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Other software tools | RNA sequencing data analysis

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Sequins
Dataset

Sequins Sequencing spike-ins

A set of spike-in RNA standards that represent full-length spliced mRNA…

A set of spike-in RNA standards that represent full-length spliced mRNA isoforms. Sequins have an entirely artificial sequence with no homology to natural reference genomes, but they align to gene…

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TROM
Desktop

TROM Transcriptome Overlap Measure

Identifies both protein-coding and non-coding indicators. TROM performs a…

Identifies both protein-coding and non-coding indicators. TROM performs a comprehensive transcriptome mapping for diverse tissues and cell types within and across four mammalian species. It also…

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GenomicFeatures
Desktop

GenomicFeatures

Enables access and manipulation of gene models and other annotations.…

Enables access and manipulation of gene models and other annotations. GenomicFeatures is a set of tools and methods that allows to make and manipulate transcript centric annotations. The software…

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GRridge
Desktop

GRridge

Improves the predictive performances of ordinary logistic ridge regression and…

Improves the predictive performances of ordinary logistic ridge regression and the group lasso. GRridge allows the use of multiple sources of co-data (e.g. external p-values, gene lists, annotation)…

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V'DJer
Desktop

V'DJer

A software for inference of B-cell receptor (BCR) repertoires using short-read…

A software for inference of B-cell receptor (BCR) repertoires using short-read RNA sequencing data. V'DJer uses customized read extraction, assembly and V(D)J rearrangement detection and…

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FocalScan
Desktop

FocalScan

A tool designed to simultaneously uncover patterns of focal copy number…

A tool designed to simultaneously uncover patterns of focal copy number alteration and coordinated expression change, thus combining both principles. FocalScan outputs a ranking of tentative cancer…

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GISPA
Desktop

GISPA Gene Integrated Set Profile Analysis

Combines and compares several genome-wide data types from three or more sample…

Combines and compares several genome-wide data types from three or more sample classes in order to find the drivers of each class. GISPA produces ranked gene sets within the context of an a priori…

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SeqTU
Desktop
Web

SeqTU

Identifies transcription units (Tus) with given RNA-seq data of any bacterium…

Identifies transcription units (Tus) with given RNA-seq data of any bacterium using a machine-learning approach. SeqTU can serve as the baseline information for studying transcriptional and…

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sigQC
Desktop

sigQC

Simplifies the quality control metrics used to evaluate the applicability of a…

Simplifies the quality control metrics used to evaluate the applicability of a gene signature to a given dataset. sigQC can evaluate a published gene signature for breast cancer metastasis and a…

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MAJIQ-SPEL
Web

MAJIQ-SPEL MAJIQ for Sampling Primers and Evaluating Local splicing variations

Helps in the visualization, interpretation, and experimental validation of both…

Helps in the visualization, interpretation, and experimental validation of both classical and complex splicing variations. MAJIQ-SPEL offers researchers fast and accurate primer design for de novo…

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RNASeq-er
Web

RNASeq-er

Accesses the results of a systematically and continually updated and…

Accesses the results of a systematically and continually updated and continually growing analysis of public RNA-seq data in European Nucleotide Archive (ENA). RNASeq-er enables ontology-powered…

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MLSeq
Desktop

MLSeq

Allows classification of the RNAseq data. MLSeq is a machine learning interface…

Allows classification of the RNAseq data. MLSeq is a machine learning interface that provides several methods, such as support vector machine (SVM), bagSVM, Random Forest (RF) and CART. The software…

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Seq2pathway
Desktop

Seq2pathway

An R/Python wrapper for pathway (or functional gene-set) analysis of genomic…

An R/Python wrapper for pathway (or functional gene-set) analysis of genomic loci, adapted for advances in genome research. Seq2pathway associates the biological significance of genomic loci with…

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globalSeq
Desktop

globalSeq

A powerful test for finding eQTL effects based upon RNA-seq data. globalSeq can…

A powerful test for finding eQTL effects based upon RNA-seq data. globalSeq can be computed efficiently and is able to handle sets of highly correlated covariates. The proposed test can detect…

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ChloroSeq
Desktop

ChloroSeq

Analyses the chloroplast transcriptome using RNA-Seq. ChloroSeq uses RNA-Seq…

Analyses the chloroplast transcriptome using RNA-Seq. ChloroSeq uses RNA-Seq alignment data to deliver detailed analyses of organelle transcriptomes, which can be fed into statistical software for…

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mRIN
Desktop

mRIN mRNA integrity number

A computational method to assess a quantitative measure of mRNA integrity. This…

A computational method to assess a quantitative measure of mRNA integrity. This is done by quantitatively modeling of the 3' bias of read coverage profiles along each mRNA transcript. A…

Informatics…
Desktop

Informatics for RNA-seq

Stores code and certain raw materials for a detailed RNA-seq tutorial.…

Stores code and certain raw materials for a detailed RNA-seq tutorial. Informatics for RNA-seq is an educational tutorial and working demonstration pipeline for RNA-seq analysis including an…

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ToNER
Desktop

ToNER Transformation of Nucleotide Enrichment Ratios

Identifies enriched sites from differential RNA-seq experiments comprising…

Identifies enriched sites from differential RNA-seq experiments comprising enriched and unenriched libraries. ToNER uses a global distribution model to report statistics of enrichment for all…

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Zipper plot
Web

Zipper plot

A visualization and analysis method to interrogate putative transcription start…

A visualization and analysis method to interrogate putative transcription start sites (TSSs) in relation to various features that are indicative for transcriptional activity. The Zipper plot enables…

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ROP
Desktop

ROP Read Origin Protocol

A computational protocol aimed to discover the source of all reads, which…

A computational protocol aimed to discover the source of all reads, which originate from complex RNA molecules, recombinant antibodies and microbial communities. The ROP accounts for 98.8% of all…

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phASER
Desktop

phASER phasing and Allele Specific Expression from RNA-seq

A fast and accurate approach for phasing variants that are overlapped by…

A fast and accurate approach for phasing variants that are overlapped by sequencing reads, including those from RNA-sequencing (RNA-seq), which often span multiple exons due to splicing. phASER…

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TcellClonality
Desktop

TcellClonality

An R script for processing MiTCR-derived CDR3 data from Peripheral T Cell…

An R script for processing MiTCR-derived CDR3 data from Peripheral T Cell Lymphoma (PTCL) RNA-seq. TcellClonality will remove non-productive CDR3 sequences, calculate the relative abundance of each…

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SPEQC
Desktop

SPEQC Structure Probing Experiment Quality Control

Rapid and quantitative metrics for evaluating structure probing data quality.…

Rapid and quantitative metrics for evaluating structure probing data quality. SPEQC uses metrics to rapidly and quantitatively evaluate data quality from structure probing experiments, demonstrating…

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NVT
Desktop

NVT

Provides a fast and simple way to analyze and evaluate multiple normalization…

Provides a fast and simple way to analyze and evaluate multiple normalization methods via visualization and representation of correlation values, based on a user-defined set of uniformly expressed…

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PINCAGE
Desktop

PINCAGE Probabilistic INTegration of CAncer GEnomics data

Allows candidate biomarker identification and sample classification. PINCAGE is…

Allows candidate biomarker identification and sample classification. PINCAGE is a flexible model for integration of multiple gene-level genomic data types. It separately models the relationships…

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CAMUR
Desktop

CAMUR Classifier with Alternative and MUltiple Rule-based models

Extracts multiple and equivalent classification models. CAMUR iteratively…

Extracts multiple and equivalent classification models. CAMUR iteratively computes a rule-based classification model, calculates the power set of the genes present in the rules, iteratively…

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LaSSO
Desktop

LaSSO Lariat Sequence Site Origin

An R script that creates a FASTA database containing all possible lariat…

An R script that creates a FASTA database containing all possible lariat signatures from a given set of introns.

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FIXSEQ
Desktop

FIXSEQ

An over-dispersion correction technique that serves as a smarter way to…

An over-dispersion correction technique that serves as a smarter way to de-duplicate counts.

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Parseq
Desktop

Parseq

A statistical approach for transcription landscape reconstruction at a basepair…

A statistical approach for transcription landscape reconstruction at a basepair resolution from RNA Seq read counts.

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dbHT-Trans
Desktop

dbHT-Trans

Filters the protein-encoding transcripts assembled by RNA-Seq according to…

Filters the protein-encoding transcripts assembled by RNA-Seq according to homology search. dbHT-Trans can generate metadata for each processing step and store them into a MySQL database. It has been…

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UClncR
Desktop

UClncR Ultrafast and Comprehensive lncRNA

Detects and analyzes long non-coding RNAs from RNA-seq, both known and…

Detects and analyzes long non-coding RNAs from RNA-seq, both known and predicted ones. UClncR is a quantifcation pipeline that works with both stranded and un-stranded RNA-seq protocols and is…

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CLIFinder
Desktop

CLIFinder Chimeric LIne Finder

Recognizes chimeras corresponding to potential L1 Chimeric Transcripts (LCTs)…

Recognizes chimeras corresponding to potential L1 Chimeric Transcripts (LCTs) in RNA-seq data from one or several samples. CLIFinder aims to analyze stranded paired-end RNA-seq data. It can be useful…

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SeqBox
Desktop

SeqBox

Allows to conduct most common analyses of RNAseq and ChIPseq data. SeqBox can…

Allows to conduct most common analyses of RNAseq and ChIPseq data. SeqBox can be useful for genomic mapping, experimental power evaluation, differential expression, or transcription…

EpiDenovo
Web

EpiDenovo

Investigates developmental epigenomes and transcriptomes that are related to De…

Investigates developmental epigenomes and transcriptomes that are related to De novo mutations (DNMs) in developmental disorders. EpiDenovo is a database for exploring the associations between…

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TrUC
Desktop

TrUC Transcription Units by Coverage

Permits to predict transcription units. TrUC uses oriented data to make its…

Permits to predict transcription units. TrUC uses oriented data to make its predictions. It predicts introns from un-oriented RNA-Seq data. It allows to improve Paramecium gene models not only by…

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The RNASeq-er…
Desktop

The RNASeq-er API

Permits to access to the results of a systematically and continually updated…

Permits to access to the results of a systematically and continually updated standardized alignment. The RNASeq-er API enables ontology-powered search for and retrieval of CRAM, bigwig and bedGraph…

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DeepBound
Desktop

DeepBound

Identifies boundaries of expressed transcripts from RNA-seq reads alignment.…

Identifies boundaries of expressed transcripts from RNA-seq reads alignment. DeepBound is an effective approach to employs deep convolutional neural fields to learn the hidden distributions and…

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HapIso
Desktop

HapIso Haplotype-specific Isoform Reconstruction

Reconstructs the haplotype-specific isoforms from long single-molecule reads.…

Reconstructs the haplotype-specific isoforms from long single-molecule reads. HapIso is a comprehensive method for the accurate reconstruction of the haplotype-specific isoforms of a diploid cell…

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rnaSeqAssumptio…
Desktop

rnaSeqAssumptions

Contains simulation code for evaluating RNA-Seq normalization methods when…

Contains simulation code for evaluating RNA-Seq normalization methods when assumptions are violated. rnaSeqAssumptions code is implemented in R and is freely available for download. Normalization…

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BIRD
Desktop

BIRD Big data Regression for predicting DNase I hypersensitivity

Predicts DNase I hypersensitivity. BIRD handles the prediction problem where…

Predicts DNase I hypersensitivity. BIRD handles the prediction problem where both predictors and responses are ultra-high-dimensional. It groups correlated predictors into clusters and transforms…

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HTSFilter
Desktop

HTSFilter

Calculates a filtering threshold for replicated RNA sequencing data. HTSFilter…

Calculates a filtering threshold for replicated RNA sequencing data. HTSFilter provides an intuitive data-driven way to filter RNA-seq data and to effectively remove genes with low constant…

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KABOOM
Desktop

KABOOM

An algorithm for finding candidate pairs for clustering gene expression data.…

An algorithm for finding candidate pairs for clustering gene expression data. The idea is that two sequences are candidates for comparison if they share α many common k-words, where the leftmost and…

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GigaTON
Dataset

GigaTON Gigas TranscriptOme pipeliNe

Studies the genome of the Pacific oyster, Crassostrea gigas. GigaTON provides a…

Studies the genome of the Pacific oyster, Crassostrea gigas. GigaTON provides a web browser that allows a convenient view of the target contig counterparts in numerous other databases at a single…

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TIN
Desktop

TIN Transcript Integrity Number

A reliable measurement of RNA integrity and a valuable approach used to…

A reliable measurement of RNA integrity and a valuable approach used to neutralize in vitro RNA degradation effect and improve differential gene expression analysis. The TIN metric is not only a…

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mseq
Desktop

mseq

An R package for modeling non-uniformity in short-read rates in RNA-Seq data.…

An R package for modeling non-uniformity in short-read rates in RNA-Seq data. mseq can lead to improved estimates of gene and isoform expressions for both Illumina and Applied Biosystems data.

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TACO
Desktop

TACO Transcriptome Assemblies Combined into One

Reconstructs a consensus transcriptome from a collection of individual…

Reconstructs a consensus transcriptome from a collection of individual assemblies. TACO is an algorithm that employs change point detection to break apart complex loci and correctly delineate…

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Seqnature
Desktop

Seqnature

A set of programs to create custom sequences from a reference sequence and a…

A set of programs to create custom sequences from a reference sequence and a pair of VCF files containing SNP and Indel information.

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Barnacle
Desktop

Barnacle Browsing Assembled RNA for Chimeras with Localized Evidence

Resolves conflicts due to repeated sequences in RNA. Barnacle is a pipeline for…

Resolves conflicts due to repeated sequences in RNA. Barnacle is a pipeline for detecting and characterizing chimeric transcripts from long RNA sequences, such as those generated by de novo…

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XSAnno
Desktop

XSAnno

A computational framework that integrates previous approaches with multiple…

A computational framework that integrates previous approaches with multiple filters to improve the accuracy of inter-species transcriptome comparisons.

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TSSpredator
Desktop

TSSpredator

A Java program for the automated detection and classification of transcription…

A Java program for the automated detection and classification of transcription start sites (TSS) from RNA-seq data. TSSpredator reads RNA-seq data in the form of simple wiggle files and performs a…

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TReNA
Desktop

TReNA

Permits to reconstruct transcriptional regulatory networks. TReNA uses gene…

Permits to reconstruct transcriptional regulatory networks. TReNA uses gene expression, priors, machine learning to process. It is particularly useful in species for which genome-wide transcription…

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DAFS
Algorithm

DAFS

A data-adaptive approach was developed to estimate the lower bound of high…

A data-adaptive approach was developed to estimate the lower bound of high expression for RNA-seq data. The Kolmgorov-Smirnov statistic and multivariate adaptive regression splines were used to…

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TruHmm
Desktop

TruHmm TRanscription Units assembly by a Hidden Markov Model

A reference based transcriptome assembler for prokaryotes, and is suitable for…

A reference based transcriptome assembler for prokaryotes, and is suitable for assembling transcripts for directional RNA-seq library. Furthermore, with the recognition of the highly complex nature…

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N-of-1-pathways
Desktop

N-of-1-pathways

A global framework relying on three principles: (i) the statistical universe is…

A global framework relying on three principles: (i) the statistical universe is a single patient; (ii) significance is derived from geneset/biomodules powered by paired samples from the same patient;…

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Tail Tools
Desktop

Tail Tools

Performs a pipeline for Illumina or SOLiD sequencing reads with poly(A) tails…

Performs a pipeline for Illumina or SOLiD sequencing reads with poly(A) tails analysis. Tail Tools includes multiple tools that permit to generating an HTML report of the analysis, a way for results…

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PVT
Desktop

PVT PAVFinder_transcriptome

Locates structural variants in transcriptome assemblies. PVT infers variants…

Locates structural variants in transcriptome assemblies. PVT infers variants from non-contiguous contig sequence alignments to the reference genome. It can classify different classes of variants such…

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Genome2Seq
Web

Genome2Seq

Finds a FASTA file corresponding to sequences based on genome co-ordinates.…

Finds a FASTA file corresponding to sequences based on genome co-ordinates. Genome2Seq can retrieve genes data generated from RNA-Seq data and Gene Ontology (GO) annotations.

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HTS-Tools
Desktop

HTS-Tools

Tools and scripts for basic analysis of NGS data. This is a collection of tools…

Tools and scripts for basic analysis of NGS data. This is a collection of tools for the analysis of NGS data (ChIP-Seq, RNA-Seq, methylation analysis and motif scanning). They are written mostly in…

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CHIP-RNA-SEQPRO
Desktop

CHIP-RNA-SEQPRO

A strategy for identifying regions of epigenetic deregulation associated with…

A strategy for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing sites. CHIP-RNA-SEQPRO is a tool for comparative analysis of a broad variety…

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genCAT
Desktop

genCAT Gene's Comprehensive Annotation Tool

It is an open platform that allows users to incorporate as many datasets…

It is an open platform that allows users to incorporate as many datasets (concepts) as possible to annotate the input gene list, as long as these datasets are prepared in bigwig, BED, BAM/SAM formats.

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BAMStats
Desktop

BAMStats

A GUI desktop tool for calculating and displaying metrics to assess the success…

A GUI desktop tool for calculating and displaying metrics to assess the success of Next Generation Sequencing mapping tools.

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iRNA-seq
Desktop

iRNA-seq intron RNA-seq

An easy, sensitive and accurate computational method for genome-wide assessment…

An easy, sensitive and accurate computational method for genome-wide assessment of transcriptional activity based on analysis of intron coverage from total RNA-seq data. iRNA-seq offers an attractive…

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