Biocview "Sequencing"

Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing

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 Inference of Genetic Ancestry from Cancer Sequencing

A collection of single-cell V(D)J 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 container (S4 class) for matrix-like assays

Adaptive Dropout Imputer (ADImpute)

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

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 lecture on sequence count data

Alikeness Based on Regression on Transciptome DECOnvolution

alpine

A metagenomic pipeline for systems biology

Analysis for short time-series 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 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 Cap Analysis of Gene Expression (CAGE) data using Bioconductor

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 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 sequencing data from ribosome profiling experiments

ANalysis Of Translational Activity (ANOTA).

Analysis of Transposable Elements

AnaLysis routines for ePigenomicS data

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 massively parallel reporter assays

Analyze Microbiome Data

Analyze Transcription Factor Enrichment

An Easy-to-use Systematic pipeline for ATACseq data analysis

An effective identification of alternative splicing events using junction arrays and RNA-Seq 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 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.

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 of Genetic Variants

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 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 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 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 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 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 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

Approximate posterior estimation for GLM coefficients

A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend

A R/Bioconductor package to detect the interaction nodes from HiC/HiChIP/HiCAR data

ArrayExpress High Throughput Sequencing Processing Pipeline

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

Assess epigenetic heterogeneity with proportion of intermediate methylation

Assessment of duplication rates in RNA-Seq datasets

Assess Tumor Microsatellite Instability with a Decision Tree Classifier from Exome Somatic Mutations

Association Plots

A suite for analysis of rare genomic variants in whole genome sequencing 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

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 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 toolkit for APA analysis using RNA-seq data

A toolkit for single-cell immune receptor profiling

a tool set for pathway based data integration and visualization

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

BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage

BANDITS: Bayesian ANalysis of DIfferenTial Splicing

Base NanoString Experiment Class

Base package for enabling powerful shiny web displays of Bioconductor objects

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

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 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 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

Binding site defintion based on iCLIP data

Binomial test for Hi-C data analysis

Bioc2019PanCancerStudy

Biological Network Analysis

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

Brings Seurat to the Tidyverse

Brings SingleCellExperiment to the Tidyverse

Brings SummarizedExperiment to the Tidyverse

Brings transcriptomics to the tidyverse

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

Calculate, visualize and analyse overlap between genomic regions

Call wide peaks for sequencing data

Candidate gene prioritization based on convergent evidence

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

ccImpute: an accurate and scalable consensus clustering based approach to impute dropout events in the single-cell RNA-seq data (https://doi.org/10.1186/s12859-022-04814-8)

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

Cellular DNA Barcode Analysis toolkit

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

ChIPexoQual

ChIP-Seq Analysis with Windows

chipseq: A package for analyzing chipseq data

ChIP-Seq data scaling according to spike-in control

Chip-seq Signal Quantifier Pipeline

ChIP-Seq Statistical Power

ChIPUtils - A package to perform exploratory analysis of ChIP data and most commonly used QC measures

Chromatin Variation Across Regions

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

cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data

Client for GREAT Analysis

Clone Identification from Single Cell Data

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 of high-throughput sequencing data by identifying co-expression patterns

Clustering of Time Series Gene Expression data

cn.mops - Mixture of Poissons for CNV detection in NGS 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-Expression Analysis of Sequencing Data

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

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 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

Compute coverage matrices from recount quickly using bwtool

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

Container for PhIP-Seq Experiments

Context-Aware Transcript Quantification from Long Read RNA-Seq data

Conveniently import and query gene models

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 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

Covariate Assisted Large-scale Multiple testing

Coverage visualization package for R

Create Copy-Number Plots using karyoploteR functionality

Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them

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 resource for package "TRESS"

DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication

Decomposing Heterogeneous Cohorts using Omic Data Profiling

Decomposition of individual tumors into mutational signatures by signature refitting

DegNorm: degradation normalization for RNA-seq data

Delineate outstanding genomic zones of differential gene activity

de novo motif discovery

Density-Preserving Data Visualization via Non-Linear Dimensionality Reduction

derfinder helper package

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 patterns of post-transcriptional modifications using machine learning

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 consensus regions inside a group of experiences using genomic positions and genomic ranges

Detection of de novo deletion in targeted sequencing trios

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 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.

Detect the correlated mutations based on selection pressure

Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data

DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates

dgeAnalysis

Differential Analyis of Hi-C 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 Enrichment Scan 2

Differential Expressed Windows Based on Negative Binomial Distribution

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 gene expression analysis based on the negative binomial distribution

Differential gene expression data formats converter

Differentially Expressed Gene-Gene pairs

Differentially Methylated CpG using Hidden Markov Model

Differentially Methylated Cytosines via a Bayesian Functional Approach

Differentially Methylated Regions caller

Differentially regulated genes from scRNA-seq data

Differential methylation anlsysis for bisulfite sequencing 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

Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data

Discriminant Analysis for Evolutionary Inference

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

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 methylation analysis from high-throughput bisulfite sequencing results

doseLM

doseR

dPeak (Deconvolution of Peaks in ChIP-seq Analysis)

dplyr-based Access to Bioconductor Annotation Resources

Dual redundant reference sequencing

Easy Analysis of RNASeq DE

Easy single cell analysis platform for enrichment

Easy Use R

Efficient manipulation of biological strings

ELBOW - Evaluating foLd change By the lOgit Way

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)

Ensemble of Gene Set Enrichment Analyses

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

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

Exon Based Strategy for Expression Analysis of genes

Experimental Design in Differential Abundance analysis

Exploration of marker-gene sequence taxonomic annotations

Exploratory analysis and differential expression for RNA-seq data

Exploratory Data Analysis and Normalization for RNA-Seq

Explore and download data from the recount3 project

Explore and download data from the recount project

External data sets for clustifyr

Extract read count signals from bam files

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 single cell whole genome bisulfate data

Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms

FASTQ2OTU: Automate microbiome analyses

FASTQ input and manipulation

FASTQ Quality Control

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

Feature-Wise Normalization for Microbiome Sequencing Data

FFPE Artificial Chimeric Read Filter for NGS data

Filtering of coding and non-coding genetic variants

Filtering of Lowly Expressed Features

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 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)

Framework for Storing and Accessing Hi-C Data Through HDF Files

Functional annotation-driven unsupervised clustering for single-cell data

functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets

Functional interpretation of single cell RNA-seq latent manifolds

Functionality Visualization for Motifs

Functions for Analyzing Cellular Barcoding Data

Functions to creation of low dimensional comparative matrices of Amino Acid Sequence occurrences

Functions to help analyze data as phyloseq objects

Functions to process LM-PCR reads from 454/Illumina data

Functions used to preprocess datasets stored in BioDataome

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

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

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 Quality Surrogate Variable Analysis for Degradation Correction

Generate Summary Plots of FastQC Reports

Generate synthetic nucleosome maps

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

Genetic Algorithms for Understanding Clonal Heterogeneity and Ordering

Genome Intervals and Read Alignments for Functional Exploration

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 visualization tool of genomic data

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

gRx Differential Clustering

GUIDE-seq analysis pipeline

GUIDE-seq and PEtag-seq analysis pipeline

Guitar

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

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 datasets as array-like objects in R

Heterogeneity-Induced Pre-Processing tOol

Hexbin plots for single cell omics data

HiC analysis using data.table

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 Chromosome Conformation Capture analysis

High Throughput Sequencing Cell Authentication Toolkit

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 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

Identify Contaminants in Marker-gene and Metagenomics Sequencing Data

Identify differential APA usage from RNA-seq alignments

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

Implementation of the dot bracket annotations with Biostrings

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 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

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

Integrating Cap Enrichment with Transcript Expression Analysis

Integrative Analysis and Visualization of Epigenomic Sequencing Data

Integrative analysis of Multi-omics data for Alternative Splicing

Integrative analysis of structural variations

Integrative Statistics of alleLe Dependent Expression

interactive analysis and visualization of alternative splicing in R

Interactive Differential Expresion Analysis Browser

Interactive Differential Expression AnaLysis

Interactive HTML graphics

Interactive visualization in genomics

interactive visualization of genomics data

Interact with the Broad Institute Cromwell workflow manager

Interface for Popular Multiple Sequence Alignment Tools

Interface to the RDP Classifier

Interpretation of RNA-seq experiments through robust, efficient comparison to public databases

Introduce *Ranges to bedtools users

Introduction to Tidy Transcriptomics

Intron-Exon Retention Estimator

Investigates Allele Specific Expression

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

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

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

Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs

Locus overlap analysis for enrichment of genomic ranges

LowMACA - Low frequency Mutation Analysis via Consensus Alignment

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

MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data

Make Complex Heatmaps

Make Interactive Complex Heatmaps

Make read coverage plots from BigWig files

Making 2D Hilbert Curve

Making Complex Heatmaps

Making Enriched Heatmaps

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, quantification and variant analysis of sequencing data

MBDDiff for processing MBDcap-seq datasets

Measuring the reproducibility of Hi-C data

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 TCR single-cell embedding

Methylation Analysis Based on Signal Detection

Methylation array and sequencing spatial analysis methods

Methylation-Based Inference of Regulatory Activity

MethylIT utility

Michaelis-Menten Modelling of Dropouts in single-cell RNASeq

Microbial Assemblage Normalized Transcript Analysis

Microbial Community Analysis GUI

Microbiome Analytics

Microbiome Data Simulation

Microbiome differential abudance and correlation analyses with bias correction

Microbiome Exploration App

Microbiome Time Series Analysis

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

Modeling RNA synthesis, processing and degradation with RNA-seq data

Monte Carlo Reference-based Consensus Clustering

Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data

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

Multimodal Mediation Analysis

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

Multivariate analysis of microarray data using ADE4

NanoString GeoMx Tools

Negative Binomial Additive Model for RNA-Seq Data

Negative Binomial Beta t-Test

Negative binomial model for scRNA-seq

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

NIH / NCI Genomic Data Commons Access

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

Nucleosome Dynamics

Nucleosome positioning package for R

Obtain Raw Read Counts from RNASeq Data

Omics Data Integration Project

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-aware and Count-based Compositional Analysis of Single-cell Data.

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

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 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 filtration for microbiome data

Phase template strands from Strand-seq data

Phenotype Consensus ANalysis (PCAN)

Phenotypic EMD for comparison of single-cell samples

Phylogenetic partitioning based ILR transform for metagenomics data

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

Plots of Statistics Collected by Qualimap from RNASeq Data

Plot stacked logos for single or multiple DNA, RNA and amino acid sequence

Plotting data and annotation information along genomic coordinates

Plotting functions for derfinder

PolyA counting and differential transcript usage analysis for scRNA-seq data

Pooling RNA-seq datasets for assembling transcript models

Position-Dependent Kernel Association Test

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

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 combinding m6A reader binding information

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

Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data

Probabilistic inference of ChIP-seq

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

Promoter identification from large-scale TSS profiling data

PROspective Power Evaluation for RNAseq

Provides structure and functions for the analysis of OTU data

QA/QC of a gVCF or VCF file

QC for enrichment based NGS

QTL mapping using Bulk Segregant Analysis of Next Generation Sequencing data.

Quality Assessment Tools for Oxford Nanopore MinION data

Quality Control for Single-Cell RNA-seq Data

Quality control for target capture experiments

Quality Control Tool for High-Throughput Sequencing Data

Quality Control, Visualization and Processing for High-Throughput Sequencing data

Quality metrics for ChIPseq data

Quantification of the Tumor Immune contexture from RNA-seq data

Quantify and Annotate Short Reads in R

Quantifying Differential Features

Quantitative comparison of multiple ChIP-seq datasets

Quantitative DNA Sequencing for Chromosomal Aberrations

Quasispecies Diversity

Query the gene models of a given organism/assembly

Quick Read Quality Control

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

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 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

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

Reliable CNV detection in targeted sequencing applications

Repetitive Element Methylation Prediction

Replicate oriented Visualization of a genomic region

Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries

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 short genomic alignments

Representing GDS files as array-like objects

Representing on-disk / remote VCF files as array-like objects

Retrotransposed transcript detection from structural variants

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

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

RLSeq: An analysis package for R-loop mapping data

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

RnaSeqSampleSize

rnaSeq secondary analyses

RnBeads

Robust Inference for Absolute Abundance in Microbiome Analysis

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

R SDK for BaseSpace RESTful API

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

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

samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation

Sample Size Calculation for RNA-Seq Experimental Design

sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R

"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"

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

Scaling normalization based on the Pareto distribution

Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences

scMerge: Merging multiple batches of scRNA-seq data

scraps output import and processing in R

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

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

Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP 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 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)

Significance-based Modules Integrating the Transcriptome and Epigenome

SILVA SSR rRNA release 128.1 Annotation Data

SIMLR: Single-cell Interpretation via Multi-kernel LeaRning

Simple Simulation of Single-cell RNA Sequencing Data

Simulate RNA-seq reads

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 Batch Correction Methods

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 RNA-Seq Analysis Utilities

Single-cell RNA sequencing data normalization

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

Smooth modeling of bisulfite sequencing

Smooth quantile normalization

Somatic Signatures

Somatic structural variant analysis

Sparse Contrastive Principal Component Analysis

spatialHeatmap

Spatial Transcriptomics Analysis

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 of MPRA data

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 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

Subsampling of high-throughput sequencing count data

Subtype Identification with Survival Data

Summarize, Analyze and Visualize MAF Files

SummarizedExperiment container

Summary, annotation and visualization of genomic data

Supervised mutational signatures

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 Environment for Data Analysis and Report Generation

systemPipeShiny: An Interactive Framework for Workflow Management and Visualization

TADCompare: Identification and characterization of differential TADs

Targeted Learning with Moderated Statistics for Biomarker Discovery

Targeted scRNA-seq primer design for TAP-seq

TARgeted SEQuencing Experiment Quality Control

TCC: Differential expression analysis for tag count data with robust normalization strategies

TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC 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

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 sequencing data analysis

Tissue-specific gene enrichment analysis

Tomo-seq data analysis

Toolkit for Single-Cell Velocity

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 finding Total RNA Expression Genes in single nucleus RNA-seq data

Tools for Managing Seurat Objects

Tools for ordering single-cell sequencing

Tools for performing taxonomic assignment.

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 variant data

Tools for visualizing genomics 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

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 sequencing data analysis

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

uORF prediction in R

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

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 EHT Data

Visual comparison of mutational processes in a set of tumors

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 microarray and RNAseq data using gene ontology annotations

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

Visualization of Methylation Data

What the Package Does (TODO)

Wind: weighted indexes for clustering evaluation

Working with Illumina Basecalling and Demultiplexing input and output files

Working with modified nucleotide sequences

Wrench normalization for sparse count data

XCI-inference

xcore expression regulators inference

YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization

Yet Another Package for Signature Analysis

Zero-Inflated Negative Binomial Model for RNA-Seq Data

Biocview "Sequencing"

R Package Documentation

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