Biocview "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
Accurate, high-resolution sample inference from amplicon sequencing data
Accurate, high-resolution sample inference from amplicon sequencing data
Accurate, high-resolution sample inference from amplicon sequencing data
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 compilation of metadata from NCBI SRA and tools
Add-on to DESeq to improve p-values and q-values
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 graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops
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 graphical interface for the metagene package
alpine
alpine
alpine
A metagenomic pipeline for systems biology
A metagenomic pipeline for systems biology
Analysis of 4sU-seq and RNA-seq time-course data
Analysis of 4sU-seq and RNA-seq time-course data
Analysis of 4sU-seq and RNA-seq time-course data
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 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 Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)
Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)
Analysis of Copy Number Variation in Single-Cell-Sequencing Data
Analysis Of Differential Abundance Taking Sample Variation Into Account
Analysis Of Differential Abundance Taking Sample 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 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 nucleotide, sequence and quality content on fastq files.
Analysis of sequencing data from ribosome profiling experiments
Analysis of sequencing data from ribosome profiling experiments
ANalysis Of Translational Activity (ANOTA).
ANalysis Of Translational Activity (ANOTA).
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 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
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
A new tool for exporting TCGA Firehose data
An integrated analysis package of Gene expression and Copy number alteration
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 integrated analysis package of miRNA and mRNA expression data
An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification
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
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-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
Annotation and gene expression data retrieval from Bgee database
Annotation Database Interface
Annotation Database Interface
Annotation Database Interface
Annotation of Genetic Variants
Annotation of Genetic Variants
Annotation of Genetic Variants
Annotation of Genetic Variants
A normalization method for Copy Number Aberration in cancer samples
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 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 creation of complex genomic profile plots
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 creation of complex genomic profile plots
An R package for the creation of complex genomic profile plots
An R Package for Unbiased Splicing Pathway Analysis
An R Package for Unbiased Splicing Pathway Analysis
An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
An R package to Identify, Annotate and Visualize Isoform Switches with Functional Consequences (from RNA-seq 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
A package for importing and analyzing data from Roche's Genome Sequencer System
A package for importing and analyzing data from Roche's Genome Sequencer System
A package to produce metagene plots
A package to produce metagene plots
A package to produce metagene plots
Approximate posterior estimation for GLM coefficients
Approximate posterior estimation for GLM coefficients
ArrayExpress High Throughput Sequencing Processing Pipeline
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 Shiny App to accompany clusterExperiment
A small RNA-seq visualizer and analysis toolkit
A small RNA-seq visualizer and analysis toolkit
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
Assess Tumor Microsatellite Instability with a Decision Tree Classifier from Exome Somatic Mutations
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
ATAC-seq Quality Control
ATAC-seq Quality Control
ATAC-seq Quality Control
ATAC sequencing Quality Control
A test for when to use quantile normalization
A test for when to use quantile normalization
A test for when to use quantile normalization
A tool for creating and analysing DNA barcodes used in Next Generation Sequencing multiplexing experiments
A tool for creating and analysing DNA barcodes used in Next Generation Sequencing multiplexing experiments
A tool for quantification of associations between genotypes and phenotypes with statistical learning techniques such as random forests and support vector machines as well as with Bayesian inference using hierarchical models
A tool for quantification of associations between genotypes and phenotypes with statistical learning techniques such as random forests and support vector machines as well as with Bayesian inference using hierarchical models
A tool for quantification of associations between genotypes and phenotypes with statistical learning techniques such as random forests and support vector machines as well as with Bayesian inference using hierarchical models
A tool for unsupervised projection of single cell RNA-seq data
A tool for unsupervised projection of single cell RNA-seq data
A tool for unsupervised projection of single cell RNA-seq data
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
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
BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage
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
Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
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 for identifying gene or isoform expression changes in ordered RNA-seq experiments
Bayesian Analysis of Differential Expression in RNA Sequencing Data
Bayesian Analysis of Differential Expression in RNA Sequencing Data
Bayesian Analysis of Single-Cell Sequencing data
Bayesian Analysis of Single-Cell Sequencing data
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 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 Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models
Bayesian Inference of Regulation of Transcriptional Activity
Bayesian Inference of Regulation of Transcriptional Activity
Bayesian Inference of Regulatory Influence on Expression (biRte)
Bayesian Inference of Regulatory Influence on Expression (biRte)
BBCAnalyzer: an R/Bioconductor package for visualizing base counts
BBCAnalyzer: an R/Bioconductor package for visualizing base counts
Big Data Management of Whole-genome Sequence Variant Calls
Big Data Management of Whole-genome Sequence Variant Calls
Big Data Management of Whole-genome Sequence Variant Calls
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
Binomial test for Hi-C data analysis
Binomial test for Hi-C data analysis
BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data
BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data
Build IGV tracks and HTML reports
Build IGV tracks and HTML reports
Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data
Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data
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
Candidate gene prioritization based on convergent evidence
Characterization of Alternative Splicing based on Paired-End Reads
Characterization of Alternative Splicing based on Paired-End Reads
CHiCAGO: Capture Hi-C Analysis of Genomic Organization
CHiCAGO: Capture Hi-C Analysis of Genomic Organization
ChIPanalyser: Predicting Transcription Factor Binding Sites
ChIPanalyser: Predicting Transcription Factor Binding Sites
ChIPexoQual
ChIPexoQual
ChIP-Seq Analysis with Windows
ChIP-Seq Analysis with Windows
ChIP-Seq Analysis with Windows
chipseq: A package for analyzing chipseq data
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 Statistical Power
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.
Classification of alternative splicing and prediction of coding potential from RNA-seq data.
Client for GREAT Analysis
Client for GREAT Analysis
Client for GREAT Analysis
Client for GREAT Analysis
Clonal Analysis of Cells Using 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 and Visualizing RNA-Seq Expression Data using Grade of Membership Models
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
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 high-throughput sequencing data by identifying co-expression patterns
Clustering of Time Series Gene Expression data
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.
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-expressed gene-set enrichment analysis
Co-Expression Analysis of Sequencing Data
Co-Expression Analysis of Sequencing Data
Co-Expression Analysis of Sequencing Data
Co-Expression Analysis of Sequencing 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
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns.
Compare Clusterings for Single-Cell Sequencing
Compare Clusterings for Single-Cell Sequencing
Compare Clusterings for Single-Cell Sequencing
Compare Clusterings for Single-Cell Sequencing
Computational pipeline for computing probability of modification from structure probing experiment data
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
Copy number analysis of high-throughput sequencing cancer data
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 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 study and Segmentation for multivariate biological data
Copy Number study and Segmentation for multivariate biological data
Copy number variant detection from exome sequencing read depth
Copy number variant detection from exome sequencing read depth
Coverage visualization package for R
Coverage visualization package for R
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
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 for the alpine package vignette
Data Mining for RNA-seq data: normalization, feature selection and classification
Data Mining for RNA-seq data: normalization, feature selection and classification
Data Mining for RNA-seq data: normalization, feature selection and classification
DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication
DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication
DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication
debrowser: Interactive Differential Expresion Analysis Browser
debrowser: Interactive Differential Expresion Analysis Browser
debrowser: Interactive Differential Expresion Analysis Browser
debrowser: Interactive Differential Expresion Analysis Browser
de novo motif discovery
de novo motif discovery
de novo motif discovery
derfinder helper package
derfinder helper package
derfinder helper package
detect different methylation level (DMR)
detect different methylation level (DMR)
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing
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 consensus regions inside a group of experiences using genomic positions and genomic ranges
Detection of Differentially Methylated Regions
Detection of Differentially Methylated Regions
Detection of Differentially Methylated Regions
Detection of focal aberrations in DNA copy number data
Detection of focal aberrations in DNA copy number data
Detection of subclonal SNVs in deep sequencing data.
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
DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates
DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates
Differential Analyis of Hi-C Data
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 Analysis of ChIP-Seq Peak Data
Differential Binding Estimation for Protein Complexes
Differential Binding of Transcription Factor with ChIP-seq
Differential Binding of Transcription Factor with ChIP-seq
Differential expression analysis and model fitting for single-cell RNA-seq data
Differential expression analysis of longitudinal count data sets
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 analysis based on the negative binomial distribution
Differential gene expression data formats converter
Differential gene expression data formats converter
Differential gene expression data formats converter
Differentially Methylated CpG using Hidden Markov Model
Differentially Methylated CpG using Hidden Markov Model
Differentially Methylated Regions caller
Differentially Methylated Regions caller
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
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
Dispersion shrinkage for sequencing data
Dispersion shrinkage for sequencing data
Dispersion shrinkage for sequencing data.
Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles
Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles
Distributed computing by file or by range
Distributed computing by file or by range
Distributed computing by file or by range
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
dplyr-based Access to Bioconductor Annotation Resources
dplyr-based Access to Bioconductor Annotation Resources
dplyr-based Access to Bioconductor Annotation Resources
Easy Analysis of RNASeq DE
Easy Analysis of RNASeq DE
Efficient manipulation of biological strings
Efficient manipulation of biological strings
ELBOW - Evaluating foLd change By the lOgit Way
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 Bayesian analysis of patterns of differential expression in count data
Empirical Bayesian analysis of patterns of differential expression in count data
Engineering Evaluation by Gene Categorization (eegc)
Engineering Evaluation by Gene Categorization (eegc)
Engineering Evaluation by Gene Categorization (eegc)
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
Estimate the cell composition of whole blood in DNA methylation samples
Estimation of per-position bias in high-throughput sequencing data
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
Exon Based Strategy for Expression Analysis of genes
Experimental Design in Differential Abundance analysis
Experimental Design in Differential Abundance analysis
Exploration of marker-gene sequence taxonomic annotations
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
Exploratory Data Analysis and Normalization for RNA-Seq
Explore and download data from the recount project
Explore and download data from the recount project
Explore and download data from the recount project
Extract read count signals from bam files
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 Methylome-Wide Association Study Pipeline for Enrichment Platforms
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
FASTQ input and manipulation
FASTQ input and manipulation
FASTQ input and manipulation
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
Feature-based association and gene-set enrichment for copy number alteration analysis in cancer
Feature-based association and gene-set enrichment for copy number alteration analysis in cancer
Filtering of coding and non-coding genetic variants
Filtering of coding and non-coding genetic variants
Filtering of coding and non-coding genetic variants
Filter replicated high-throughput transcriptome sequencing data
Filter replicated high-throughput transcriptome sequencing data
Filter replicated high-throughput transcriptome sequencing 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 SNV/Indel differences between two bam files with near relationship
Find SNV/Indel differences between two bam files with near relationship
functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets
functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets
Functions to process LM-PCR reads from 454/Illumina data
Functions to process LM-PCR reads from 454/Illumina data
Functions to process LM-PCR reads from 454/Illumina data
GC Aware Peak Caller
GC Aware Peak Caller
GC Aware Peak Caller
Gene Break Detection
Gene Break Detection
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 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 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 HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Generate Summary Plots of FastQC Reports
Generate synthetic nucleosome maps
Generate synthetic nucleosome maps
Generate synthetic nucleosome maps
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
Genetic Algorithms for Understanding Clonal Heterogeneity and Ordering
Genome Intervals and Read Alignments for Functional Exploration
Genome Intervals and Read Alignments for Functional Exploration
Genome Level Trellis Layout
Genome Level Trellis Layout
Genome Level Trellis Layout
Genome Level Trellis Layout
Genomic Visualisation Routines
Global visualization tool of genomic data
Global visualization tool of genomic data
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Greengenes 13.5 16S rRNA Database Annotation Data
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
Grey Lists -- Mask Artefact Regions Based on ChIP Inputs
GRO-seq Analysis Pipeline
GRO-seq Analysis Pipeline
GRO-seq Analysis Pipeline
GRO-seq Analysis Pipeline
gRx Differential Clustering
gRx Differential Clustering
GUIDE-seq analysis pipeline
GUIDE-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
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
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
hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data
HDF5 back end for DelayedArray objects
HDF5 back end for DelayedArray objects
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
High throughput analysis of T cell antigen receptor sequences
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
htslib high-throughput sequencing library as an R package
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 Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies
Identification of genetic Variants affecting Alternative Splicing
Identification of genetic Variants affecting Alternative Splicing
Identification of Novel alternative PolyAdenylation Sites (PAS)
Identification of Novel alternative PolyAdenylation Sites (PAS)
Identification of Novel alternative PolyAdenylation Sites (PAS)
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
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
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
Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
Inference of differential exon usage in RNA-Seq
Inference of differential exon usage in RNA-Seq
Infers clonal composition of a tumor
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
Infrastructure to work with genomewide position-specific scores
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 Multi-omics data for Alternative Splicing
Integrative analysis of structural variations
Integrative analysis of structural variations
Integrative analysis of structural variations
Integrative analysis pipeline for pooled CRISPR functional genetic screens
Integrative Statistics of alleLe Dependent Expression
Integrative Statistics of alleLe Dependent Expression
Interactive Differential Expression AnaLysis
Interactive Differential Expression AnaLysis
Interactive HTML graphics
Interactive HTML graphics
Interactive HTML graphics
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 Basic Local Alignment Search Tool (BLAST)
Interface to the RDP Classifier
Interface to the RDP Classifier
Introduce *Ranges to bedtools users
Introduce *Ranges to bedtools users
Introduce *Ranges to bedtools users
Intron-Exon Retention Estimator
Intron-Exon Retention Estimator
Intron-Exon Retention Estimator
Investigates Allele Specific Expression
Investigates Allele Specific Expression
Investigates Allele Specific Expression
IP-seq data analysis and vizualization
IP-seq data analysis and vizualization
IP-seq data analysis and vizualization
Isoform expression estimation based on RNA-seq data
Joint analysis of multiple ChIP-Seq data sets
JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data
JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data
L1-regularization based methods for detection of differential splicing
L1-regularization based methods for detection of differential splicing
L1-regularization based methods for detection of differential splicing
Learning from DNA to Predict Enhancers
Learning from DNA to Predict Enhancers
Linear model and normality based transformation method (Linnorm)
Linear model and normality based transformation method (Linnorm)
Location overlap analysis for enrichment of genomic ranges
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
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
Machine learning interface for RNA-Seq data
Machine learning interface for RNA-Seq data
Machine Learning Interface for RNA-Seq Data
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 2D Hilbert Curve
Making Complex Heatmaps
Making Complex Heatmaps
Making Complex Heatmaps
Making Complex Heatmaps
Making Enriched Heatmaps
Making Enriched Heatmaps
Making Enriched Heatmaps
Making Enriched Heatmaps
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
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
Measuring the reproducibility of Hi-C data
MetaAnalysis for High Throughput Experiments
MetaAnalysis for High Throughput Experiments
MetaAnalysis for High Throughput Experiments
Meta-analysis of RNA-Seq count data in multiple studies
Meta-analysis of RNA-Seq count data in multiple studies
Methods for identifying small RNA loci from high-throughput sequencing data
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 Single-Cell RNA-Seq Data Analysis
Methylation-Based Inference of Regulatory Activity
Methylation-Based Inference of Regulatory Activity
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
Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
Microbial Assemblage Normalized Transcript Analysis
Microbial Assemblage Normalized Transcript Analysis
Microbial Community Analysis GUI
Microbial Community Analysis GUI
Microbiome Analytics
Microbiome Analytics
MiRNA Ranking by Gene Expression
MiRNA Ranking by Gene Expression
miRNAtap: microRNA Targets - Aggregated Predictions
miRNAtap: microRNA Targets - Aggregated Predictions
Model higher-order methylation profiles
Model higher-order methylation profiles
Model higher-order methylation profiles
Model higher-order methylation profiles
Monte Carlo Consensus Clustering
Monte Carlo Consensus Clustering
Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data
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)
MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)
Multiple Beta t-Tests
Multiple Beta t-Tests
Multiple Sample Peak Calling: Using combined evidence from replicates to evaluate ChIP-seq peaks
Multiple Sequence Alignment
Multiple Sequence Alignment
Multiple Sequence Alignment with MUSCLE
Multiple Sequence Alignment with MUSCLE
NGScopy: Detection of Copy Number Variations in Next Generation Sequencing sequencing
NGScopy: Detection of Copy Number Variations in Next Generation Sequencing sequencing
NIH / NCI Genomic Data Commons Access
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
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
Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq
Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq
Package analyse 4C sequencing data
Package analyse 4C sequencing data
Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection
Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection
Package for enabling powerful shiny web displays of Bioconductor objects
Package for enabling powerful shiny web displays of Bioconductor objects
Parallel implmentation of bounded memory GEE
Parse and analyze Illumina SAV files
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
PathoStat Statistical Microbiome Analysis Package
patternCNV: a versatile tool for detecting copy number changes from exome-seq data
Perform Methylation Analysis on Next Generation Sequencing Data
Perform Methylation Analysis on Next Generation Sequencing Data
Permutation-Based Analysis associating Conserved Differentially Methylated Elements from One Generation to the Next to a Treatment Effect
Permutation-Based Analysis associating Conserved Differentially Methylated Elements from One Generation to the Next to a Treatment Effect
Phase template strands from Strand-seq data
Phenotype Consensus ANalysis (PCAN)
Phenotype Consensus ANalysis (PCAN)
Phylogenetic partitioning based ILR transform for metagenomics data
Phylogenetic partitioning based ILR transform for metagenomics data
Phylogenetic partitioning based ILR transform for metagenomics data
pipeline for single cell RNA-seq data analysis
pipeline for single cell RNA-seq data analysis
Plot customizable linear genomes displaying arbitrary data
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
Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
Plotting functions for derfinder
Plotting functions for derfinder
Plotting functions for derfinder
Position-Dependent Kernel Association Test
Position-Dependent Kernel Association Test
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 for Nucleosome Positioning with MNase-based or Sonicated Short-read Data
Probabilistic inference of ChIP-seq
Probabilistic inference of ChIP-seq
Probabilistic inference of ChIP-seq
Probe region expression estimation for RNA-seq data for improved microarray comparability
Probe region expression estimation for RNA-seq data for improved microarray comparability
Processing and analyzing bisulfite sequencing data
Processing and analyzing bisulfite sequencing data
Promoter identification from large-scale TSS profiling data
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
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
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 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 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 Tool for High-Throughput Sequencing Data
Quality Control, Visualization and Processing 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
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 comparison of multiple ChIP-seq datasets
Quantitative DNA sequencing for chromosomal aberrations
Quantitative DNA sequencing for chromosomal aberrations
Quantitative DNA sequencing for chromosomal aberrations
Quick Read Quality Control
Quick Read Quality Control
Quick Read Quality Control
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
R bowtie wrapper
R bowtie wrapper
Rcpp Integration Surrogate Variable Analysis
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
Recalibrating Quality Of Nucleotides
Recalibrating Quality Of Nucleotides
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
Repetitive Element Methylation Prediction
Representation and manipulation of genomic intervals and variables defined along a genome
Representation and manipulation of genomic intervals and variables defined along a genome
Representation and manipulation of genomic intervals and variables defined along a genome
Representation and manipulation of genomic intervals and variables defined along a genome
Representation and Manipulation of Genomic Tuples
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
Representation and manipulation of short genomic alignments
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
Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation
Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation
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
RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments
RNA-seq data analysis using the Poisson-Tweedie family of distributions
RNA-seq data analysis using the Poisson-Tweedie family of distributions
RnaSeqSampleSize
RnaSeqSampleSize
rnaSeq secondary analyses
rnaSeq secondary analyses
RnBeads
RnBeads
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data
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
rqt: utilities for gene-level meta-analysis
R SDK for BaseSpace RESTful API
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
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 metabarcoding alalyses for multiple amplicons
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
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
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
Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data
Segmentation of Bis-seq data
Segmentation of Bis-seq data
Segvis: A package for visualization of high throughout sequencing data along genomic segments
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
Shape-based Analysis of Variation in ChIP-seq using Functional PCA
Shape-based Analysis of Variation in ChIP-seq using Functional PCA
Significance-based Modules Integrating the Transcriptome and Epigenome
Significance-based Modules Integrating the Transcriptome and Epigenome
Significance-based Modules Integrating the Transcriptome and Epigenome
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
Simulate RNA-seq reads
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
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 Overview of Normalized Expression data
Single Cell Overview of Normalized Expression data
Single Cell Overview of Normalized Expression data
Smooth quantile normalization
Smooth quantile normalization
SomatiCA: identifying, characterizing, and quantifying somatic copy number aberrations from cancer genome sequencing
Somatic Signatures
Somatic Signatures
Somatic Signatures
Statistical analysis for sparse high-throughput sequencing
Statistical analysis for sparse high-throughput sequencing
Statistical analysis for sparse high-throughput sequencing
Statistical analysis of Solexa sequencing 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 about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)
Statistical Testing for ChIP-Seq data sets
Statistical Testing for ChIP-Seq data sets
String objects representing biological sequences, and matching algorithms
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
Subread sequence alignment for R
Subread sequence alignment for R
Subsampling of high-throughput sequencing count data
Subsampling of high-throughput sequencing count data
Subsampling of high-throughput sequencing count 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
SummarizedExperiment container
Summary, annotation and visualization of genomic data
Summary, annotation and visualization of genomic data
Summary, annotation and visualization of genomic data
Surrogate Variable Analysis
Surrogate Variable Analysis
Surrogate Variable Analysis
systemPipeRdata: NGS workflow templates and sample data
systemPipeR: NGS workflow and report generation environment
systemPipeR: NGS workflow and report generation environment
Targeted Learning for Biomarker Discovery with Moderated Statistics
Targeted Learning for Biomarker Discovery with Moderated Statistics
Targeted Learning for Biomarker Discovery with Moderated Statistics
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"
"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"
TCGA Workflow Analyze cancer genomics and epigenomics data using Bioconductor packages
TCGA Workflow Analyze cancer genomics and epigenomics data using Bioconductor packages
Test for differential expression for RNA-seq data
Test for differential expression for RNA-seq data
Testing for association between RNA-Seq and high-dimensional data
Testing for association between RNA-Seq and high-dimensional data
Testing for association between RNA-Seq and high-dimensional data
The Genomic STate ANnotation Package
The Genomic STate ANnotation Package
This package classifies putative polyadenylation sites as true or false/internally oligodT primed
This package classifies putative polyadenylation sites as true or false/internally oligodT primed
This package classifies putative polyadenylation sites as true or false/internally oligodT primed
Time course sequencing data analysis
Time course sequencing data analysis
Time course sequencing data analysis
Title: SIMLR: Single-cell Interpretation via Multi-kernel LeaRning
Title: SIMLR: Single-cell Interpretation via Multi-kernel LeaRning
Tool for converting GFF3 file format data to a GRanges Object
Tools for computational epigenomics
Tools for computational epigenomics
Tools for curating, analyzing, and manipulating biological sequences
Tools for curating, analyzing, and manipulating biological sequences
Tools for Exploratory Analysis of Variant Calls
Tools for Exploratory Analysis of Variant Calls
Tools for Exploratory Analysis of Variant Calls
Tools for making and manipulating transcript centric annotations
Tools for making and manipulating transcript centric annotations
Tools for making and manipulating transcript centric annotations
Tools for ordering single-cell sequencing
Tools for performing taxonomic assignment.
Tools for performing taxonomic assignment.
Tools for Sanger Sequencing Data in R
Tools for Sanger Sequencing Data in R
Tools for variant data
Tools for variant data
Tools for variant data
Tools for visualizing genomics data
Tools for visualizing genomics data
Tools for visualizing genomics data
Transcript expression inference and differential expression analysis for RNA-seq data
Transcript expression inference and differential expression analysis for RNA-seq data
Transcription Start Site Identification
Transcription Start Site Identification
Transcriptome-guided quality assessment of m6A-seq data
Transcriptomic View of Genomic Features
Transcriptomic View of Genomic Features
Triform finds enriched regions (peaks) in transcription factor ChIP-sequencing data
Triform finds enriched regions (peaks) in transcription factor ChIP-sequencing data
TVTB: The VCF Tool Box
TVTB: The VCF Tool Box
TVTB: The VCF Tool Box
TVTB: The VCF Tool Box
Two dimensional visualization of single-cell data
Two phase differential expression for singel-cell RNA-seq
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
Varying-Censoring Aware Matrix Factorization
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
Visualise microarray and RNAseq data using gene ontology annotations
Visualization of high-throughput assays in microtitre plate or slide format
Visualization of high-throughput assays in microtitre plate or slide format
Working with Illumina Basecalling and Demultiplexing input and output files
Working with Illumina Basecalling and Demultiplexing input and output files
Working with Illumina Basecalling and Demultiplexing input and output files
YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
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
Zero-Inflated Negative Binomial Model for RNA-Seq Data