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Read count software tools | RNA sequencing data analysis

Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to each…
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SAMtools
Desktop

SAMtools

A suite of programs for interacting with high-throughput sequencing data. It…

A suite of programs for interacting with high-throughput sequencing data. It can manipulate alignments in the SAM/BAM/CRAM formats : reading, writing, editing, indexing, viewing and converting…

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BEDTools
Desktop

BEDTools

A software suite for the comparison, manipulation and annotation of genomic…

A software suite for the comparison, manipulation and annotation of genomic features in browser extensible data (BED) and general feature format (GFF) format. BEDTools also supports the comparison of…

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EISA
Desktop

EISA Exon-Intron Split Analysis

A computational approach that measures changes in mature RNA and pre-mRNA reads…

A computational approach that measures changes in mature RNA and pre-mRNA reads across different experimental conditions to quantify transcriptional and post-transcriptional regulation of gene…

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rMATS
Desktop

rMATS replicate Multivariate Analysis of Transcript Splicing

A statistical model and computer program designed for detection of differential…

A statistical model and computer program designed for detection of differential alternative splicing from replicate RNA-Seq data. rMATS uses a hierarchical model to simultaneously account for…

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DEXSeq
Desktop

DEXSeq

Tests for differential usage of exons and hence of isoforms in RNA-seq samples.…

Tests for differential usage of exons and hence of isoforms in RNA-seq samples. DEXSeq uses generalized linear models and offers reliable control of false discoveries by taking biological variation…

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IRanges
Desktop

IRanges

A package that provides efficient low-level and highly reusable S4 classes for…

A package that provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding) and, more generally, data that can be organized…

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featureCounts
Desktop

featureCounts

A read summarization program, which counts mapped reads for the genomic…

A read summarization program, which counts mapped reads for the genomic features such as genes and exons.

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rnaseqcomp
Desktop

rnaseqcomp

Evaluates the performance of RNA-seq measurements in terms of specificity and…

Evaluates the performance of RNA-seq measurements in terms of specificity and sensitivity. Rnaseqcomp is a package that offers several quantitative and visualized benchmarks for RNA-seq…

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JuncBASE
Desktop

JuncBASE

It is used to identify and classify alternative splicing events from RNA-Seq…

It is used to identify and classify alternative splicing events from RNA-Seq data.

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SeqGSEA
Desktop

SeqGSEA

Provides methods for gene set enrichment analysis of high-throughput RNA-Seq…

Provides methods for gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing. It uses negative binomial distribution to model read count data,…

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aRNApipe
Desktop

aRNApipe automated RNA-seq pipeline

Provides an integrated and efficient workflow for analyzing single-end and…

Provides an integrated and efficient workflow for analyzing single-end and stranded or unstranded paired-end RNA-seq data. Unlike previous pipelines, aRNApipe is focused on high performance computing…

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Chipster
Desktop

Chipster

A user-friendly analysis software tool for high-throughput data. Chipster…

A user-friendly analysis software tool for high-throughput data. Chipster contains over 350 analysis tools for next generation sequencing (NGS), microarray, proteomics and sequence data. Users can…

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NGS-Trex
Web

NGS-Trex NGS TRanscriptome profile EXplorer

Allows user to upload raw sequences and obtain an accurate characterization of…

Allows user to upload raw sequences and obtain an accurate characterization of the transcriptome profile. NGS-Trex can assess differential expression at both gene and transcript level. It compares…

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QuickRNASeq
Desktop

QuickRNASeq

Advances the automation and visualization of RNA-seq data analyses results.…

Advances the automation and visualization of RNA-seq data analyses results. QuickRNASeq is a pipeline that significantly reduces data analysts’ hands-on time, which results in a substantial…

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FineSplice
Desktop

FineSplice

A pipeline based on TopHat2 combined with a splice junction detection algorithm.

A pipeline based on TopHat2 combined with a splice junction detection algorithm.

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GENE-counter
Desktop

GENE-counter

A computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for…

A computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression of eukaryotes, prokaryotes, as well as organisms with no available genome reference sequence.

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expressRNA
Web

expressRNA

Processes 3’ mRNA sequencing data. expressRNA classifies the sites where…

Processes 3’ mRNA sequencing data. expressRNA classifies the sites where cleavage and polyadenylation take place. It is able to identify the differentially regulated poly(A) sites. This tool…

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rDiff
Desktop

rDiff

An open source tool for accurate detection of differential RNA processing from…

An open source tool for accurate detection of differential RNA processing from RNA-Seq data.

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CANEapp
Desktop

CANEapp Comprehensive automated Analysis of Next-generation sequencing Experiments

Integrates data from different sources and experiments. CANEapp is a platform…

Integrates data from different sources and experiments. CANEapp is a platform for integrating next-generation sequencing (NGS) analysis pipelines and tools into a user-friendly suite that can be…

TEtools
Desktop

TEtools transposable elements tools

Provides analysis of TE expression. TEtools takes into account the TE sequence…

Provides analysis of TE expression. TEtools takes into account the TE sequence diversity of the genome. It can be applied to unannotated or unassembled genomes and is freely available under the GPL3.…

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EQP
Desktop

EQP Exon Quantification Pipeline

Allows estimation of the expression level of genes, exons and exon-exon…

Allows estimation of the expression level of genes, exons and exon-exon junctions in RNA-seq experiments. EQP performs the steps of alignment and quantification to generate three types of counts. It…

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ST Pipeline
Desktop

ST Pipeline

Permits to process and analyze the raw files generated with the Spatial…

Permits to process and analyze the raw files generated with the Spatial Transcriptomics (ST) method. ST Pipeline enables demultiplexing of spatially-resolved RNA-seq data and robust quality filtering…

SPLICIFY
Desktop

SPLICIFY

Identifies differentially expressed splice variants on RNA and protein level.…

Identifies differentially expressed splice variants on RNA and protein level. SPLICIFY is able to identify condition-specific aberrant splicing events on protein level by performing comparative…

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RNAMiner
Web

RNAMiner

A multi-level bioinformatics protocol and pipeline. RNAMiner includes five…

A multi-level bioinformatics protocol and pipeline. RNAMiner includes five steps: Mapping RNA-Seq reads to a reference genome, calculating gene expression values, identifying differentially expressed…

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miARma-Seq
Desktop

miARma-Seq

Designed for mRNA, miRNA and circRNA identification and differential expression…

Designed for mRNA, miRNA and circRNA identification and differential expression analysis, applicable to any sequenced organism. miARma-Seq is presented as a stand-alone tool that provides different…

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voom
Desktop

voom

Estimates, from RNA-seq experiments, the mean-variance relationship of the…

Estimates, from RNA-seq experiments, the mean-variance relationship of the log-counts, generates a precision weight for each observation and enters these into the limma empirical Bayes analysis…

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DSGseq
Desktop

DSGseq

This program is aimed to identify differentially spliced genes from two groups…

This program is aimed to identify differentially spliced genes from two groups of RNA-seq samples.

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LSTrAP
Desktop

LSTrAP Large-Scale Transcriptome Analysis Pipeline

Pre-processes RNA-seq data and maps it to the genome. LSTrAP performs quality…

Pre-processes RNA-seq data and maps it to the genome. LSTrAP performs quality control and produces co-expression networks. It provides functional and comparative genomics data to enable a host of…

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NGS-pipe
Desktop

NGS-pipe

Allows to develop tailored workflows for the analysis of whole-exome (WES),…

Allows to develop tailored workflows for the analysis of whole-exome (WES), whole-genome (WGS), and transcriptome (RNA-seq) sequencing data. NGS-pipe is an automated framework for the design of…

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RNA workbench
Server

RNA workbench

Establishes a central, redistributable workbench for scientists and programmers…

Establishes a central, redistributable workbench for scientists and programmers working with RNA-related data. The RNA workbench builds a sustainable community around it. This platform is unique in…

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viGEN
Desktop

viGEN

Combines existing well-known and novel RNA-seq tools for not only detection and…

Combines existing well-known and novel RNA-seq tools for not only detection and quantification of viral RNA, but also variants in the viral transcripts. ViGEN includes 4 major modules: the first…

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HTSeq
Desktop

HTSeq

A Python library to facilitate the rapid development of scripts. HTSeq offers…

A Python library to facilitate the rapid development of scripts. HTSeq offers parsers for many common data formats in HTS projects, as well as classes to represent data, such as genomic coordinates,…

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RAP
Web

RAP RNA-seq Analysis Pipeline

Allows users to analyze sequencing data in multiple steps. The RAP purpose is…

Allows users to analyze sequencing data in multiple steps. The RAP purpose is to investigate the complex transcriptional landscape of eukaryotic transcriptomes through a computationally optimized…

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IRAP
Desktop

IRAP integrated RNA-seq Analysis Pipeline

A flexible RNA-seq analysis pipeline that allows the user to select and apply…

A flexible RNA-seq analysis pipeline that allows the user to select and apply their preferred combination of existing tools for mapping reads, quantifying expression and testing for differential…

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VERSE
Desktop

VERSE

An RNA-seq read counting tool which builds upon the speed of featureCounts and…

An RNA-seq read counting tool which builds upon the speed of featureCounts and implements the counting modes of HTSeq. VERSE is more than 30x faster than HTSeq when computing the same gene counts.…

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OncoRep
Desktop

OncoRep Oncogenomics Report

A fully automated RNA-Seq based report for patients with (breast) cancer, which…

A fully automated RNA-Seq based report for patients with (breast) cancer, which includes molecular classification, detection of altered genes, detection of altered pathways, identification of gene…

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SPARTA
Desktop

SPARTA

Extracts raw Illumina reads to differentially expressed genes. SPARTA is a…

Extracts raw Illumina reads to differentially expressed genes. SPARTA is a bacterial RNA-seq analysis tool performing transcriptional profiling experiments using RNA-seq. It enables microbiologists…

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RACKJ
Desktop

RACKJ Read Analysis & Comparison Kit in Java

A set of Java programs that analyze and compare RNA-seq data made by NGS…

A set of Java programs that analyze and compare RNA-seq data made by NGS technologies. In addition to RPKM (Reads Per Kbp per Million reads) values, RACKJ computes read counts for exons and splicing…

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IntEREst
Desktop

IntEREst Intron Exon Retention Estimator

Performs intron-exon retention analysis on RNA-seq data. IntEREst facilitates…

Performs intron-exon retention analysis on RNA-seq data. IntEREst facilitates estimation and comparison of splicing efficiency of various transcripts across several samples. It can estimate the…

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ASpli
Desktop

ASpli

Simplifies the characterization of genome-wide changes in alternative splicing…

Simplifies the characterization of genome-wide changes in alternative splicing (AS) under different experimental conditions. ASpli analyzes the differential usage of introns, exons, and splice…

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sRAP
Desktop

sRAP

Provides a pipeline for gene expression analysis (primarily for RNA-Seq data).…

Provides a pipeline for gene expression analysis (primarily for RNA-Seq data). The normalization function is specific for RNA-Seq analysis, but all other functions of sRAP (Quality Control Figures,…

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GenomicRanges
Desktop

GenomicRanges

Defines general purpose containers for storing and manipulating genomic…

Defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. GenomicRanges builds upon the IRanges package to add biological semantics to…

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multi mapping…
Desktop

multi mapping counter

Allows users to record the number of readings produced by RNA-Seq per gene.…

Allows users to record the number of readings produced by RNA-Seq per gene. multi mapping counter is a standalone software authorizing multi-mapping reads, that includes a function for counting a…

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PORT
Desktop

PORT Pipeline of RNA-Seq Transformations

Allows users to work on normalization or quantification of RNA-seq. PORT…

Allows users to work on normalization or quantification of RNA-seq. PORT enables to realize two types of normalization: (1) exon-intron-junction normalization and (2) gene normalization.

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Quantas
Desktop

Quantas

A pipeline to analyze alternative splicing using RNA-Seq. gapless and countit…

A pipeline to analyze alternative splicing using RNA-Seq. gapless and countit are collectively named Quantas. The pipeline has been tested quite extensively, but the document is still at its…

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bcbio-nextgen
Desktop

bcbio-nextgen

A python toolkit providing best-practice pipelines for fully automated high…

A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. You write a high level configuration file specifying your inputs and analysis parameters.…

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Array Studio
Desktop

Array Studio

Provides the premier enterprise solution for data content, framework and…

Provides the premier enterprise solution for data content, framework and graphical user interface for omic and next-generation sequencing data analysis. Array Suite (Array Studio and Array Server)…

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