Tag: RNA-Seq

SeqGSEA 1.33.0 – Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

SeqGSEA 1.33.0

:: DESCRIPTION

SeqGSEA generally provides methods for gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing.

::DEVELOPER

Xi Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • R package
  • BioConductor

:: DOWNLOAD

 SeqGSEA

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 6. [Epub ahead of print]
SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing.
Wang X1, Cairns MJ.

BMC Bioinformatics. 2013;14 Suppl 5:S16. doi: 10.1186/1471-2105-14-S5-S16. Epub 2013 Apr 10.
Gene set enrichment analysis of RNA-Seq data: integrating differential expression and splicing.
Wang X, Cairns MJ.

FX 1.0.5 – RNA-Seq analysis tool on the Cloud

FX 1.0.5

:: DESCRIPTION

FX is a user-Frendly RNA-Seq gene eXpression analysis tool, empowered by the concept of cloud-computing. With FX, you can simply upload your RNA-Seq raw FASTQ data on the cloud, and let the computing infra to do the heavy analysis.

::DEVELOPER

Genomic Medicine Institute, Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 FX

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Mar 1;28(5):721-3. doi: 10.1093/bioinformatics/bts023. Epub 2012 Jan 17.
FX: an RNA-Seq analysis tool on the cloud.
Hong D1, Rhie A, Park SS, Lee J, Ju YS, Kim S, Yu SB, Bleazard T, Park HS, Rhee H, Chong H, Yang KS, Lee YS, Kim IH, Lee JS, Kim JI, Seo JS.

EMSAR v2.0.1 – Quantify Transcripts from RNA-seq data

EMSAR v2.0.1

:: DESCRIPTION

EMSAR (Estimation by Mappability-based Segmentation And Reclustering) is a new approach for quantifying transcript abundance from RNA-seq data.The software groups reads according to the set of transcripts to which they are mapped and finds maximum likelihood estimates using a joint Poisson model for each optimal set of segments of transcripts.

::DEVELOPER

Peter Park’s lab at CBMI, Harvard Medical School

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  EMSAR

:: MORE INFORMATION

Citation

EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering.
Lee S, Seo CH, Alver BH, Lee S, Park PJ.
BMC Bioinformatics. 2015 Sep 3;16(1):278. doi: 10.1186/s12859-015-0704-z.

ArrayExpressHTS 1.42.0 – RNA-seq data Processing and Quality Assessment

ArrayExpressHTS 1.42.0

:: DESCRIPTION

ArrayExpressHTS is an R and Bioconductor RNA-seq processing pipeline that highly utilizes distributed computing for data processing and quality assessment of High-Throughput Sequencing experiments and datasets

::DEVELOPER

EBI.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R package
  • Bioconductor

:: DOWNLOAD

  ArrayExpressHTS

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Mar 15;27(6):867-9. doi: 10.1093/bioinformatics/btr012. Epub 2011 Jan 13.
A pipeline for RNA-seq data processing and quality assessment.
Goncalves A, Tikhonov A, Brazma A, Kapushesky M.

Transcriptome Assembler – Transcriptome Assembly used in RNA-seq of 16 Mammalian Species

Transcriptome Assembler

:: DESCRIPTION

Transcriptome Assembler is a software for transcriptome assembly used in RNA-seq of 16 mammalian species.

::DEVELOPER

Pritchard Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  Transcriptome Assembler

:: MORE INFORMATION

RNASeqMut 0.7 – RNA-Seq Mutation Detection

RNASeqMut 0.7

:: DESCRIPTION

RNASeqMut is an easy-to-use program to detection variants in RNA-Seq read alignments. rnaseqmut is a light-weight C++ program to detect variants (or mutations, including SNPs, indels, RNA editing events) from a single or multiple RNA-Seq BAM files.

::DEVELOPER

Wei Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 RNASeqMut

:: MORE INFORMATION

EricScript 0.5.5 – Identify Chimeric Transcripts in RNA-seq data

EricScript 0.5.5

:: DESCRIPTION

EricScript is a computational framework for the discovery of gene fusions in paired end RNA-seq data.

::DEVELOPER

EricScript team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 EricScript

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Dec 15;28(24):3232-9. doi: 10.1093/bioinformatics/bts617. Epub 2012 Oct 23.
Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript.
Benelli M, Pescucci C, Marseglia G, Severgnini M, Torricelli F, Magi A.

IsoLasso 2.6.1 – A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly

IsoLasso 2.6.1

:: DESCRIPTION

IsoLasso is an algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.

::DEVELOPER

Wei Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MatLab
  • C Compiler

:: DOWNLOAD

  IsoLasso

:: MORE INFORMATION

Citation

J Comput Biol. 2011 Nov;18(11):1693-707. doi: 10.1089/cmb.2011.0171. Epub 2011 Sep 27. IsoLasso: a LASSO regression approach to RNA-Seq based transcriptome assembly. Li W1, Feng J, Jiang T.

FusionCatcher 1.33 – Fusion Genes Finder for RNA-seq data

FusionCatcher 1.33

:: DESCRIPTION

FusionCatcher searches for novel/known fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq) from diseased samples.

::DEVELOPER

FusionCatcher team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Python
  • Biopyton
  • Bowtie

:: DOWNLOAD

 FusionCatcher

:: MORE INFORMATION

Citation

S. Kangaspeska, S. Hultsch, H. Edgren, D. Nicorici, A. Murumägi, O.P. Kallioniemi,
Reanalysis of RNA-sequencing data reveals several additional fusion genes with multiple isoforms,
PLoS ONE 7(10): e48745. doi:10.1371/journal.pone.0048745