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Workflow/pipeline software tools | RNA sequencing data analysis

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AltAnalyze
Desktop

AltAnalyze

An easy-to-use application for microarray, RNA-Seq and metabolomics analysis.…

An easy-to-use application for microarray, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), AltAnalyze will assess…

oneChannelGUI
Desktop

oneChannelGUI

Facilitates analysis of microarrays and miRNA/RNA-seq data on laptops.…

Facilitates analysis of microarrays and miRNA/RNA-seq data on laptops. oneChannelGUI can be used for quality control, normalization, filtering, statistical validation and data mining for single…

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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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easyRNASeq
Desktop

easyRNASeq

An R package that simplifies the processing of RNA sequencing data, hiding the…

An R package that simplifies the processing of RNA sequencing data, hiding the complex interplay of the required packages behind a single functionality. easyRNASeq calculates the coverage of…

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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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PRADA
Desktop

PRADA

A pipeline to analyze paired end RNA-Seq data to generate gene expression…

A pipeline to analyze paired end RNA-Seq data to generate gene expression values (RPKM) and gene-fusion candidates.

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SAPAS
Desktop

SAPAS

A pipeline for RNA-seq method to research polyA. SAPAS performs a systematic…

A pipeline for RNA-seq method to research polyA. SAPAS performs a systematic search and evaluation of protocols for typical steps to investigate to what extent these can indeed facilitate RNA-seq…

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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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RseqFlow
Desktop

RseqFlow

An RNA-Seq analysis pipeline which offers an express implementation of analysis…

An RNA-Seq analysis pipeline which offers an express implementation of analysis steps for RNA sequencing datasets.

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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…

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TRAPR
Desktop

TRAPR Total RNA-Seq Analysis Package for R

Facilitates the statistical analysis and visualization of RNA-Seq expression…

Facilitates the statistical analysis and visualization of RNA-Seq expression data. TRAPR provides various functions for data management, the filtering of low-quality data, normalization,…

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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…

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QuasR
Desktop

QuasR

Provides an integrated analysis of high-throughput sequencing data in R,…

Provides an integrated analysis of high-throughput sequencing data in R, covering all steps from read preprocessing, alignment and quality control to quantification. QuasR supports different…

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TRAPLINE
Desktop

TRAPLINE Transparent Reproducible and Automated PipeLINE

Serves for RNAseq data processing, evaluation and prediction. TRAPLINE guides…

Serves for RNAseq data processing, evaluation and prediction. TRAPLINE guides researchers through the NGS data analysis process in a transparent and automated state-of-the-art pipeline. It can detect…

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systemPipeR
Desktop

systemPipeR

An extensible environment for both building and running end-to-end analysis…

An extensible environment for both building and running end-to-end analysis workflows with automated report generation for a wide range of next-generation sequencing (NGS) applications. Its unique…

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hppRNA
Desktop

hppRNA

Converts the raw fastq files into gene/isoform expression matrix and…

Converts the raw fastq files into gene/isoform expression matrix and differentially expressed genes or isoforms. hppRNA is a one-in-all solution composed of four scenarios such as pre-mapping,…

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SePIA
Desktop

SePIA Sequence Processing Integration and Analysis

Automates RNA-seq processing, integration and analysis. SePIA allows…

Automates RNA-seq processing, integration and analysis. SePIA allows reproducible analysis of total RNA, poly(A)-derived RNA, small RNA, and integrated microRNA (miRNA) and mRNA data. It provides a…

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wapRNA
Desktop
Web

wapRNA

This is a free web-based application for the processing of high-throughput…

This is a free web-based application for the processing of high-throughput RNA-Seq data from next generation sequencing (NGS) platforms, such as Genome Analyzer of Illumina Inc. (Solexa) and SOLiD of…

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RNA CoMPASS
Desktop

RNA CoMPASS

A web-based GUI distributed computational pipeline, provides all-in-one…

A web-based GUI distributed computational pipeline, provides all-in-one functionality including human transcriptome quantification and the typical endogenous RNA-Sequencing analysis along with the…

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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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Zika-RNAseq-Pip…
Desktop

Zika-RNAseq-Pipeline

Provides an open source RNA-seq processing pipeline that can be used to extract…

Provides an open source RNA-seq processing pipeline that can be used to extract knowledge from any study that profiled gene expression using RNA-seq applied to mammalian cells, comparing two…

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MetaTrans
Desktop

MetaTrans

Analyzes the structure and functions of active microbial communities using the…

Analyzes the structure and functions of active microbial communities using the power of multi-threading computers. MetaTrans is designed to perform two types of RNA-Seq analyses: taxonomic and gene…

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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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OTP
Web

OTP One Touch Pipeline

Provides a platform for storing, handling and processing next generation…

Provides a platform for storing, handling and processing next generation sequencing (NGS) data. OTP performs both data management and processing and allows users to automate an entire process to raw…

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Oqtans
Desktop

Oqtans Online quantitative transcriptome analysis

It is based on the Galaxy-framework and provides tools for read mapping,…

It is based on the Galaxy-framework and provides tools for read mapping, transcript reconstruction and quantitation as well as differential expression analysis.

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TRAP
Desktop
Web

TRAP Time-series RNA-seq Analysis Package

A comprehensive package integrating all necessary tasks such as mapping short…

A comprehensive package integrating all necessary tasks such as mapping short reads, measuring gene expression levels, finding differentially expressed genes (DEGs), clustering and pathway analysis…

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CIPHER
Desktop

CIPHER

Automates the processing and analysis of several commonly used Next Generation…

Automates the processing and analysis of several commonly used Next Generation Sequencing (NGS) datasets including: ChIP-seq, RNA-seq, Global Run On sequencing (GRO-seq), micrococcal nuclease…

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R-SAP
Desktop

R-SAP

An automated bioinformatics pipeline that analyzes and quantifies…

An automated bioinformatics pipeline that analyzes and quantifies high-throughput RNA-Seq datasets.

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RNA-seq portal
Web

RNA-seq portal

Includes three types of workflows for different tasks. RNA-seq portal permits…

Includes three types of workflows for different tasks. RNA-seq portal permits users to perform computing and analysis, including sequence quality control, read-mapping, transcriptome assembly,…

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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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necklace
Desktop

necklace

Automatically combines transcriptomes from difference sources, such as assembly…

Automatically combines transcriptomes from difference sources, such as assembly and annotation, into a compact and unified reference. necklace is applicable to any species with an incomplete…

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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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exceRpt
Web

exceRpt

Allows users to processing of RNA-Seq data. exceRpt is a pipeline for RNA-Seq…

Allows users to processing of RNA-Seq data. exceRpt is a pipeline for RNA-Seq library preparation. The software processes each sample independently through a cascade of read-alignment steps designed…

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zUMIs
Desktop

zUMIs

Processes raw reads to count tables for RNA-seq data using Unique Molecular…

Processes raw reads to count tables for RNA-seq data using Unique Molecular Identifiers (UMIs). zUMIs is a pipeline applicable for most experimental designs of RNA-seq data, such as single-nuclei…

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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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Bio-Docklets
Desktop

Bio-Docklets

Aims to perform basic analysis and interpretation of datasets with minimal…

Aims to perform basic analysis and interpretation of datasets with minimal effort. Bio-Docklets is an approach for abstracting the complex data operations of multi-step, bioinformatics pipelines for…

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TRUFA
Web

TRUFA TRanscriptome User-Friendly Analysis

Offers a web-based interface that generates the outputs commonly used in de…

Offers a web-based interface that generates the outputs commonly used in de novo RNA-seq analysis and comparative transcriptomics. TRUFA provides a comprehensive service that allows performing…

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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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RNA-Rocket
Web

RNA-Rocket

A free service that provides access to RNA-Seq and ChIP-Seq analysis tools for…

A free service that provides access to RNA-Seq and ChIP-Seq analysis tools for studying infectious diseases. The site makes available thousands of pre-indexed genomes, their annotations, and the…

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TCW
Desktop

TCW Transcriptome Computational Workbench

A software package for assembling, annotating, querying, and comparing…

A software package for assembling, annotating, querying, and comparing transcript and expression level data.

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QuickNGS
Desktop
Web

QuickNGS

A workflow system for laboratories with the need to analyze data from multiple…

A workflow system for laboratories with the need to analyze data from multiple NGS projects at a time. QuickNGS takes advantage of parallel computing resources, a comprehensive back-end database, and…

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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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Glbase
Desktop

Glbase

Allows the user to perform many common analyses on ChIP-seq, microarray and…

Allows the user to perform many common analyses on ChIP-seq, microarray and RNA-seq data. Glbase is a flexible and multifunctional toolkit which includes many functions to intersect two lists of…

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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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READemption
Desktop

READemption

Permits the computational evaluation of RNA-Seq data. READemption is an…

Permits the computational evaluation of RNA-Seq data. READemption is an automated RNA-Seq processing with the initial purpose to handle differential RNA-Seq (dRNA-Seq) data for the determination of…

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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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Guide
Desktop

Guide

A desktop application for the bench biologists to analyse RNA-Seq and…

A desktop application for the bench biologists to analyse RNA-Seq and microarray expression data.

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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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rnaSeqMap
Desktop

rnaSeqMap

A toolbox for analyses that may be performed with the use of gene annotations…

A toolbox for analyses that may be performed with the use of gene annotations or alternatively, in an unsupervised mode, on any genomic region to find novel or non-standard transcripts. The data…

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ViennaNGS
Desktop

ViennaNGS

An integrated collection of Perl modules focused on building efficient…

An integrated collection of Perl modules focused on building efficient pipelines for NGS data processing. ViennaNGS comes with functionality for extracting and converting features from common NGS…

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r-make
Desktop

r-make

A pipeline that processes RNA sequencing reads. r-make estimates the expression…

A pipeline that processes RNA sequencing reads. r-make estimates the expression levels for exons, genes, and splice junctions. In the process, it prints a range of quality metrics and statistics,…

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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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Pyicos
Desktop

Pyicos

Analyses mapped reads from diverse High-throughput sequencing (HTS)…

Analyses mapped reads from diverse High-throughput sequencing (HTS) experiments: ChIP-Seq, either punctuated or broad signals, CLIP-Seq and RNA-Seq. Pyicos is a command line utility for the…

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Grape
Desktop

Grape Grape RNA-Seq Analysis Pipeline Environment

Allows analysis of millions of short reads obtained from high-throughput…

Allows analysis of millions of short reads obtained from high-throughput RNA-Seq experiments. Grape is a workflow that automates the steps from RNA-Seq reads to transcript quantification and…

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RSEQtools
Desktop

RSEQtools

A suite of tools that use this format for the analysis of RNA-Seq experiments.

A suite of tools that use this format for the analysis of RNA-Seq experiments.

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RiboPip
Desktop

RiboPip

Enables users to process Ribosome Profiling (Ribo-seq) and RNA sequencing…

Enables users to process Ribosome Profiling (Ribo-seq) and RNA sequencing (RNA-seq) datasets. RiboPip computes a splice-aware alignment to a reference database along with a read summarization and…

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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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DuffyRNAseq
Desktop

DuffyRNAseq

Implements an analysis pipeline for processing RNA-seq data from Illumina…

Implements an analysis pipeline for processing RNA-seq data from Illumina NextGen sequencers, to measure gene transcription and differential expression. DuffyRNAseq offers a multistep read assignment…

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Partek Flow
Desktop

Partek Flow

Enable researchers to self-sufficiently perform data analysis. Partek Flow…

Enable researchers to self-sufficiently perform data analysis. Partek Flow software is designed specifically for the analysis needs of next generation sequencing (NGS) applications including RNA,…

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AIR
Web

AIR Artificial intelligence RNAseq

Offers a solution to close the gap between data production and data…

Offers a solution to close the gap between data production and data interpretation, making it possible for researchers to do their own analysis in the simplest possible way and giving them the…

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QRNAseq
Desktop

QRNAseq

A tool to manage huge amounts of RNA-seq data in an integrative way which…

A tool to manage huge amounts of RNA-seq data in an integrative way which includes RNA-seq data quality control, read alignment, gene fusion, gene mutation, isoform identification and function…

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Maverix…
Desktop

Maverix Analytic Platform

A unique cloud-based analytic environment that integrates current,…

A unique cloud-based analytic environment that integrates current, industry-standard open source tools into pre-configured pipelines designed to be easy-to-use by any scientist/biologist.

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Tuxedo
Desktop

Tuxedo

Handles RNA-sequencing pipeline that is based on TopHat suite. The Tuxedo…

Handles RNA-sequencing pipeline that is based on TopHat suite. The Tuxedo protocol allows to assess alternative splicing inferred on fragments per kilobase per million (FPKM) values.

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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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Strand NGS
Desktop

Strand NGS

Provides analysis, management and visualization tools for next-generation…

Provides analysis, management and visualization tools for next-generation sequencing (NGS) data. Strand NGS supports extensive workflows for alignment, RNA-seq, small RNA-seq, DNA-seq, Methyl-seq,…

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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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RobiNA
Desktop

RobiNA

A User Friendly Graphical Interface to Powerful Open Source Microarray and…

A User Friendly Graphical Interface to Powerful Open Source Microarray and RNA-Seq Processing.

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MAP-RSEQ
Desktop

MAP-RSEQ

A computational workflow that leverages data from an RNA-Seq experiment to…

A computational workflow that leverages data from an RNA-Seq experiment to provide comprehensive reports on genomic features for secondary data analysis.

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