Biocview "Sequencing"

Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing
Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing
Access matrix-like HDF5 server content or BigQuery content through a SummarizedExperiment interface
Access matrix-like HDF5 server content or BigQuery content through a SummarizedExperiment interface
Access matrix-like HDF5 server content or BigQuery content through a SummarizedExperiment interface
Accessory Methods for the Analysis of Oxford Nanopore Technologies DNA Sequence Data
Accurate, high-resolution sample inference from amplicon sequencing data
Accurate, high-resolution sample inference from amplicon sequencing data
Accurate Inference of Genetic Ancestry from Cancer Sequencing
A collection of single-cell V(D)J tools
A collection of single-cell V(D)J tools
A compilation of metadata from NCBI SRA and tools
A compilation of metadata from NCBI SRA and tools
A compilation of metadata from NCBI SRA and tools
A complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)
A complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)
Adaptive Dropout Imputer (ADImpute)
Adaptive Dropout Imputer (ADImpute)
Adaptive Dropout Imputer (ADImpute)
Additional functions for working with ChIP-Seq data
Additional functions for working with ChIP-Seq data
Add-on to DESeq to improve p-values and q-values
Adjust for positional and batch effects using ComBat
Adjust for positional and batch effects using ComBat
A Fast Scalable and Flexible Non Negative Matrix Factorization Method
A framework to prioritize DNA methylation aberrations based on conformational and cis-regulatory element enrichment
A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops
A graphical interface for the metagene package
A graphical interface for the metagene package
A lecture on sequence count data
Alikeness Based on Regression on Transciptome DECOnvolution
Alikeness Based on Regression on Transciptome DECOnvolution
alpine
alpine
A metagenomic pipeline for systems biology
Analysis for short time-series data
Analysis for short time-series data
Analysis for short time-series data
Analysis, interpretation, and visualization of DamID-seq data
Analysis, interpretation, and visualization of DamID-seq data
Analysis of alternative poly A site usage
Analysis of alternative splicing using RNA-Seq
Analysis of alternative splicing using RNA-Seq
Analysis of Alternative Splicing Using RNA-Seq
Analysis of Alternative Splicing Using RNA-Seq
Analysis of amplicon enrichment panels
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)
Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)
Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)
Analysis of compositions of microbiomes with bias correction
Analysis of Copy Number Variation in Single-Cell-Sequencing Data
Analysis of Copy Number Variation in Single-Cell-Sequencing Data
Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account
Analysis Of Differential Abundance Taking Sample Variation Into Account
Analysis of high-throughput sequencing data processed by restriction enzyme digestion
Analysis of nucleotide, sequence and quality content on fastq files
Analysis of nucleotide, sequence and quality content on fastq files.
Analysis of nucleotide, sequence and quality content on fastq files.
Analysis of sequencing data from ribosome profiling experiments
ANalysis Of Translational Activity (ANOTA).
Analysis of Transposable Elements
AnaLysis routines for ePigenomicS data
AnaLysis routines for ePigenomicS data
Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies
Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies
Analyze high-throughput sequencing of T and B cell receptors
Analyze high-throughput sequencing of T and B cell receptors
Analyze high-throughput sequencing of T and B cell receptors
Analyze massively parallel reporter assays
Analyze massively parallel reporter assays
Analyze Microbiome Data
Analyze Transcription Factor Enrichment
Analyze Transcription Factor Enrichment
An Easy-to-use Systematic pipeline for ATACseq data analysis
An Easy-to-use Systematic pipeline for ATACseq data analysis
An Easy-to-use Systematic pipeline for ATACseq data analysis
An Easy-to-use Systematic pipeline for ATACseq data analysis
An Easy-to-use Systematic pipeline for ATACseq data analysis
An effective identification of alternative splicing events using junction arrays and RNA-Seq data
An effective identification of alternative splicing events using junction arrays and RNA-Seq data
A new tool for exporting TCGA Firehose data
A new tool for exporting TCGA Firehose data
A new tool for exporting TCGA Firehose data
An integrated analysis package of Gene expression and Copy number alteration
An integrated analysis package of miRNA and mRNA expression data
An integrated analysis package of miRNA and mRNA expression data
An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification
An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps
An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps
An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps.
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
Annotation and gene expression data retrieval from Bgee database
Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology
Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology
Annotation of Genetic Variants
Annotation of Genetic Variants
Annotation of Genetic Variants
A normalization and copy number estimation method for single-cell DNA sequencing
A normalization and copy number estimation method for single-cell DNA sequencing
A normalization-invariant minimum enclosing ball method to detect differentially expressed genes for RNA-seq data
A normalization-invariant minimum enclosing ball method to detect differentially expressed genes for RNA-seq data
A normalization method for Copy Number Aberration in cancer samples
A novel algorithm for calling mRNA m6A peaks by modeling biological variances in MeRIP-seq data
An package for identification of novel peptides by customized database derived from RNA-Seq
An package for identification of novel peptides by customized database derived from RNA-Seq
An package for identification of novel peptides by customized database derived from RNA-Seq
An R Package for Adjusting Bias in Gene Set Enrichment Analysis
An R package for analysis of massive parallel sequencing based RNA structure probing data
An R package for analysis of massive parallel sequencing based RNA structure probing data
An R package for gene and isoform differential expression analysis of RNA-seq data
An R package for gene and isoform differential expression analysis of RNA-seq data
An R package for gene and isoform differential expression analysis of RNA-seq data
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
An R package for the creation of complex genomic profile plots
An R package for the creation of complex genomic profile plots
An R package for the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms
An R Package for Unbiased Splicing Pathway Analysis
An R Package for Unbiased Splicing Pathway Analysis in RNAseq data
An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates
An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates
An R Wrapper for Bowtie2 and AdapterRemoval
An Ultra-Fast and All-in-One Fastq Preprocessor (Quality Control, Adapter, low quality and polyX trimming) and UMI Sequence Parsing).
A package for importing and analyzing data from Roche's Genome Sequencer System
A package for the CLIP data visualization
A package to produce metagene plots
A package to produce metagene plots
A package to produce metagene plots
A pipeline especially built for computing several single-cell datasets
Application of t-sne to NGS Genomic Signal Profiles
appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity and high PPV
appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity and high PPV
Approximate posterior estimation for GLM coefficients
Approximate posterior estimation for GLM coefficients
A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend
A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend
A R/Bioconductor package to detect the interaction nodes from HiC/HiChIP/HiCAR data
A R/Bioconductor package to detect the interaction nodes from HiC/HiChIP/HiCAR data
A R/Bioconductor package to detect the interaction nodes from HiC/HiChIP/HiCAR data
ArrayExpress High Throughput Sequencing Processing Pipeline
ArrayExpress High Throughput Sequencing Processing Pipeline
A search tool for single cell RNA-seq data by gene lists
A search tool for single cell RNA-seq data by gene lists
A sensitive and fast tool for detection of TAD boundaries
A Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files
A Shiny App to accompany clusterExperiment
A small RNA-seq visualizer and analysis toolkit
A Software Suite for Shallow Sequencing Copy Number Analysis
ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events
ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events
Assess epigenetic heterogeneity with proportion of intermediate methylation
Assess epigenetic heterogeneity with proportion of intermediate methylation
Assessment of duplication rates in RNA-Seq datasets
Assessment of duplication rates in RNA-Seq datasets
Assessment of duplication rates in RNA-Seq datasets
Assess Tumor Microsatellite Instability with a Decision Tree Classifier from Exome Somatic Mutations
Association Plots
Association Plots
Association Plots
A suite for analysis of rare genomic variants in whole genome sequencing data
A suite for analysis of rare genomic variants in whole genome sequencing data
A SummarizedExperiment for Ivy-GAP data
A SummarizedExperiment for Ivy-GAP data
A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data
A Supervised Approach for Predicting Cell Cycle Progression Using Single-Cell RNA-seq Data
ASURAT database builder
Asymmetric Within-Sample Transformation
ATAC-seq Quality Control
ATAC-seq Quality Control
ATAC-seq Quality Control
A test for when to use quantile normalization
A test for when to use quantile normalization
A Tidy Transcriptomics introduction to RNA-Seq analyses
A tool for creating and analysing DNA barcodes used in Next Generation Sequencing multiplexing experiments
A Tool for Customizable and Reproducible Plotting of Sequencing Coverage Data
A Tool for Integration of Big Bio Data
A Tool for Optimizing Combinations of DNA Barcodes Used in Multiplexed Experiments on Next Generation Sequencing Platforms
A Tool for Optimizing Combinations of DNA Barcodes Used in Multiplexed Experiments on Next Generation Sequencing Platforms
A tool for quantification of associations between genotypes and phenotypes in genome wide association studies (GWAS) with Bayesian inference and statistical learning
A tool for unsupervised projection of single cell RNA-seq data
A tool for unsupervised projection of single cell RNA-seq data
A toolkit for APA analysis using RNA-seq data
A toolkit for APA analysis using RNA-seq data
A toolkit for single-cell immune receptor profiling
A toolkit for single-cell immune receptor profiling
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
A Tool to Analyze and Design NGS Based Custom Gene Panels
A Tool to Analyze and Design NGS Based Custom Gene Panels
A Tool to Analyze and Design NGS Based Custom Gene Panels
A unified computational framework for genomic feature annotation, differential expression analysis of circular RNAs
A visualization tool for single cell data of C.elegans embrogenesis
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes
BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage
BANDITS: Bayesian ANalysis of DIfferenTial Splicing
BANDITS: Bayesian ANalysis of DIfferenTial Splicing
Base NanoString Experiment Class
Base package for enabling powerful shiny web displays of Bioconductor objects
Base package for enabling powerful shiny web displays of Bioconductor objects
Base package for enabling powerful shiny web displays of Bioconductor objects
Base resolution DNA methylation data analysis
Base resolution DNA methylation data analysis
Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
Basic4CSim: Simulation of 4C-seq data
Basic and advanced bioinformatics for RegenerationNEXT
Batch Effects Quality Control Software
Batch Effects Quality Control Software
Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments
Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments
Bayesian Analysis of Differential Expression in RNA Sequencing Data
Bayesian Analysis of Single-Cell Sequencing data
Bayesian Analysis of Single-Cell Sequencing data
Bayesian clustering and imputationa of single cell methylomes
Bayesian clustering and imputationa of single cell methylomes
Bayesian Enrichment Estimation in R
Bayesian Hidden Markov Model for the detection of differentially methylated regions
Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)
Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)
Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models
Bayesian Inference of Regulation of Transcriptional Activity
Bayesian Inference of Regulatory Influence on Expression (biRte)
Bayesian modelling of cell-to-cell DNA methylation heterogeneity
BBCAnalyzer: an R/Bioconductor package for visualizing base counts
Bias Awared Peak Calling and Quantification for MeRIP-Seq
Big multivariate data plotted interactively
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
Binding site defintion based on iCLIP data
Binomial test for Hi-C data analysis
Binomial test for Hi-C data analysis
Bioc2019PanCancerStudy
Biological Network Analysis
Biological Network Analysis
BioTIP: An R package for characterization of Biological Tipping-Point
BioTIP: An R package for characterization of Biological Tipping-Point
BioTIP: An R package for characterization of Biological Tipping-Point
Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution
Brain Span Atlas in Biobase Expressionset R toolset
Brain Span Atlas in Biobase Expressionset R toolset
Brings Seurat to the Tidyverse
Brings Seurat to the Tidyverse
Brings SingleCellExperiment to the Tidyverse
Brings SingleCellExperiment to the Tidyverse
Brings SingleCellExperiment to the Tidyverse
Brings SummarizedExperiment to the Tidyverse
Brings SummarizedExperiment to the Tidyverse
Brings SummarizedExperiment to the Tidyverse
Brings transcriptomics to the tidyverse
Brings transcriptomics to the tidyverse
Brings transcriptomics to the tidyverse
Brings transcriptomics to the tidyverse
Browse the Human Cell Atlas data portal
Browse the Human Cell Atlas data portal
Browse the Human Cell Atlas data portal
Browse the Human Cell Atlas data portal
BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data
Build IGV tracks and HTML reports
Building Expression Atlas from RNA-Seq data
Building Expression Atlas from RNA-Seq data
Building Expression Atlas from RNA-Seq data
Building Expression Atlas from RNA-Seq data
Calculate, visualize and analyse overlap between genomic regions
Call wide peaks for sequencing data
Call wide peaks for sequencing data
Call wide peaks for sequencing data
Candidate gene prioritization based on convergent evidence
Candidate gene prioritization based on convergent evidence
Candidate gene prioritization based on convergent evidence
Candidate gene prioritization based on convergent evidence
Category encoding method for selecting feature genes for the classification of single-cell RNA-seq
Category encoding method for selecting feature genes for the classification of single-cell RNA-seq
CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data
CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data
Cell-Cycle using Mixture Models
CellRanger Input/Output
Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms
Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms
Cellular DNA Barcode Analysis toolkit
Cellular DNA Barcode Analysis toolkit
Cellular DNA Barcode Analysis toolkit
CEllular Latent Dirichlet Allocation
CEllular Latent Dirichlet Allocation
CEllular Latent Dirichlet Allocation
Cepo for the identification of differentially stable genes
cfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-free DNA
Characterization of Alternative Splicing based on Paired-End Reads
CHiCAGO: Capture Hi-C Analysis of Genomic Organization
ChIPanalyser: Predicting Transcription Factor Binding Sites
ChIPanalyser: Predicting Transcription Factor Binding Sites
ChIPanalyser: Predicting Transcription Factor Binding Sites
ChIPexoQual
ChIPexoQual
ChIP-Seq Analysis with Windows
ChIP-Seq Analysis with Windows
chipseq: A package for analyzing chipseq data
chipseq: A package for analyzing chipseq data
ChIP-Seq data scaling according to spike-in control
ChIP-Seq data scaling according to spike-in control
Chip-seq Signal Quantifier Pipeline
ChIP-Seq Statistical Power
ChIP-Seq Statistical Power
ChIPUtils - A package to perform exploratory analysis of ChIP data and most commonly used QC measures
Chromatin Variation Across Regions
Chromatin Variation Across Regions
Chromosome Instability Index
Chromosome Instability Index
Classification of alternative splicing and prediction of coding potential from RNA-seq data.
Classifier for Single-cell RNA-seq Using Cell Clusters
Classifier for Single-cell RNA-seq Using Cell Clusters
Classifier for Single-cell RNA-seq Using Cell Clusters
Classifier for Single-cell RNA-seq Using Cell Clusters
Classifier for Single-cell RNA-seq Using Cell Clusters
cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data
cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data
Client for GREAT Analysis
Client for GREAT Analysis
Clone Identification from Single Cell Data
Clone Identification from Single Cell Data
Clone Identification from Single Cell Data
Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models
Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models
Clustering Deviation Index (CDI)
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Clustering of high-throughput sequencing data by identifying co-expression patterns
Clustering of high-throughput sequencing data by identifying co-expression patterns
Clustering of Time Series Gene Expression data
Clustering of Time Series Gene Expression data
cn.mops - Mixture of Poissons for CNV detection in NGS data
cn.mops - Mixture of Poissons for CNV detection in NGS data
CNV detection tool for targeted NGS panel data
CNV detection tool for targeted NGS panel data
CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.
co-expressed gene-set enrichment analysis
co-expressed gene-set enrichment analysis
Co-Expression Analysis of Sequencing Data
Co-Expression Analysis of Sequencing Data
Co-Expression Analysis of Sequencing Data
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns.
CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems
Compare Clusterings for Single-Cell Sequencing
Compare Clusterings for Single-Cell Sequencing
Compare Clusterings for Single-Cell Sequencing
Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets
Comparing Differential Abundance/Expression Methods
Computational pipeline for computing probability of modification from structure probing experiment data
Computational pipeline for computing probability of modification from structure probing experiment data
Compute coverage matrices from recount quickly using bwtool
ComSeq: An ensemble method for RNA-Seq differential analysis
ComSeq: An ensemble method for RNA-Seq differential analysis
Conducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocation
Conducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocation
Container for PhIP-Seq Experiments
Context-Aware Transcript Quantification from Long Read RNA-Seq data
Conveniently import and query gene models
Conveniently import and query gene models
Conveniently import and query gene models
Coordinate Covariation Analysis
Coordinate Covariation Analysis
Coordinate Covariation Analysis
CopyKit
Copy number analysis of high-throughput sequencing cancer data
Copy number calling and SNV classification using targeted short read sequencing
Copy number calling and SNV classification using targeted short read sequencing
Copy number prediction with correction for GC and mappability bias for HTS data
Copy number prediction with correction for GC and mappability bias for HTS data
Copy number prediction with correction for GC and mappability bias for HTS data
Copy Number study and Segmentation for multivariate biological data
Copy number variant detection from exome sequencing read depth
Copy Number Visualization
Correspondence Analysis for Single Cell Data
Correspondence Analysis for Single Cell Data
Covariate Assisted Large-scale Multiple testing
Covariate Assisted Large-scale Multiple testing
Coverage visualization package for R
Create Copy-Number Plots using karyoploteR functionality
Create Copy-Number Plots using karyoploteR functionality
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
Data-Adaptive Statistics for High-Dimensional Multiple Testing
Data-Adaptive Statistics for High-Dimensional Multiple Testing
Data-driven Annotation of the Transcriptome
Data for the alpine package vignette
Data management of large-scale whole-genome sequence variant calls
Data Management of Large-Scale Whole-Genome Sequence Variant Calls
Data Mining for RNA-seq data: normalization, feature selection and classification
Data Mining for RNA-seq data: normalization, feature selection and classification
Data resource for package "TRESS"
DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication
DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication
Decomposing Heterogeneous Cohorts using Omic Data Profiling
Decomposing Heterogeneous Cohorts using Omic Data Profiling
Decomposition of individual tumors into mutational signatures by signature refitting
Decomposition of individual tumors into mutational signatures by signature refitting
DegNorm: degradation normalization for RNA-seq data
DegNorm: degradation normalization for RNA-seq data
Delineate outstanding genomic zones of differential gene activity
Delineate outstanding genomic zones of differential gene activity
de novo motif discovery
de novo motif discovery
Density-Preserving Data Visualization via Non-Linear Dimensionality Reduction
derfinder helper package
derfinder helper package
DEsingle for detecting three types of differential expression in single-cell RNA-seq data
DEsingle for detecting three types of differential expression in single-cell RNA-seq data
Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions
detect different methylation level (DMR)
Detecting abberant splicing events from RNA-sequencing data
Detecting abberant splicing events from RNA-sequencing data
Detecting patterns of post-transcriptional modifications using machine learning
Detecting patterns of post-transcriptional modifications using machine learning
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing
Detection, Characterization and Visualization of Kataegis in Sequencing Data
Detection of 2'-O methylations by RiboMethSeq
Detection of 2'-O methylations by RiboMethSeq
Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges
Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges
Detection of de novo deletion in targeted sequencing trios
Detection of de novo deletion in targeted sequencing trios
Detection of de novo deletion in targeted sequencing trios
Detection of Differentially Methylated Regions
Detection of Differentially Methylated Regions
Detection of focal aberrations in DNA copy number data
Detection of m7G, m3C and D modification by AlkAnilineSeq
Detection of m7G, m3C and D modification by AlkAnilineSeq
Detection of post-transcriptional modifications in high throughput sequencing data
Detection of post-transcriptional modifications in high throughput sequencing data
Detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing
Detection of subclonal SNVs in deep sequencing data.
Detection of subclonal SNVs in deep sequencing data.
Detection of subclonal SNVs in deep sequencing data.
Detect the correlated mutations based on selection pressure
Detect the correlated mutations based on selection pressure
Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates
dgeAnalysis
dgeAnalysis
Differential Analyis of Hi-C Data
Differential Analyis of Hi-C Data
Differential analysis for MeRIP-seq data
Differential analysis for MeRIP-seq data
Differential Binding Analysis of ChIP-Seq Peak Data
Differential Binding Estimation for Protein Complexes
Differential Binding of Transcription Factor with ChIP-seq
Differential cell type change analysis using Logistic/linear Regression
Differential cell-type-specific allelic imbalance
Differential Co-expression Analysis
Differential Co-expression Analysis
Differential Enrichment Scan 2
Differential Enrichment Scan 2
Differential Expressed Windows Based on Negative Binomial Distribution
Differential Expressed Windows Based on Negative Binomial Distribution
Differential expression analysis and model fitting for single-cell RNA-seq data
Differential expression analysis and model fitting for single-cell RNA-seq data
Differential Expression Analysis for RNA-seq data through a robust variance component test
Differential expression analysis of longitudinal count data sets
Differential expression analysis of longitudinal count data sets
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression data formats converter
Differential gene expression data formats converter
Differentially Expressed Gene-Gene pairs
Differentially Methylated CpG using Hidden Markov Model
Differentially Methylated CpG using Hidden Markov Model
Differentially Methylated Cytosines via a Bayesian Functional Approach
Differentially Methylated Cytosines via a Bayesian Functional Approach
Differentially Methylated Regions caller
Differentially Methylated Regions caller
Differentially regulated genes from scRNA-seq data
Differential methylation anlsysis for bisulfite sequencing data
Differential methylation anlsysis for bisulfite sequencing data
Differential methylation anlsysis for bisulfite sequencing data
Differential pattern analysis for Ribo-seq data
Differential pattern analysis for Ribo-seq data
Differential Topology, Progression and Differentiation
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
Discriminant Analysis for Evolutionary Inference
Discriminant Analysis for Evolutionary Inference
Dispersion shrinkage for sequencing data
Dispersion shrinkage for sequencing data
Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles
distinct: a method for differential analyses via hierarchical permutation tests
Distributed computing by file or by range
Distributed computing by file or by range
distSTRING calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA methylation analysis from high-throughput bisulfite sequencing results
DNA methylation analysis from high-throughput bisulfite sequencing results
DNA methylation analysis from high-throughput bisulfite sequencing results
doseLM
doseR
doseR
doseR
doseR
doseR
doseR
dPeak (Deconvolution of Peaks in ChIP-seq Analysis)
dPeak (Deconvolution of Peaks in ChIP-seq Analysis)
dplyr-based Access to Bioconductor Annotation Resources
dplyr-based Access to Bioconductor Annotation Resources
Dual redundant reference sequencing
Dual redundant reference sequencing
Easy Analysis of RNASeq DE
Easy Analysis of RNASeq DE
Easy single cell analysis platform for enrichment
Easy single cell analysis platform for enrichment
Easy Use R
Efficient manipulation of biological strings
Efficient manipulation of biological strings
Efficient manipulation of biological strings
ELBOW - Evaluating foLd change By the lOgit Way
Empirical Analysis of Digital Gene Expression Data in R
Empirical Analysis of Digital Gene Expression Data in R
Empirical Analysis of Digital Gene Expression Data in R
Empirical Bayesian analysis of patterns of differential expression in count data
Engineering Evaluation by Gene Categorization (eegc)
Engineering Evaluation by Gene Categorization (eegc)
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
Environment for Gene Expression Searching Combined with Functional Enrichment Analysis
Environment for Gene Expression Searching Combined with Functional Enrichment Analysis
Environment for Gene Expression Searching Combined with Functional Enrichment Analysis
Error correction tool for noisy genotyping by sequencing (GBS) data
Estimates Isoform Specific RPF Footprint Densities
Estimate the cell composition of whole blood in DNA methylation samples
Estimate the cell composition of whole blood in DNA methylation samples
Estimation of per-position bias in high-throughput sequencing data
Example experimental microarray data set for the "biotmle" R package
exome-based anlaysis of MeRIP-Seq data: peak calling and differential analysis
exome-based anlaysis of MeRIP-Seq data: peak calling and differential analysis
exome-based anlaysis of MeRIP-Seq data: peak calling and differential analysis
Exon Based Strategy for Expression Analysis of genes
Experimental Design in Differential Abundance analysis
Exploration of marker-gene sequence taxonomic annotations
Exploration of marker-gene sequence taxonomic annotations
Exploratory analysis and differential expression for RNA-seq data
Exploratory analysis and differential expression for RNA-seq data
Exploratory Data Analysis and Normalization for RNA-Seq
Exploratory Data Analysis and Normalization for RNA-Seq
Explore and download data from the recount3 project
Explore and download data from the recount3 project
Explore and download data from the recount project
Explore and download data from the recount project
External data sets for clustifyr
Extract read count signals from bam files
Extract read count signals from bam files
Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data
Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data
Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data
Fast and efficient summarization of generic bedGraph files from Bisufite sequencing
Fast and efficient summarization of generic bedGraph files from Bisufite sequencing
Fast and efficient summarization of single cell whole genome bisulfate data
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
FASTQ2OTU: Automate microbiome analyses
FASTQ input and manipulation
FASTQ input and manipulation
FASTQ Quality Control
FASTQ Quality Control
Fast Reading and Processing of Common Gene Annotation and Next Generation Sequencing Format Files
Fast Reading and Processing of Common Gene Annotation and Next Generation Sequencing Format Files
Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens
Feature-based association and gene-set enrichment for copy number alteration analysis in cancer
FEAture SelcTion (FEAST) for Single-cell clustering
FFPE Artificial Chimeric Read Filter for NGS data
FFPE Artificial Chimeric Read Filter for NGS data
Filtering of coding and non-coding genetic variants
Filtering of coding and non-coding genetic variants
Filtering of Lowly Expressed Features
Filter replicated high-throughput transcriptome sequencing data
Filter replicated high-throughput transcriptome sequencing data
Find breakpoints in Strand-seq data
Find breakpoints in Strand-seq data
Find breakpoints in Strand-seq data
Finding the DNA and protein sequences in a list of genomic or proteomic loci
Finding the DNA and Protein Sequences of Any Genomic or Proteomic Loci
Find RAre Splicing Events in RNA-Seq Data
Find RAre Splicing Events in RNA-Seq Data
Find RAre Splicing Events in RNA-Seq Data
Find SNV/Indel differences between two bam files with near relationship
Fishpond: differential transcript and gene expression with inferential replicates
Fishpond: downstream methods and tools for expression data
Fix gene symbols that are messed up by Excel
Flexible, probabilistic metrics for quality control of scRNA-seq data
Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)
Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)
Framework for Storing and Accessing Hi-C Data Through HDF Files
Framework for Storing and Accessing Hi-C Data Through HDF Files
Framework for Storing and Accessing Hi-C Data Through HDF Files
Framework for Storing and Accessing Hi-C Data Through HDF Files
Functional annotation-driven unsupervised clustering for single-cell data
Functional annotation-driven unsupervised clustering for single-cell data
functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets
functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets
Functional interpretation of single cell RNA-seq latent manifolds
Functional interpretation of single cell RNA-seq latent manifolds
Functionality Visualization for Motifs
Functions for Analyzing Cellular Barcoding Data
Functions for Analyzing Cellular Barcoding Data
Functions to creation of low dimensional comparative matrices of Amino Acid Sequence occurrences
Functions to creation of low dimensional comparative matrices of Amino Acid Sequence occurrences
Functions to creation of low dimensional comparative matrices of Amino Acid Sequence occurrences
Functions to help analyze data as phyloseq objects
Functions to help analyze data as phyloseq objects
Functions to process LM-PCR reads from 454/Illumina data
Functions to process LM-PCR reads from 454/Illumina data
Functions used to preprocess datasets stored in BioDataome
GC Aware Peak Caller
GC Aware Peak Caller
Gene Break Detection
GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data
GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data
Gene Ontology analyser for RNA-seq and other length biased data
Gene Ontology analyser for RNA-seq and other length biased data
Gene Ontology analyser for RNA-seq and other length biased data
Gene Ontology analyser for RNA-seq and other length biased data
Generally Applicable Gene-set Enrichment for Pathway Analysis
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq
Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Generate Quality Surrogate Variable Analysis for Degradation Correction
Generate Summary Plots of FastQC Reports
Generate synthetic nucleosome maps
Generate synthetic nucleosome maps
Generating Tree Hierarchy Visualizations from Gene Expression Data
Generating Tree Hierarchy Visualizations from Gene Expression Data
Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences
Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
Genetic Algorithms for Understanding Clonal Heterogeneity and Ordering
Genome Intervals and Read Alignments for Functional Exploration
Genome Level Trellis Layout
Genome Level Trellis Layout
Genome Level Trellis Layout
GenomicDistributions: fast analysis of genomic intervals with Bioconductor
Genomic Visualisation Routines
genphen: tool for quantification of genotype-phenotype associations in genome wide association studies (GWAS)
Global Test for Counts
Global Test for Counts
Global visualization tool of genomic data
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
GREAT Analysis - Functional Enrichment on Genomic Regions
Greengenes 13.8 85% similarity OTU threshold 16S rRNA Database Annotation Data
Greengenes 13.8 88% similarity OTU threshold 16S rRNA Database Annotation Data
Greengenes 13.8 91% similarity OTU threshold 16S rRNA Database Annotation Data
Greengenes 13.8 94% similarity OTU threshold 16S rRNA Database Annotation Data
Greengenes 13.8 97% similarity OTU threshold 16S rRNA Database Annotation Data
Grey Lists -- Mask Artefact Regions Based on ChIP Inputs
GRO-seq Analysis Pipeline
GRO-seq Analysis Pipeline
GRO-seq Analysis Pipeline
gRx Differential Clustering
GUIDE-seq analysis pipeline
GUIDE-seq and PEtag-seq analysis pipeline
Guitar
Guitar
GWAS-based Mendelian Randomization and Path Analyses
GWAS-based Mendelian Randomization and Path Analyses
GWAS trait-associated SNP enrichment analyses in genomic intervals
Handling and analysis of high-throughput microbiome census data
Handling and analysis of high-throughput microbiome census data
hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data
HDF5 backend for DelayedArray objects
HDF5 backend for DelayedArray objects
Heterogeneity-Induced Pre-Processing tOol
Heterogeneity-Induced Pre-Processing tOol
Hexbin plots for single cell omics data
Hexbin plots for single cell omics data
HiC analysis using data.table
HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets
HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets
HiCdiff: Joint normalization and comparative analysis of multiple Hi-C datasets
Higher-Order Deconvolution Survival Analyses
High throughput analysis of T cell antigen receptor sequences
High throughput analysis of T cell antigen receptor sequences
High Throughput Chromosome Conformation Capture analysis
High Throughput Chromosome Conformation Capture analysis
High Throughput Sequencing Cell Authentication Toolkit
High Throughput Sequencing Cell Authentication Toolkit
HMM-Based Model for Genotyping and Cross-Over Identification
HMM-Based Model for Genotyping and Cross-Over Identification
HMMRATAC - a semi-supervised machine learning approach for identifying open chromatin regions from ATAC-Seq data using Hidden Markov Models
htslib high-throughput sequencing library as an R package
HTSlib high-throughput sequencing library as an R package
Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies
Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies
Identification and classification of plant transcription factors
Identification of genetic Variants affecting Alternative Splicing
Identification of putative mammalian orthologs to given enhancer
Identifies false positives of CNV calling tools by using SNV calls
Identifies false positives of CNV calling tools by using SNV calls
Identify Contaminants in Marker-gene and Metagenomics Sequencing Data
Identify Contaminants in Marker-gene and Metagenomics Sequencing Data
Identify differential APA usage from RNA-seq alignments
Identify differential APA usage from RNA-seq alignments
Identifying Genes Overexpressed in Subsets of Tumors from Tumor-Normal mRNA Expression Data
Identifying Genes Overexpressed in Subsets of Tumors from Tumor-Normal mRNA Expression Data
igvShiny: a wrapper of Integrative Genomics Viewer (IGV - an interactive tool for visualization and exploration integrated genomic data)
ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers
immune Cell Analysis Tool
immune Cell Analysis Tool
Implementation of the dot bracket annotations with Biostrings
Implementation of the dot bracket annotations with Biostrings
Imputation-guided re-construction of complete methylomes from WGBS data
Imputation-guided re-construction of complete methylomes from WGBS data
Imputation-guided re-construction of complete methylomes from WGBS data
Indentification of significantly activated ligand-receptor interactions across clusters of cells from single-cell RNA sequencing data
Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
Inference of Chromosome-length Haplotypes using Genomic Data of Single Gamete Cells
Inference of Chromosome-length Haplotypes using Genomic Data of Single Gamete Cells
Inference of Chromosome-Length Haplotypes Using Genomic Data of Single Gamete Cells
Inference of differential exon usage in RNA-Seq
Inference of differential exon usage in RNA-Seq
Inferring the Tree of Cells
Infers clonal composition of a tumor
Infrastructure for microfluidic oscillatory washing-based ChIP
Infrastructure to work with genomewide position-specific scores
Infrastructure to work with genomewide position-specific scores
InPAS: a bioconductor package for the identification of novel alternative PolyAdenylation Sites (PAS) using RNA-seq data
In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data
In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data
Integrating Cap Enrichment with Transcript Expression Analysis
Integrating Cap Enrichment with Transcript Expression Analysis
Integrative Analysis and Visualization of Epigenomic Sequencing Data
Integrative Analysis and Visualization of Epigenomic Sequencing Data
Integrative analysis of Multi-omics data for Alternative Splicing
Integrative analysis of Multi-omics data for Alternative Splicing
Integrative analysis of structural variations
Integrative analysis of structural variations
Integrative Statistics of alleLe Dependent Expression
Integrative Statistics of alleLe Dependent Expression
interactive analysis and visualization of alternative splicing in R
Interactive Differential Expresion Analysis Browser
Interactive Differential Expresion Analysis Browser
Interactive Differential Expresion Analysis Browser
Interactive Differential Expression AnaLysis
Interactive Differential Expression AnaLysis
Interactive Differential Expression AnaLysis
Interactive HTML graphics
Interactive HTML graphics
Interactive visualization in genomics
Interactive visualization in genomics
interactive visualization of genomics data
Interact with the Broad Institute Cromwell workflow manager
Interact with the Broad Institute Cromwell workflow manager
Interface for Popular Multiple Sequence Alignment Tools
Interface to the RDP Classifier
Interface to the RDP Classifier
Interpretation of RNA-seq experiments through robust, efficient comparison to public databases
Interpretation of RNA-seq experiments through robust, efficient comparison to public databases
Introduce *Ranges to bedtools users
Introduce *Ranges to bedtools users
Introduction to Tidy Transcriptomics
Introduction to Tidy Transcriptomics
Introduction to Tidy Transcriptomics
Introduction to Tidy Transcriptomics
Introduction to Tidy Transcriptomics
Introduction to Tidy Transcriptomics
Introduction to Tidy Transcriptomics
Introduction to Tidy Transcriptomics
Intron-Exon Retention Estimator
Intron-Exon Retention Estimator
Investigates Allele Specific Expression
Investigates Allele Specific Expression
IP-seq data analysis and vizualization
IP-seq data analysis and vizualization
Isoform expression estimation based on RNA-seq data
JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data
KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline
KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline
L1-regularization based methods for detection of differential splicing
L1-regularization based methods for detection of differential splicing
Label-Free Identification of Endogenous Informative Single Cell Mitochondrial RNA Mutation for Lineage Analysis and Clonal Evolution
Landscape Expression Visualization Interface
Landscape Expression Visualization Interface
Learn and Apply Cell Type Signatures
Learn and Apply Cell Type Signatures
Learning from DNA to Predict Enhancers
Linear model and normality based normalization and transformation method (Linnorm)
Linear Models for Microarray Data
Linear Models for Microarray Data
Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs
Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs
Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs
Locus overlap analysis for enrichment of genomic ranges
Locus overlap analysis for enrichment of genomic ranges
Locus overlap analysis for enrichment of genomic ranges
LowMACA - Low frequency Mutation Analysis via Consensus Alignment
LowMACA - Low frequency Mutation Analysis via Consensus Alignment
LowMACA - Low frequency Mutation Analysis via Consensus Alignment
LPEseq: local-pooled-error test for RNA-seq data with a small number of replicates
LPEseq: local-pooled-error test for RNA-seq data with a small number of replicates
m6Aboost
m6Aexpress-BHM: Predicting m6A regulation of gene expression in multiple-groups context by a Bayesian Hierarchical Mixture model
Machine Learning Interface for RNA-Seq Data
Machine Learning Interface for RNA-Seq Data
Machine Learning Interface for RNA-Seq Data
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data
Make Complex Heatmaps
Make Complex Heatmaps
Make Complex Heatmaps
Make Interactive Complex Heatmaps
Make read coverage plots from BigWig files
Make read coverage plots from BigWig files
Making 2D Hilbert Curve
Making 2D Hilbert Curve
Making 2D Hilbert Curve
Making Complex Heatmaps
Making Enriched Heatmaps
Making Enriched Heatmaps
Making Enriched Heatmaps
Manipulation of SQLite-based annotations in Bioconductor
Manipulation of SQLite-based annotations in Bioconductor
Manipulation of SQLite-based annotations in Bioconductor
Mapping of Phyloseq Information
Mapping protein-DNA interactions in highly repetitive regions of the genomes with prior-enhanced read mapping
Mapping protein-DNA interactions in highly repetitive regions of the genomes with prior-enhanced read mapping
Mapping, quantification and variant analysis of sequencing data
MBDDiff for processing MBDcap-seq datasets
Measuring the reproducibility of Hi-C data
Measuring the reproducibility of Hi-C data
Measuring the reproducibility of Hi-C data
MetaAnalysis for High Throughput Experiments
MetaAnalysis for High Throughput Experiments
Meta-analysis of RNA-Seq count data in multiple studies
Metabarcoding and microbiome analysis using multiple amplicons
Methods for identifying small RNA loci from high-throughput sequencing data
Methods for Single-Cell RNA-Seq Data Analysis
Methods for Single-Cell RNA-Seq Data Analysis
Methods for TCR single-cell embedding
Methylation Analysis Based on Signal Detection
Methylation array and sequencing spatial analysis methods
Methylation array and sequencing spatial analysis methods
Methylation-Based Inference of Regulatory Activity
Methylation-Based Inference of Regulatory Activity
MethylIT utility
Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
Microbial Assemblage Normalized Transcript Analysis
Microbial Assemblage Normalized Transcript Analysis
Microbial Community Analysis GUI
Microbiome Analytics
Microbiome Analytics
Microbiome Data Simulation
Microbiome differential abudance and correlation analyses with bias correction
Microbiome Exploration App
Microbiome Exploration App
Microbiome Time Series Analysis
Mini-batch K-means Clustering for Single-Cell RNA-seq
Mini-batch K-means Clustering for Single-Cell RNA-seq
MiRNA Ranking by Gene Expression
miRNAtap: microRNA Targets - Aggregated Predictions
mirTarRnaSeq
Miscellaneous Functions for Metabarcoding Analysis
Model higher-order methylation profiles
Model higher-order methylation profiles
Model higher-order methylation profiles
Modeling RNA synthesis, processing and degradation with RNA-seq data
Modeling RNA synthesis, processing and degradation with RNA-seq data
Monte Carlo Reference-based Consensus Clustering
Monte Carlo Reference-based Consensus Clustering
Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data
Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data
MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)
MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)
MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis
Multiple Beta t-Tests
Multiple Beta t-Tests
Multiple Sample Peak Calling
Multiple Sample Peak Calling: Using combined evidence from replicates to evaluate ChIP-seq peaks
Multiple Sequence Alignment
Multiple Sequence Alignment with MUSCLE
Multi-sample multi-group scRNA-seq data analysis tools
Multi-sample multi-group scRNA-seq data analysis tools
Multi-sample multi-group scRNA-seq data analysis tools
Multivariate analysis of microarray data using ADE4
NanoString GeoMx Tools
Negative Binomial Additive Model for RNA-Seq Data
Negative Binomial Additive Model for RNA-Seq Data
Negative Binomial Beta t-Test
Negative binomial model for scRNA-seq
Negative binomial model for scRNA-seq
Network smoothing for scRNAseq
Network smoothing for scRNAseq
NEUral network-based single-Cell Annotation tool
NGScopy: Detection of Copy Number Variations in Next Generation Sequencing sequencing
NGS Read Simulator for FFPE Tissue
NGS Read Simulator for FFPE Tissue
NIH / NCI Genomic Data Commons Access
NIH / NCI Genomic Data Commons Access
Normalisation Tools for Inter-Condition Variability of ChIP-Seq Data
Normalisation Tools for Inter-Condition Variability of ChIP-Seq Data
Normalization of Single-Cell mRNA Sequencing Data
Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available
Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available
Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available
Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available
Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available
Nucleosome Dynamics
Nucleosome positioning package for R
Nucleosome positioning package for R
Nucleosome positioning package for R
Nucleosome positioning package for R
Obtain Raw Read Counts from RNASeq Data
Obtain Raw Read Counts from RNASeq Data
Omics Data Integration Project
Omics Data Integration Project
Omics Data Integration Project
Open Reading Frames in Genomics
Open Reading Frames in Genomics
Open Reading Frames in Genomics
Optimising the Definition of Expressed Regions
Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq
Outlier Analysis for pairwise differential comparison
Outlier Analysis for pairwise differential comparison
Outlier Analysis for pairwise differential comparison
Outlier-aware and Count-based Compositional Analysis of Single-cell Data.
OUTRIDER - OUTlier in RNA-Seq fInDER
OUTRIDER - OUTlier in RNA-Seq fInDER
Overlay omics data onto SBGN pathway diagram
Package analyse 4C sequencing data
Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection
Package for enabling powerful shiny web displays of Bioconductor objects
Packaging common Seurat analysis tasks
Parallel implmentation of bounded memory GEE
Parse and analyze Illumina SAV files
Parse and analyze Illumina SAV files
Parse and analyze Illumina SAV files
PathoStat Statistical Microbiome Analysis Package
PathoStat Statistical Microbiome Analysis Package
patternCNV: a versatile tool for detecting copy number changes from exome-seq data
Peak Calling and differential analysis for MeRIP-Seq
Peak Calling and differential analysis for MeRIP-Seq
Peak Refinement Metric Gathering and Evalutation by Motif Enrichment
Peak saturation processing and analysis
Perform co-DE gene analysis
Perform Methylation Analysis on Next Generation Sequencing Data
Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect
Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect
Permutation filtration for microbiome data
Permutation filtration for microbiome data
Phase template strands from Strand-seq data
Phenotype Consensus ANalysis (PCAN)
Phenotypic EMD for comparison of single-cell samples
Phenotypic EMD for comparison of single-cell samples
Phenotypic EMD for comparison of single-cell samples
Phylogenetic partitioning based ILR transform for metagenomics data
Phylogenetic partitioning based ILR transform for metagenomics data
Pipeline for augmented co-expression analysis
Pipeline for augmented co-expression analysis
Pipeline for single cell multi-omic data pre-processing
pipeline for single cell RNA-seq data analysis
Plot customizable linear genomes displaying arbitrary data
Plot customizable linear genomes displaying arbitrary data
Plots of Statistics Collected by Qualimap from RNASeq Data
Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
Plotting data and annotation information along genomic coordinates
Plotting data and annotation information along genomic coordinates
Plotting functions for derfinder
Plotting functions for derfinder
PolyA counting and differential transcript usage analysis for scRNA-seq data
Pooling RNA-seq datasets for assembling transcript models
Pooling RNA-seq datasets for assembling transcript models
Position-Dependent Kernel Association Test
Position-Dependent Kernel Association Test
Power Estimation Tool for RNA-Seq and proteomics data
Power Estimation Tool for RNA-Seq and proteomics data
Precict cis-co-accessibility from single-cell chromatin accessibility data
preciseTAD: A machine learning framework for precise TAD boundary prediction
preciseTAD: A machine learning framework for precise TAD boundary prediction
preciseTAD: A machine learning framework for precise TAD boundary prediction
Predict cis-co-accessibility from single-cell chromatin accessibility data
Predict cis-co-accessibility from single-cell chromatin accessibility data
Predicting context-specific m6A regulation of gene expression
Predicting context-specific m6A regulation of gene expression
Predicting context-specific m6A regulation of gene expression combinding m6A reader binding information
Prediction of pri-miRNA Transcription Start Site
Prediction of pri-miRNA Transcription Start Site
Prediction of Protein Conserved Regions Using NADDA Algorithm
Predict open reading frames in nucleotide sequences
Pre-process DNA Copy Number (CN) Data for Detection of CN Events
Prioritization of potentially bioactive metabolic features from epidemiological and environmental metabolomics datasets
Prioritization of potentially bioactive metabolic features from epidemiological and environmental metabolomics datasets
Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data
Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data
Probabilistic inference of ChIP-seq
Probabilistic inference of ChIP-seq
Probabilistic Outlier Identification for RNA Sequencing Generalized Linear Models
Probabilistic Outlier Identification for RNA Sequencing Generalized Linear Models
Probe region expression estimation for RNA-seq data for improved microarray comparability
Processing and analyzing bisulfite sequencing data
Programmatic access to the DEE2 RNA expression dataset
Programmatic access to the DEE2 RNA expression dataset
Promoter identification from large-scale TSS profiling data
Promoter identification from large-scale TSS profiling data
PROspective Power Evaluation for RNAseq
PROspective Power Evaluation for RNAseq
Provides structure and functions for the analysis of OTU data
QA/QC of a gVCF or VCF file
QA/QC of a gVCF or VCF file
QC for enrichment based NGS
QTL mapping using Bulk Segregant Analysis of Next Generation Sequencing data.
QTL mapping using Bulk Segregant Analysis of Next Generation Sequencing data.
Quality Assessment Tools for Oxford Nanopore MinION data
Quality Assessment Tools for Oxford Nanopore MinION data
Quality Control for Single-Cell RNA-seq Data
Quality Control for Single-Cell RNA-seq Data
Quality Control for Single-Cell RNA-seq Data
Quality control for target capture experiments
Quality control for target capture experiments
Quality Control Tool for High-Throughput Sequencing Data
Quality Control Tool for High-Throughput Sequencing Data
Quality Control, Visualization and Processing for High-Throughput Sequencing data
Quality metrics for ChIPseq data
Quality metrics for ChIPseq data
Quality metrics for ChIPseq data
Quantification of the Tumor Immune contexture from RNA-seq data
Quantify and Annotate Short Reads in R
Quantify and Annotate Short Reads in R
Quantifying Differential Features
Quantitative comparison of multiple ChIP-seq datasets
Quantitative DNA Sequencing for Chromosomal Aberrations
Quantitative DNA Sequencing for Chromosomal Aberrations
Quasispecies Diversity
Quasispecies Diversity
Quick Read Quality Control
Quick Read Quality Control
Random Rotation Methods for High Dimensional Data with Batch Structure
Random Rotation Methods for High Dimensional Data with Batch Structure
Rank Constrained Similarity Learning for single cell RNA sequencing data
Rank Constrained Similarity Learning for Single Cell RNA Sequencing Data
R-based analysis of ChIP-seq And Differential Expression - a tool for integrating a count-based ChIP-seq analysis with differential expression summary data
R-based analysis of ChIP-seq And Differential Expression - a tool for integrating a count-based ChIP-seq analysis with differential expression summary data
Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities
R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts
R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts
R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts
R bowtie wrapper
Rcpp Integration Surrogate Variable Analysis
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
Recalibrating Quality Of Nucleotides
Recipes using seqsetvis
Reconstruction, visualization and analysis of branching trajectories
Reconstruction, visualization and analysis of branching trajectories
Reconstruction, visualization and analysis of branching trajectories
Reference-guided isoform reconstruction and quantification for long read RNA-Seq data
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
Reliable CNV detection in targeted sequencing applications
Reliable CNV detection in targeted sequencing applications
Reliable CNV detection in targeted sequencing applications
Repetitive Element Methylation Prediction
Repetitive Element Methylation Prediction
Replicate oriented Visualization of a genomic region
Replicate oriented Visualization of a genomic region
Replicate oriented Visualization of a genomic region
Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries
Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries
Representation and manipulation of genomic intervals
Representation and manipulation of genomic intervals
Representation and manipulation of genomic intervals; demo with github actions binary generation
Representation and Manipulation of Genomic Tuples
Representation and Manipulation of Genomic Tuples
Representation and manipulation of short genomic alignments
Representation and manipulation of short genomic alignments
Representing GDS files as array-like objects
Representing GDS files as array-like objects
Representing on-disk / remote VCF files as array-like objects
Representing on-disk / remote VCF files as array-like objects
Representing on-disk / remote VCF files as array-like objects
Retrotransposed transcript detection from structural variants
Retrotransposed transcript detection from structural variants
Revealing differentially expressed genes using nonlinear dimensionality reduction for single cell RNA-Seq data
Revealing differentially expressed genes using nonlinear dimensionality reduction for single cell RNA-Seq data
R functions
RiboseQC, a Comprehensive Ribo-Seq Analysis Tool
Ribosomal Database Project 16S rRNA release 11.5 Annotation Data
Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation
Ribosome Profiling Quality Control
Ribosome Profiling Quality Control
R implementation of the LEfSE method for microbiome biomarker discovery
R implementation of the LEfSE method for microbiome biomarker discovery
R Interface for the Basic Local Alignment Search Tool
RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments
RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments
RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments
RLSeq: An analysis package for R-loop mapping data
RNA-seq analysis using multiple algorithms
RNA-seq analysis using multiple algorithms
RNA-seq data analysis using the Poisson-Tweedie family of distributions
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
RnaSeqSampleSize
RnaSeqSampleSize
rnaSeq secondary analyses
RnBeads
Robust Inference for Absolute Abundance in Microbiome Analysis
Robust Inference for Absolute Abundance in Microbiome Analysis
Robust Inference for Absolute Abundance in Microbiome Analysis
Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data
R package for CRAG
R package for CRAG
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data
rqt: utilities for gene-level meta-analysis
rqt: utilities for gene-level meta-analysis
rqt: utilities for gene-level meta-analysis
R SDK for BaseSpace RESTful API
rSFFreader reads in sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers
rSFFreader reads in sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers
RSVSim: an R/Bioconductor package for the simulation of structural variations
RSVSim: an R/Bioconductor package for the simulation of structural variations
runibic: row-based biclustering algorithm for analysis of gene expression data in R
Run `magic-impute` on scRNA Seq dataset in R
R Wrapper for HISAT2 Aligner
R wrapper for the python openTSNE library
R wrapper for the python openTSNE library
samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation
samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation
Sample Size Calculation for RNA-Seq Experimental Design
Sample Size Calculation for RNA-Seq Experimental Design
sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R
sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"
Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications
Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications
Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs
Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data
Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data
Scaling normalization based on the Pareto distribution
Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences
scMerge: Merging multiple batches of scRNA-seq data
scMerge: Merging multiple batches of scRNA-seq data
scraps output import and processing in R
scRecover for imputation of single-cell RNA-seq data
scRecover for imputation of single-cell RNA-seq data
scRecover for imputation of single-cell RNA-seq data
ScRNA-seq Workflow CONCLUS - From CONsensus CLUSters To A Meaningful CONCLUSion
Seamless visualization of complex genomic variations in GMOs and edited cell lines
Search for correlation between epigenetic signals and gene expression in TADs
Search for correlation between epigenetic signals and gene expression in TADs
Segmentation of Bis-seq data
Segmentation of Bis-seq data
Segvis: A package for visualization of high throughput sequencing data along genomic segments
Selecting the number of mutational signatures using a perplexity-based measure and cross-validation
Semi-parametric simulation tool for bulk and single-cell RNA sequencing data
Semi-parametric simulation tool for bulk and single-cell RNA sequencing data
Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data
Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data
Set Based Visualizations for Next-Gen Sequencing Data
Set Based Visualizations for Next-Gen Sequencing Data
Set of tools to identify periodic occurrences of k-mers in DNA sequences
Set of tools to identify periodic occurrences of k-mers in DNA sequences
Set of tools to make V-plots and compute footprint profiles
Set of tools to make V-plots and compute footprint profiles
Shape-based Analysis of Variation in ChIP-seq using Functional PCA
Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)
Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)
Significance-based Modules Integrating the Transcriptome and Epigenome
Significance-based Modules Integrating the Transcriptome and Epigenome
Significance-based Modules Integrating the Transcriptome and Epigenome
SILVA SSR rRNA release 128.1 Annotation Data
SILVA SSR rRNA release 128.1 Annotation Data
SILVA SSR rRNA release 128.1 Annotation Data
SIMLR: Single-cell Interpretation via Multi-kernel LeaRning
Simple Simulation of Single-cell RNA Sequencing Data
Simple Simulation of Single-cell RNA Sequencing Data
Simple Simulation of Single-cell RNA Sequencing Data
Simple Simulation of Single-cell RNA Sequencing Data
Simple Simulation of Single-cell RNA Sequencing Data
Simulate RNA-seq reads
Simulate RNA-seq reads
Simulate RNA-seq reads
Simulate RNA-seq reads
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
Simulation of Rare Variant Genetic Data
SingCellaR: an integrative analysis tool for single-cell RNA sequencing (scRNA-seq) data
Single-cell analysis toolkit for gene expression data in R
Single-Cell Analysis Toolkit for Gene Expression Data in R
Single-Cell Analysis Toolkit for Gene Expression Data in R
Single-Cell Analysis Toolkit for Gene Expression Data in R
Single-Cell Analysis Toolkit for Gene Expression Data in R
Single-Cell Batch Correction Methods
Single-Cell Batch Correction Methods
single-cell higher order testing
single-cell higher order testing
Single-cell Interpretation via Multi-kernel LeaRning (SIMLR)
Single-Cell Operation for Neat Enrichment
Single Cell Overview of Normalized Expression data
Single Cell Overview of Normalized Expression data
Single-Cell RNA-Seq Analysis Utilities
Single-Cell RNA-Seq Analysis Utilities
Single-cell RNA sequencing data normalization
Single-cell RNA sequencing data normalization
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data
Single-cell Targetted Network Inference
Small-Count Analysis Methods for High-Dimensional Data
Small-Count Analysis Methods for High-Dimensional Data
Smooth modeling of bisulfite sequencing
Smooth quantile normalization
Smooth quantile normalization
Smooth quantile normalization
Somatic Signatures
Somatic Signatures
Somatic Signatures
Somatic structural variant analysis
Sparse Contrastive Principal Component Analysis
Sparse Contrastive Principal Component Analysis
spatialHeatmap
spatialHeatmap
Spatial Transcriptomics Analysis
Spatial Transcriptomics Analysis
SpectralTAD: Hierarchical TAD detection using spectral clustering
SpectralTAD: Hierarchical TAD detection using spectral clustering
SpectralTAD: Hierarchical TAD detection using spectral clustering
Spike-in calibration for cell-free MeDIP
SpotClean adjusts for spot swapping in spatial transcriptomics data
spsBio: A systemPipeShiny plugin for biological data visualization
Stan implementation of BASiCS
Statistical analysis for sparse high-throughput sequencing
Statistical analysis for sparse high-throughput sequencing
Statistical Analysis of MPRA data
Statistical Analysis of MPRA data
Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)
Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)
Statistical Inference of Associations between Microbial Communities And host phenoTypes
Statistical Inference of Associations between Microbial Communities And host phenoTypes
Statistical Inference of Associations between Microbial Communities And host phenoTypes
Statistical Testing for ChIP-Seq data sets
Statistical Testing for ChIP-Seq data sets
Statistical Utility for RBP (RNA binding protein) Functions
Structure Learning for Count Data
Subclonal copy number and LOH prediction from whole genome sequencing of tumours
Subclonal copy number and LOH prediction from whole genome sequencing of tumours
Subclonal copy number and LOH prediction from whole genome sequencing of tumours
Subsampling of high-throughput sequencing count data
Subsampling of high-throughput sequencing count data
Subtype Identification with Survival Data
Summarize, Analyze and Visualize MAF Files
Summarize, Analyze and Visualize MAF Files
Summarize, Analyze and Visualize MAF Files
SummarizedExperiment container
SummarizedExperiment container
SummarizedExperiment container
Summary, annotation and visualization of genomic data
Summary, annotation and visualization of genomic data
Supervised mutational signatures
Surrogate Variable Analysis
Surrogate Variable Analysis
Surrogate Variable Analysis
svpluscnv: analysis and visualization of complex structural variation data
systemPipeRdata: Workflow templates and sample data
systemPipeR: NGS workflow and report generation environment
systemPipeR: workflow management and report generation environment
systemPipeShiny: An Interactive Framework for Workflow Management and Visualization
systemPipeShiny: An Interactive Framework for Workflow Management and Visualization
systemPipeShiny: An Interactive Framework for Workflow Management and Visualization
TADCompare: Identification and characterization of differential TADs
TADCompare: Identification and characterization of differential TADs
TADCompare: Identification and characterization of differential TADs
Targeted Learning with Moderated Statistics for Biomarker Discovery
Targeted Learning with Moderated Statistics for Biomarker Discovery
Targeted scRNA-seq primer design for TAP-seq
Targeted scRNA-seq primer design for TAP-seq
TARgeted SEQuencing Experiment Quality Control
TARgeted SEQuencing Experiment Quality Control
TCC: Differential expression analysis for tag count data with robust normalization strategies
TCC: Differential expression analysis for tag count data with robust normalization strategies
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"
"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"
Test for differential expression for RNA-seq data
The Genomic STate ANnotation Package
The slim version of signac
The tidyomics blog
The tidyomics blog
This package classifies putative polyadenylation sites as true or false/internally oligodT primed
this package collects r fxns useful in my daily coding life
This package contains the NGS-Panel-Analyzer R package
This Package Helps Characterise and Visualise Whole Genome Sequencing Data from Liquid Biopsy
Tidy Transcriptomics for Single-cell RNA Sequencing Analyses
Tidyverse functions for SummarizedExperiment
Time-Course Multi-Omics data integration
Time-Course Multi-Omics data integration
Time-Course Multi-Omics data integration
Time course sequencing data analysis
Time course sequencing data analysis
Tissue-specific gene enrichment analysis
Tissue-specific gene enrichment analysis
Tomo-seq data analysis
Tomo-seq data analysis
Toolkit for Single-Cell Velocity
Toolkit for Single-Cell Velocity
Tools for computational epigenomics
Tools for computational epigenomics
Tools for curating, analyzing, and manipulating biological sequences
Tools for data visualization
Tools for Exploratory Analysis of Variant Calls
Tools for Exploratory Analysis of Variant Calls
Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data
Tools for ordering single-cell sequencing
Tools for ordering single-cell sequencing
Tools for performing taxonomic assignment.
Tools for Sanger Sequencing Data in R
Tools for Sanger Sequencing Data in R
tools for spike-in UMI analysis
Tools for the Efficient Analysis of High-Resolution Genomics Data
Tools for the Efficient Analysis of High-Resolution Genomics Data
Tools for variant data
Tools for variant data
Tools for visualizing genomics data
Tools for visualizing genomics data
Tools for visualizing genomics data
trajectory-based differential expression analysis for sequencing data
trajectory-based differential expression analysis for sequencing data
Trajectory functions for visualization and interpretation.
Transcript abundance linear modeling from compressed coverage information
Transcript Annotation Tool (TransAT): an R package for retrieving annotations for transcript specific genetic variants
Transcript expression inference and differential expression analysis for RNA-seq data
Transcription Factor Enrichment Analysis for ATAC-seq
Transcription Start Site Identification
Transcriptome CUTteR
Transcriptome-guided quality assessment of m6A-seq data
Transcriptomic View of Genomic Features
Transcriptomic View of Genomic Features
Translational control assessment from ribosome footprint and total RNA libraries
Triform finds enriched regions (peaks) in transcription factor ChIP-sequencing data
TSS and TSR Analysis
TSS and TSR Analysis
TSS sequencing data analysis
TVTB: The VCF Tool Box
TVTB: The VCF Tool Box
Two phase differential expression for singel-cell RNA-seq
Two phase differential expression for single-cell RNA-seq
UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data
UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data
uORF prediction in R
Utilities for Handling Single-Cell Droplet Data
Utilities for Handling Single-Cell Droplet Data
Utilities to create and use an Ensembl based annotation database
Utilities to create and use Ensembl-based annotation databases
Utilities to create and use Ensembl-based annotation databases
Utilities to create and use Ensembl-based annotation databases
Utilities to create and use Ensembl-based annotation databases
Variant annotations for structural variants
Variant annotations for structural variants
Variant annotations for structural variants
Varying-Censoring Aware Matrix Factorization
VeloViz: RNA-velocity informed 2D embeddings for visualizing cell state trajectories
Viral Evolution ReconStructiOn (VERSO)
Viscello for Visualization of Single Cell Data
Viscello for Visualization of Single Cell Data
Viscello for Visualization of Single Cell EHT Data
Visual comparison of mutational processes in a set of tumors
Visual Exploration of Omic Datasets Using a Shiny App
Visual Exploration of Omic Datasets Using a Shiny App
Visual Exploration of Omic Datasets Using a Shiny App
Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic Intervals
Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic Intervals
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualization and annotation of read signal over genomic ranges with profileplyr
Visualization and annotation of read signal over genomic ranges with profileplyr
Visualization of genomic structural variants
Visualization of high-throughput assays in microtitre plate or slide format
What the Package Does (TODO)
Wind: weighted indexes for clustering evaluation
Working with Illumina Basecalling and Demultiplexing input and output files
Working with Illumina Basecalling and Demultiplexing input and output files
Working with modified nucleotide sequences
Working with modified nucleotide sequences
Wrench normalization for sparse count data
Wrench normalization for sparse count data
XCI-inference
XCI-inference
xcore expression regulators inference
YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
Yet Another Package for Signature Analysis
Yet Another Package for Signature Analysis
Yet Another Package for Signature Analysis
Yet Another Package for Signature Analysis
Zero-Inflated Negative Binomial Model for RNA-Seq Data
Zero-Inflated Negative Binomial Model for RNA-Seq Data