Visualization

Web-based

expVIP

• Description : expVIP is a web-based tool for RNA-seq data visualization and analysis of differential expression. The features include a generation of a custom web browser for sorting, filtering, and visualization of RNA-seq data.

spongeScan

• Description : spongeScan is a web-based tool for identification and visualization of long non-coding RNAs (lncRNAs) response elements (MREs) that function as miRNA sponges.

ASCOT

• Description : ASCOT is a web-based tool for querying, summarizing, and visualization of alternative splicing models in public human and mouse RNA-Seq data. ASCOT uses Snaptron and Recount2.

DEIVA

• Description : DEIVA (Differential Gene Expression Interactive Visual Analysis) is a tool for visualizing differential gene expression (DGE) results. Both web-based and stand-alone versions are available.

JBrowse

• Description : JBrowse is a tool for visualizing genomic data and aligned high-throughput sequencing reads using a web-based browser. It has an AJAX interface.

ATGC transcriptomics

• Description : ATGC transcriptomics is a tool for visualization and analysis of RNA-seq data.

RNASeqExpressionBrowser

• Description : RNASeqExpressionBrowser is a tool for visualization of RNA-seq data. The RNASeqExpressionBrowser package contains functions for browsing genes using identifiers, annotations, sequence similarity, and searching differentially and co-expressed genes.

ReadXplorer

• Description : ReadXplorer is a tool for visualization of genomic and transcriptomic mapped data. The ReadXplorer algorithm has functions for computing quality and quantity of alignments for classification, single nucleotide polymorphism (SNP) and transcription start site (TSS) detection, differential expression analysis, and transcriptome identification.

SaVanT

• Description : SaVanT (Signature Visualization Too) is a web-based tool for signature visualization of RNA-seq data samples.

rMAPS

• Description : rMAPS is a web-based tool for the analysis of RNA-binding proteins (RBPs) binding sites. rMAPS has two main modules: Motif Map for enrichment analysis of RNA-binding proteins and CLIP Map for computing of RNA-maps.

BEST

• Description : BEST is a web-based tool for visualization and analysis of spatio-temporal brain expression in RNA-seq data. The visualizations methods include heatmaps, Venn-diagrams, co-expression networks, and Manhattan plots. The source code is available from the authors upon request.

START

• Description : START (Shiny Transcriptome Analysis Resource Tool) App is a web-based tool for visualization of RNA-seq data analysis results.

visTrajectory

• Description : visTrajectory is a tool to visualize high-dimensional datasets in RNA-seq data. The algorithm is based on Bayesian Unidimensional Scaling (BUDS) method to extract principal variation sources from high-dimensional data.

GraphiteWeb

• Description : GraphiteWeb is a web-based tool to analyze and visualize pathways of gene expression in RNA-seq data sets.

MeV

• Description : MeV (Multiple Experiment Viewer) is a tool to visualize differential gene expression (DGE) in RNA-seq data. The MeV tool includes functions for converting raw count data to RPKM or FPKM values.

BrowserGenome

• Description : BrowserGenome is a web-based tool for the analysis and visualization of RNA-seq data. The BrowserGenome tool includes functions for barcode deconvolution, read mapping, real-time data visualization, transcript-count analysis, and normalization.

Heatmapper

• Description : Heatmapper is a web-based tool to visualize data as heatmaps. It can generate heatmaps for a wide variety of data, for example, generate, cluster and visualize: (1) expression-based heat maps from transcriptomic, proteomic and metabolomic experiments; (2) pairwise distance maps; (3) correlation maps; (4) image overlay heat maps; (5) latitude and longitude heat maps and (6) geopolitical (choropleth) heat maps.

Stand-alone

Cascade

• Description : A web-based tool for 3D visualization of RNA-seq data sets from cancer genomic investigations. The Cascade can visualize such data, as alternative splicing frequencies, mutations, and gene expressions.

omicplotR

• Description : omicplotR is a Shiny app to visualize RNA-seq, meta-RNA-seq, and 16s rRNA data. The omicplotR package has methods for differential expression analysis using ALDEx2, biplots for principal component analysis (PCA), dendrograms, stacked bar, and effect plots.

TRAPR

• Description : A tool for visualization and statistical analysis of RNA-seg data. The TRAPR algorithm can filter low-quality data, normalize, transform, perform statistical analyses, and visualize data. The ability to visualize results supports the creation of customized computing pipelines. It additionally has functions for data management.

FastProject

• Description : FastProject is a tool to visualize single-cell RNA-seq (scRNA-seq) data to aid in interpretation. It computes a report of two-dimensional projections with annotations.

SpliceDetector

• Description : SpliceDetector is a tool to detect alternative splicing in RNA-seq. The SpliceDetector algorithm uses the Ensembl transcript IDs to identify splicing events, computes statistical analysis of alternative and differential splicing, and presents the results in a graphical view.

sleuth

• Description : sleuth, an R tool for differential analysis and benchmarking RNA-seq experiments. The sleuth package analyzes and benchmarks data, quantified by the kallisto tool (see links). sleuth also includes interactive graphical visualization tools.

AltAnalyze

• Description : AltAnalyze is a tool for the analysis of differential gene expression and alternative splicing in RNA-seq and Affymetrix (exon, gene, junction) data. The AltAnalyze includes multiple visualization functions, for example, network, pathway, splicing graph, and varying levels of abstraction: isoform, exon, protein, domain, molecular interactions.

derfinder

• Description : derfinder is a tool for differential expression analysis of RNA-seq data. The derfinder package provides single base-level F-statistics and identification at differentially expressed region (DER) levels. The derfinder algorithm uses a bump-hunting method for the identification of differentially expressed regions and among others, multi-group and time-course analyses. The derfinder package also contains visualization functions.

CountClust

• Description : CountClust is a visualization tool for expression data applying grade of membership (admixture models, topic models, Latent Dirichlet Allocation) models in RNA-seq data.

DEBrowser

• Description : DEBrowser is an R Shiny app for step-wise visualizing expression data from RNA-seq. The debrowser package has methods to plot various types of graphs, such as scatter, box, bar, heatmaps, MA, and volcano.

DomainGraph

• Description : DomainGraph is a plugin for Cytoscape to visualize molecular interaction networks. DomainGraph facilitates analysis of the effects of alternative splicing on genes, protein isoforms, molecular interactions, pathways, and miRNA binding sites. DomainGraph visualizes results produced by the AltAnalyze tool, including automatic annotation of affected genes, pathways, and miRNA binding sites. Requires: Cytoscape 2.6, and Java SE 8.

Artemis

• Description : Artemis set of software consists of 1. Artemis for browsing and annotating genomes, 2. Artemis Comparison Tool (ACT) to compare DNA sequences and to investigate synteny, 3. BamView to visualize BAM and CRAM files, and 4. DNAPlotter uses Artemis to read EMBL, GFF3, and Genbank files to generate DNA maps.

DEIVA

• Description : DEIVA (Differential Gene Expression Interactive Visual Analysis) is a tool for visualizing differential gene expression (DGE) results. Both web-based and stand-alone versions are available.

Integrated genome browser (IGB)

• Description : Integrated Genome Browser (IGB) is a desktop application for browsing genomes and large-scale related datasets. It displays annotations and position-specific graphs, among others. Affymetrix originally developed the IGB tool.

Integrative Genomics Viewer (IGV)

• Description : Integrative Genomics Viewer (IGV) is a tool for visualizing high-throughput, large sequencing data sets. It allows loading a reference genome, separate tracks, annotations from both local and remote sources. A web-tool is also available, running at https://igv.org/app/.

SplicingViewer

• Description : SplicingViewer is a tool visualizing, detection, and annotation of splicing patterns.

MeV

• Description : MeV (Multiple Experiment Viewer) is a tool to visualize differential gene expression (DGE) in RNA-seq data. The MeV tool includes functions for converting raw count data to RPKM or FPKM values.

MochiView

• Description : MochiView is a tool to visualize and analyze genomic sequences and features. MochiView is useful for the exploration of RNA-seq, ChIP-Seq, and ChIP-Chip data.

S-MART

• Description : S-MART is a tool to manage and visualize mapped RNA-seq and ChIP-seq data.

BamView

• Description : BamView is a tool to visualize data in sequence reads aligned on a reference genome sequence.

Apollo

• Description : Apollo is a tool A collaborative, real-time, genome annotation web-based editor.

PANEV

• Description : PANEV (PAthway NEtwork Visualizer) is a tool to visualize gene/pathway-based networks using KEGG.

Gene fusion

Subread

• Description : Subread is a software tool package for the alignment of both DNA-seq and RNA-seq read data, quantification, and mutation detection. The Subread package consists of five separate tools: 1. Subread, a read aligner for both RNA-seq and DNA-seq data, 2. Subjunc, read aligner for RNA-seq data, detection of exon-exon junctions and gene fusion events, 3. featureCounts, read counting, 4. Sublong, for aligning long reads using the seed-and-vote technique, and 5. exactSNP, a single-nucleotide polymorphism discovery. An R version of the Subread package is also available, Rsubread .

SOAPfusion

• Description : SOAPfusion is a tool to discover fusions in paired-endn RNA-seq data.

STARChip

• Description : STARChip (Star Chimeric Post) is a tool for detect fused sequences and circular RNA from the output of the STAR alignment tool.

Rsubread

• Description : Rsubread is an R tool for RNA-/DNA-seq data mapping, read counting, single-nucleotide polymorphism (SNP), structural variant, and gene fusion detection. The tool is also available in C language, see Subread.

FusionHunter

• Description : FusionHunter is a tool to identify gene fusion in RNA-seq data sets.

DeFuse

• Description : DeFuse is a tool for the identification of gene fusions in RNA-seq data. The deFuse algorithm examines all conflicting paired-end sequence alignments to find fusion boundaries.

BreakFusion

• Description : BreakFusion is a tool to identify gene fusions in whole transcriptome paired-end sequencing data. The BreakFusion algorithm uses a combination of alignment strength and paired-end read alignment analyses.

TopHat-Fusion

• Description : TopHat-Fusion is a tool for the detection of gene fusion transcripts in RNA-seq data.

Pipelines

RSEQREP

• Description : RSEQREP (RNA-Seq Reports) is a tool for complete RNA-seq analysis. The RSEQREP algorithm runs on an RSEQREP Amazon Virtual Machine Image (AMI) hosted by AWS, or on a local Linux machine (Ubuntu). The RSEQREP has automated, customizable analysis methods for reference alignment, reference alignment quality control, data normalization, data compression, identification of differentially expressed genes, identification of co-expressed gene clusters, enriched pathways, and heatmaps. The algorithm outputs a PDF report, publication-ready tables, and figures.

DRAP

• Description : DRAP (de novo RNA-Seq Assembly Pipeline) pipeline tool uses two separate assemblers, Trinity and Oasis, to make de novo RNA-seq assemblies. The DRAP algorithm has three modules: runDrap, runMeta, and runAssessment.

zUMIs

• Description : A pipeline tool for analysis of RNA-seq data comprising sample-specific barcodes and unique molecular identifiers. The zUMIs algorithm can identify cells by a read distribution. Besides, it has a function to downsample varying library sizes.

TRAPR

• Description : A tool for visualization and statistical analysis of RNA-seg data. The TRAPR algorithm can filter low-quality data, normalize, transform, perform statistical analyses, and visualize data. The ability to visualize results supports the creation of customized computing pipelines. It additionally has functions for data management.

NGScloud

• Description : A tool for analysis of RNA-seq data at Amazon cloud computing services. The NGScloud has an interface for controlling Amazon's hardware resources and analysis workflow. The NGScloud algorithm can run workflows in numerous different instances.

SPARTA

• Description : SPARTA (Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis), is a tool for transcriptomic analysis of bacterial Illumina RNA-seq data. SPARTA can analyze single-end data. The Pipeline includes FastQC, Bowtie, HTSeq, edgeR, and output consists of QC reports, gene feature counts, differential gene expression, and scatterplots.

RUM

• Description : RUM (RNA-Seq Unified Mapper) is a pipeline to map Illumina RNA-seq data. The RUM algorithm Bowtie to map the reads onto a genome and to a transcriptome database. It uses BLAT for mapping against the genome and merges all three mappings into one. Note that the usage of BLAT requires a separate license.

FRAMA

• Description : A pipeline tool to assemble and annotate transcriptomes for RNA-seq data. The FRAMA algorithm uses a reference transcriptome and makes de novo assemblies, assigns gene symbols, detects fusions and constructs scaffolds, and annotates contigs.

RseqFlow

• Description : RseqFlow is a pipeline tool for RNA-seq data analysis for single-ended reads produced by the Illumina platform. The RseqFlow includes functions for sequencing quality control, mapped reads signal tracks, post mapping quality control, expression level computation, identification of differentially expressed genes, and calling single-nucleotide polymorphism (SNPs). RseqFlow is run by the Pegasus Workflow Management System and is available as a complete Virtual Machine. It can also run in a UNIX command-line mode and users can run each analysis separately. However, the authors no longer support the project.

BSeq-sc

• Description : BSeq-sc is a pipeline tool for the estimation of differential expression and cell types from single-cell RNA-seq data as bulk tissue samples.

RPASuite

• Description : RPASuite (RNA Processing Analysis Suite) is a pipeline tool for the identification of differential expression in RNA-seq data. RPASuite suite processes Differentially Processed Loci (DPL) and Coherently Processed Loci (CPL).

RobiNA

• Description : RobiNA is a pipeline tool for RNA-seq differential expression analysis, covering all analysis RNA-seq steps. RobiNA can use data from Illumina/Solexa, Affymetrix, and generic tabular two-color or single-channel array data. The package includes quality control, filtering, analysis of differential gene expression, and visualization of results. RobiNA uses bowtie for mapping of reads, DESeq, and edgeR for differential gene expression analysis. The output is compatible with MapMan and PageMan.

RAP

• Description : RAP is a web-based tool for RNA-seq data analysis. The RAP workflow includes FastQC, NGS QC Toolkit, Tophat, Cufflinks, HTSeq, SpliceTrap, Cuffdiff2, DESeq, and ChimeraScan tools.

IDEAMEX

• Description : IDEAMEX (Integrative Differential Expression Analysis for Multiple EXperiments) is a web-based pipeline tool for the analysis and visualization of differential gene expression in RNA-seq data sets.

hppRNA-a

• Description : hppRNA-a is a pipeline tool for RNA-seq data analysis. The workflow uses Snakemake pipeline management software and includes Tophat-Cufflink-Cuffdiff, Subread-featureCounts-DESeq2, STAR-RSEM-EBSeq, Bowtie-eXpress-edgeR, Kallisto-sleuth, and HISAT-StringTie-Ballgown tools. The pipeline can analyze mRNAs, lncRNAs, circRNAs, and also can handle gene fusions and SNPs.

ExpressionPlot

• Description : ExpressionPlot is a web-based tool for RNA-seq analysis.

bcbioRNASeq

• Description : bcbioRNASeq is a tool for the analysis deferentially expressed genes in RNA-seq data. The package includes a workflow for pre-processing, identification of deferentially expressed genes, annotation, and reporting .

LSTrAP

• Description : LSTrAP (Large-Scale Transcriptome Analysis Pipeline) is a pipeline tool combining all required tools for the computation of co-expression networks in RNA_seq data sets. The LSTrAP also supports parallel and cluster computing.

Myrna

• Description : Myrna is a pipeline tool to compute differential gene expression (DGE) in RNA-seq data. Myrna uses Bowtie, R, and runs as a parallel pipeline on a cluster or on a single computer.

ArrayExpressHTS

• Description : ArrayExpressHTS is a pipeline tool to pre-process, estimate expression, and quality assessment of RNA-seq data. The ArrayExpressHTS can run in a local computer or remotely on the R-cloud farm at the European Bioinformatics Institute. You can use your own data or public data in the ArrayExpress Archive.

IRIS-EDA

• Description : IRIS-EDA is a comprehensive tool for differential gene expression (DGE) analysis for RNA-seq and single-cell RNA-seq (scRNA-seq) data. The IRIS-EDA algorithm implements edgeR, DESeq2, and limma tools. IRIS-EDA package also includes correlation analysis, heatmap, clustering, biclustering, Principal Component Analysis (PCA), Multidimensional Scaling (MDS), t-distributed Stochastic Neighbor Embedding (t-SNE), and several visualization tools.

RNASeqGUI

• Description : RNASeqGUI is a graphical user interface tool for the analysis of differentially expressed genes in RNA-seq data. The RNASeqGUI package includes EdgeR Exact Test, EdgeR GLM for Multi Factors, DESeq, DESeq for Complex Design, DESeq2, DESeq2 for Complex Design, NoiSeq, and BaySeq tools.

cufflinks (cloudIFB)

• Description : cufflinks (cloudIFB) is a workflow tool for various different analyses in RNA-seq data.

Grape

• Description : Grape is a pipeline environment comprising of a set of RNA-seq analysis tools.

Oqtans

• Description : Oqtans is a web-based tool to analyze transcriptomes. The Oqtans package workflows run on Galaxy. The algorithm uses machine learning for the analysis of sequence alignments, transcript identification, quantification, and differential gene expression (DGE) analysis.

CANEapp

• Description : CANEapp (application for Comprehensive automated Analysis of Next-generation sequencing Experiments) is a suite of tools for the analysis of RNA-seq data. The CANEapp package includes functions for differential gene expression analysis, the discovery of new noncoding RNAs using Cuffdiff, edgeR, and DESeq2. The package also includes a graphical user interface.

GENE-Counter

• Description : GENE-Counter is a pipeline tool for the analysis of differential gene expression in RNA-seq data. GENE-Counter is ready for use with CASHX, Bowtie, and BWA, but can use alignment tool that uses SAM file format.

Other

MINTmap

• Description : MINTmap (MItochondrial and Nuclear TRF mapping) is a tool for identification and determining the abundance of transfer RNA fragments (tRFs) in RNA-seq data. The MINTmap algorithm also classifies fragments as false positives if it finds them to originate outside the tRNA scope.

KAPAC

• Description : KAPAC (for k-mer activity on polyadenylation site choice) is a tool to detect sequence motifs that affect poly(A) site usage on the 3' end. The package also includes PAQR (polyadenylation site usage quantification from RNA sequencing data) tool for evaluation of the 3' end processing in distinct data sets.

SimBA

• Description : SimBA consists of a set of tools for benchmarking and evaluation of RNA-seq pipelines. Set contains two tools, SimCT and BenchCT. SimCT simulates RNA-seq data sets, and BenchCT does the benchmarking by comparing output from an RNA-seq pipeline against the simulated data.

kissDE

• Description : kissDE is an R tool for retrieving specific variants from RNA-seq data, such as insertions, deletions (indels), single-nucleotide variation (SNVs), and splicing variants.

ACE (Zhejiang University)

• Description : ACE (Zhejiang University) is a tool

GDCRNATools

• Description : An R package for interactive analysis of RNA -seq data, specifically lncRNA, mRNA, related to ceRNA regulatory networks in cancer data sets from the Genomic Data Commons (GDC). GDCRNATools also has functions for downloading and organizing the GDC data.

coseq

• Description : coseq is an R tool to analyze co-expression in RNA-seq data. The coseq algorithm uses modified transformations and mixture models or a k-means method.

IntEREst

• Description : IntEREst is an R tool to analyze Intron-Exon Retention in RNA-seq data sets. The IntEREst algorithm can analyze both annotated and non-annotated retention events. The IntEREst algorithm uses statistical methods, modified from DESeq2, edgeR, and DEXSeq R packages and supports single and multiple cores.

bcSeq (Duke)

• Description : bcSeq is an R tool to map short hairpin RNA ( shRNA) and CRISPR screens reference barcode library. The bcSeq parallelized algorithm uses the Trie data structure and resolves sequencing errors using Phred quality scores. It also uses a Baye's method to classify read barcode origins. It also supports user-defined probability models and supports multi-threading.

RED-ML

• Description : A tool for detection of RNA editing. The RED-ML algorithm is based on machine learning and does not require access to RNA editing databases.

CPSS

• Description : CPSS is a web-based tool for the analysis of microRNAs (miRNAs) and non-coding RNAs (ncRNAs) in RNA-seq data. It performs functional annotation, distribution of lengths, mapping, quantification, prediction of novel micro RNAs, identification of piwi-interacting and differentially expressed miRNAs, editing, prediction of signaling pathways, protein-protein interactions of predicted genes, detection of non-coding and differentially expressed RNAs (ncRNAs). CPSS also visualizes results as charts and graphs.

Subread

• Description : Subread is a software tool package for the alignment of both DNA-seq and RNA-seq read data, quantification, and mutation detection. The Subread package consists of five separate tools: 1. Subread, a read aligner for both RNA-seq and DNA-seq data, 2. Subjunc, read aligner for RNA-seq data, detection of exon-exon junctions and gene fusion events, 3. featureCounts, read counting, 4. Sublong, for aligning long reads using the seed-and-vote technique, and 5. exactSNP, a single-nucleotide polymorphism discovery. An R version of the Subread package is also available, Rsubread .

FEELnc

• Description : FEELnc (FlExible Extraction of LncRNAs) is a tool for annotation of long non-coding RNAs (lncRNAs) in assembled RNA-seq data sets. The FEELnc algorithm uses a Random Forest approach.

CancerInSilico

• Description : CancerInSilico is an R tool to compute mathematical models of tumor progression. CancerInSilico also generates expression data from the modeling results.

AllelicImbalance

• Description : A tool to identify, manage, and visualize allelic imbalances in RNA-seq data.

AltAnalyze

• Description : AltAnalyze is a tool for the analysis of differential gene expression and alternative splicing in RNA-seq and Affymetrix (exon, gene, junction) data. The AltAnalyze includes multiple visualization functions, for example, network, pathway, splicing graph, and varying levels of abstraction: isoform, exon, protein, domain, molecular interactions.

derfinder

• Description : derfinder is a tool for differential expression analysis of RNA-seq data. The derfinder package provides single base-level F-statistics and identification at differentially expressed region (DER) levels. The derfinder algorithm uses a bump-hunting method for the identification of differentially expressed regions and among others, multi-group and time-course analyses. The derfinder package also contains visualization functions.

MMAPPR

• Description : MMAPPR (MAPPR2) is a tool for mapping mutations in pooled RNA_seq data, specifically forward screens of F2 data. The MMAPPR2 algorithm is an improved version of MMAPPR, and it distinguishes differences among control and mutant RNA sequences. It also uses Ensembl's Variant Effect Predictor to predict effects and ranks candidate mutations.

pcaReduce

• Description : pcaReduce is an R tool to cluster cell expression in RNA-seq data. The pcaReduce algorithm uses a new agglomerative clustering approach to compute the hierarchies of cell states.

cellTree

• Description : a Latent Dirichlet Allocation (LDA) model

RDDpred

• Description : RDDpred is a tool to predict RNA editing with specific conditions in RNA-seq data. The RDDpred algorithm uses a Random Forest RDD classifier to find candidate RNA-editing events.

LIONS

• Description : A pipeline to detect and quantify transposable elements (TEs) initiated transcription in paired-end RNA-seq data. The LIONS pipeline uses the following software tools: Python3, pysam, Bowtie2, Tophat2, Java v8 or higher, Samtools v0.1.18, R v3.5.0 or higher, Bedtools v2.25.0, and Cufflinks v2.2.1.

ROP

• Description : ROP (Read Origin Protocol) is a tool to discover the source of all reads originating from RNA molecules in RNA-seq datasets.

MBASED

• Description : MBASED is a tool to detect allele-specific gene expression in RNA-seq data. The MBASED algorithm uses simulation to determine the statistical significance and combines single-nucleotide variants (SNVs) into the allele counts.

TANRIC

• Description : An interactive open platform to explore the function of lncRNAs in cancer.

Sequgio

• Description : Sequgio is a tool to estimate the expression of isoforms and their distribution in RNA-seq datasets. The Sequgio algorithm uses a joint statistical model to assess nonuniformly distributed reads. However, the Authors no longer maintain the package.

miARma-Seq

• Description : miARma-Seq contains a suite of tools for differential expression analysis of miRNA, mRNA, and circRNA. It can also predict functions and targets and works in any organism.

RNA CoMPASS

• Description : RNA CoMPASS is a tool to simultaneously analyze host and pathogen transcriptomes using RNA-seq datasets. The RNA CoMPASS package includes a web-based graphical interface together with a control of the computational pipeline.

RNAseqEval

• Description : RNAseqEval is a tool collection for evaluation and benchmarking of RNA-seq mapping.

QAPA

• Description : QAPA (Quantification of APA) is a tool that finds alternative polyadenylation (APA) codes from RNA-seq data sets.

Mikado

• Description : Mikado is a pipeline tool for the selection of useful transcript sequences from transcriptome assemblies. The Mikado algorithm uses several different methods to identify expressed loci, for the assignment of representative transcripts, and the selection gene model sets. The algorithm uses up to 50 different metrics, and can also use BLAST data for the scoring of transcript similarity and identify chimeras.

CellFishing

• Description : CellFishing (cell finder via hashing) is a tool for discovering cells that are alike in large-scale RNA-seq data.

recount (Bioconductor)

• Description : A tool to obtain and search data from the Recount2 Project at https://jhubiostatistics.shinyapps.io/recount/. The data consists of the gene, exon or exon-exon junctions, raw counts, the phenotype metadata, the URLs to the sample, or the mean coverage bigWig files.

Rail-dbGaP

• Description : Rail-dbGaP is a tool to analyze protected data on a commercial cloud, compliant with The National Institutes of Health (NIH) guidelines. The Rail-dbGaP protocol works with all tools that run on Amazon Web Services Elastic MapReduce. See also Rail-RNA in the links.

Boiler

• Description : A tool to compress RNA-seq alignments. The Boiler algorithm extracts summary, coverage, and distribution data from the sequence alignments. By discarding individual sequence data, the resulting data set is small.

anndata

• Description : AnnData is a Python class to manage annotated data matrices and developed for use with SCANPY (see links).

anchor

• Description : Anchor is a tool for finding unimodal, bimodal, and multimodal features in any data normalized between 0 and 1, such as alternative splicing.

SCmut

• Description : SCmut is a tool for the detection of cells that contain mutations in RNA-seq and bulk-cell DNA-sequencing data. The SCmut algorithm can use a list of somatic mutations in the absence of DNA-sequencing data.

GEM-Tools

• Description : GEM-Tools is an API and a Python API that simplify the usage of the GEM Mapper tool (See links). Besides, GEM-Tools includes a command-line interface, gemtools, for initiating the RNAseq pipeline, indexer module, statistics module, and various other tools.

Picard

• Description : Picard is a collection of command-line tools for handling high-throughput sequencing data.

MultiQC

• Description : MultiQC is a tool that aggregates results from multiple sequence aligners, post- and pre-processing, and quality control tools. Version 1.8 supports 78 separate tool packages. The MultiQC obtains the information by scanning the log files and produces an HTML report. This tool is also useful for Single-cell sequencing data and population studies.

Rsubread

• Description : Rsubread is an R tool for RNA-/DNA-seq data mapping, read counting, single-nucleotide polymorphism (SNP), structural variant, and gene fusion detection. The tool is also available in C language, see Subread.

Cufflinks

• Description : Cufflinks consist of a suite of tools for differential gene expression analysis of RNA-seq data. It assembles aligned reads in a set of transcripts and estimates the relative abundances. The Cufflinks suite consists of the following tools: cufflinks, cuffcompare, cuffmerge, cuffquant, cuffdiff, and cuffnorm.

Orione

• Description : Orione is a Galaxy-based framework that grouped together workflows and tools to perform de novo genome assembly, annotation, RNA-Seq and metagenomics analysis. This user-friendly tool is suitable for those working on microbes.

Polyester

• Description : Polyester is a tool for simulation of RNA-seq reads with replicates.

DEUS

• Description : DEUS is an R tool for profiling small non-coding RNA (sncRNA) in RNA-seq data sets.

postprocess

• Description : postprocess is an algorithm for the recovery of alternative splicing and library-specific expression data from de Bruijn graphs. The postprocess algorithm is for post-processing the Velvet assembler output. It reports the expression levels as reads per kilobase per million mapped reads (RPKM).

SeqAcademy

• Description : SeqAcademy is an educational tool based on the Jupyter notebook. The aim of this SeqAcademy is to provide an educational source for learning RNA-seq and ChIP-seq data analysis. The use does not require any prior programming skills.

countsimQC

• Description : countsimQC is a tool

BRAKER1

• Description : BRAKER1 is a tool for the annotation of genomes based on RNA-seq data. The BRAKER1 algorithm uses an unsupervised learning method and does not require pre-training.

H-DBAS

• Description : H-DBAS is a database of human-transcriptome for alternative splicing with RNA-seq tags.

DARIO

• Description : DARIO is a web-based tool to detect and analyze ncRNA, microRNA, snoRNA, and tRNA from RNA-seq data. DARIO provides various analyses from read normalization and differential expression to quantification and prediction of ncRNA.

GenomicTools

• Description : GenomicTools is a command-line tool and a C++ API to perform various analyses of RNA-seq DNA-seq, ChIP-seq, and Methyl-seq data.

SigFuge

• Description : SigFuge is a tool to identify genomic loci that display differential expression patterns among several RNA-seq datasets. The SigFuge algorithm uses hypothesis testing to asses clustered genes that manifest alternative splicing or differences of isoform expression.

globalSeq

• Description : globalSeq is a tool to test associations of genomic and RNA-seq data. The globalSeq algorithm uses the negative binomial distribution combined with a random-effects model and can detect genetic and epigenetic variations that have an effect on gene expression.

PVAAS

• Description : PVAAS is a tool for the identification of anomalous splicing variants in RNA-seq data.

compcodeR

• Description : compcodeR is a tool to benchmark differential gene expression analysis tools for RNA-seq data.

AUGUSTUS

• Description : AUGUSTUS is a tool to predict genes ab initio in eukaryote genome sequences. The AUGUSTUS algorithm uses a generalized Hidden Markov Model.

discordant

• Description : discordant is a tool for the identification of molecular feature pairs with largest difference between correlation coefficients.

Guitar

• Description : Guitar is a tool to visualize genomic features that are related to RNA in RNA-seq data. It extracts the standardized RNA coordinates with respect to the landmarks of RNA transcripts. For example, transcription start/end, and codons.

QuasR

• Description : QuasR is a tool to quantify and annotate reads from RNA-seq, ChIP-seq, and Bis-seq. The QuasR package has tools for all analysis steps from sequence read preprocessing, alignment, and quality control to quantification.

S-MART

• Description : S-MART is a tool to manage and visualize mapped RNA-seq and ChIP-seq data.

TROM

• Description : TROM (Transcriptome Overlap Measure) is a tool to compare transcriptomes within and between species. The TROM identifies molecular characteristics and evaluates the potential overlap of genes between samples.

GSEABenchmarkeR

• Description : GSEABenchmarkeR is a tool for benchmarking set- and network-based methods for enrichment analysis of gene expression data (microarray and RNA-seq). The algorithm assesses runtime, statistical significance, and relevance of the results in respect of the phenotypes.

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