Tag: RNA-Seq

FusionFinder 1.2.1 – Finding Gene Fusions In RNA-Seq Data

FusionFinder 1.2.1

:: DESCRIPTION

FusionFinder is a perl-based software package, which can be used to find fusion transcript candidates in RNA-Seq data.

::DEVELOPER

Richard Francis

:: SCREENSHOTS

 N/A

:: REQUIREMENTS

  • linux/ Windows/ MacOsX
  • Perl
  • MySQL

:: DOWNLOAD

 FusionFinder

:: MORE INFORMATION

Citation

Francis RW, Thompson-Wicking K, Carter KW, Anderson D, Kees UR, et al. (2012)
FusionFinder: A Software Tool to Identify Expressed Gene Fusion Candidates from RNA-Seq Data.
PLoS ONE 7(6): e39987. doi:10.1371/journal.pone.0039987

WASP v1.0 – Web-Accessible Single Cell RNA-Seq Processing Platform

WASP v1.0

:: DESCRIPTION

WASP is a software covering the full range of analysis steps of a typical single-cell RNA sequencing workflow for Drop-Seq-based scRNA-Seq data.

::DEVELOPER

Bioinformatics and Systems Biology, Justus-Liebig-University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows / MacOS
  • R
  • Python

:: DOWNLOAD

WASP

:: MORE INFORMATION

Citation

Hoek A, Maibach K, Özmen E, Vazquez-Armendariz AI, Mengel JP, Hain T, Herold S, Goesmann A.
WASP: a versatile, web-accessible single cell RNA-Seq processing platform.
BMC Genomics. 2021 Mar 18;22(1):195. doi: 10.1186/s12864-021-07469-6. PMID: 33736596; PMCID: PMC7977290.

CAFU – A Galaxy framework for exploring unmapped RNA-Seq data

CAFU

:: DESCRIPTION

CAFU is a Galaxy-based bioinformatics framework for comprehensive assembly and functional annotation of unmapped RNA-seq data from single- and mixed-species samples which integrates plenty of existing next-generation sequencing (NGS) analytical tools and our developed programs, and features an easy-to-use interface to manage, manipulate and most importantly, explore large-scale unmapped reads.

::DEVELOPER

Ma Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

CAFU

:: MORE INFORMATION

Citation

Chen S, Ren C, Zhai J, Yu J, Zhao X, Li Z, Zhang T, Ma W, Han Z, Ma C.
CAFU: a Galaxy framework for exploring unmapped RNA-Seq data.
Brief Bioinform. 2020 Mar 23;21(2):676-686. doi: 10.1093/bib/bbz018. PMID: 30815667; PMCID: PMC7299299.

deepTS – Exploring Transcriptional Switches from pairwise, temporal, and population RNA-Seq data

deepTS

:: DESCRIPTION

deepTS is a powerful and flexible web-based Galaxy platform for identifying, visualizing and analyzing transcriptional switch (TS) events from pairwise, temporal and population transcriptome data.

::DEVELOPER

Ma Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

deepTS

:: MORE INFORMATION

Citation

Qiu Z, Chen S, Qi Y, Liu C, Zhai J, Xie S, Ma C.
Exploring transcriptional switches from pairwise, temporal and population RNA-Seq data using deepTS.
Brief Bioinform. 2021 May 20;22(3):bbaa137. doi: 10.1093/bib/bbaa137. PMID: 32728687.

rsgcc 1.0.6 – Gini methodology-based correlation and Clustering analysis of Microarray and RNA-Seq Gene Expression data

rsgcc 1.0.6

:: DESCRIPTION

rsgcc is an R package that can be utilized as an alternative option for biologists to perform clustering analyses of gene expression patterns or transcriptional network analyses.

::DEVELOPER

Ma Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 rsgcc

:: MORE INFORMATION

Citation

Plant Physiol. 2012 Sep;160(1):192-203. doi: 10.1104/pp.112.201962. Epub 2012 Jul 13.
Application of the Gini correlation coefficient to infer regulatory relationships in transcriptome analysis.
Ma C1, Wang X.

FuMa 3.0.0 – Reporting Overlap in RNA-seq Detected Fusion Genes

FuMa 3.0.0

:: DESCRIPTION

FuMa (Fusion Matcher) is a program that reports identical fusion genes based on gene-name annotations.

::DEVELOPER

FuMa team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 FuMa

:: MORE INFORMATION

Citation

Hoogstrate Y, Böttcher R, Hiltemann S, van der Spek PJ, Jenster G, Stubbs AP.
FuMa: reporting overlap in RNA-seq detected fusion genes.
Bioinformatics. 2016 Apr 15;32(8):1226-8. doi: 10.1093/bioinformatics/btv721. Epub 2015 Dec 10. PMID: 26656567.

Chimerascan 0.4.5a – Detect Gene Fusions in Paired-end RNA Sequencing (RNA-Seq) Datasets

Chimerascan 0.4.5a

:: DESCRIPTION

Chimerascan is a  software for detecting gene fusions in paired-end RNA sequencing (RNA-Seq) datasets.

::DEVELOPER

The Michigan Center for Translational Pathology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Chimerascan

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Oct 15;27(20):2903-4. Epub 2011 Aug 11.
ChimeraScan: a tool for identifying chimeric transcription in sequencing data.
Iyer MK, Chinnaiyan AM, Maher CA.

MRFSeq 0.1 – Gene Expression Analysis using Coexpression and RNA-Seq data

MRFSeq 0.1

:: DESCRIPTION

MRFSeq is a new efficient algorithm based on a Markov random field (MRF) model that uses additional gene coexpression data to enhance the prediction power.

::DEVELOPER

Ei-Wen Yang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • G++
  • R package

:: DOWNLOAD

 MRFSeq

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Sep 1;29(17):2153-61. doi: 10.1093/bioinformatics/btt363. Epub 2013 Jun 21.
Differential gene expression analysis using coexpression and RNA-Seq data.
Yang EW1, Girke T, Jiang T.

PennSeq – Isoform-specific Gene Expression Quantification in RNA-Seq

PennSeq

:: DESCRIPTION

PennSeq is a statistical method that allows each isoform to have its own non-uniform read distribution.

::DEVELOPER

Yu Hu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Perl

:: DOWNLOAD

 PennSeq

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 Feb;42(3):e20. doi: 10.1093/nar/gkt1304. Epub 2013 Dec 20.
PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution.
Hu Y1, Liu Y, Mao X, Jia C, Ferguson JF, Xue C, Reilly MP, Li H, Li M.