MetaDiff – Differential Expression Analysis on RNA-Seq

MetaDiff

:: DESCRIPTION

MetaDiff is a Java/R-based software package that performs differential expression analysis on RNA-Seq based data.

::DEVELOPER

MetaDiff team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • JRE
  • R

:: DOWNLOAD

 MetaDiff

:: MORE INFORMATION

Citation

MetaDiff: differential isoform expression analysis using random-effects meta-regression.
Jia C, Guan W, Yang A, Xiao R, Tang WH, Moravec CS, Margulies KB, Cappola TP, Li M, Li C.
BMC Bioinformatics. 2015 Jul 2;16:208. doi: 10.1186/s12859-015-0623-z

contamDE 1.0 – Differential Expression analysis of RNA-seq data for Contaminated Tumor Samples

contamDE 1.0

:: DESCRIPTION

The R package ‘contamDE’ conducts differential expression (DE) analysis using high throughput next-generation RNA-seq read count data generated from contaminated tumor samples that are either matched or unmatched with normal samples, which estimates the proportion of pure tumor cells in each contaminated tumor sample, and provides tumor vs.

::DEVELOPER

Hong Zhang @Fudan University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 contamDE

:: MORE INFORMATION

Citation

contamDE: Differential expression analysis of RNA-seq data for contaminated tumor samples.
Shen Q, Hu J, Jiang N, Hu X, Luo Z, Zhang H.
Bioinformatics. 2015 Nov 9. pii: btv657.

KATSURA 1.0.1 – KEGG Pathway Coverage & Expression Analysis

KATSURA 1.0.1

:: DESCRIPTION

Katsura tool is a free open source Java application designed to overlay gene expression data, comparative genomics data, or quantitative shotgun proteomics data onto metabolic pathways. Katsura uses data from the Kyoto Encyclopedia of Genes and Genomes (KEGG), Kanehisa Laboratory at Kyoto University, to build a small database containing KEGG pathway and enzyme data relating to one or more user specified organisms. Katsura manages the local database allowing users to update core information, add genomes of interest, backup the database and display database status reports. Gene expression data is input to allow visualization of pathway level expression trends over time or over a series of experimental conditions. A separate table visualizes the individual enzymes and associated gene expression values for each pathway. Capabilities such as bookmarking pathways to annotate findings, saving results to reloadable files, and the ability to output pdf reports and summary files help to capture key research findings.

::DEVELOPER

KATSURA team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • JAVA

:: DOWNLOAD

KATSURA

:: MORE INFORMATION

This application is released under the GPL v3 License: View License

Citation:

  1. Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M., and Hirakawa, M.; KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 38, D355-D360 (2010).
  2. Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K.F., Itoh, M., Kawashima, S., Katayama, T., Araki, M., and Hirakawa, M.; From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34, D354-357 (2006).
  3. Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000).

FIDEA – Functional Interpretation of Differential Expression Analysis

FIDEA

:: DESCRIPTION

FIDEA has been designed to help in the functional interpretation of the results derived by differential expression analysis by assessing which functional categories are significantly enriched by the differentially expressed genes.

::DEVELOPER

the Biocomputing Unit

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W84-8. doi: 10.1093/nar/gkt516. Epub 2013 Jun 10.
FIDEA: a server for the functional interpretation of differential expression analysis.
D’Andrea D1, Grassi L, Mazzapioda M, Tramontano A.

GExposer 1.0 – Differential Expression analysis in RNA-Seq

GExposer 1.0

:: DESCRIPTION

GExposer is a software for differential expression analysis in RNA-Seq by machine learning algorithm with local normalization

::DEVELOPER

System Biology Laboratory Of Chi Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • R package

:: DOWNLOAD

 GExposer

 :: MORE INFORMATION

Treebic 1.11 – Hierarchical Generative Biclustering for MicroRNA Expression Analysis

Treebic 1.11

:: DESCRIPTION

Treebic is a Software package for hierarchical biclustering.

::DEVELOPER

José Caldas, firstname.lastname@aalto.fi.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • R package

:: DOWNLOAD

 Treebic

:: MORE INFORMATION

Citation

J. Caldas and S. Kaski.
Hierarchical generative biclustering for microRNA expression analysis.
J. Caldas and S. Kaski. Journal of Computational Biology, 18(3):251-261, 2011

ALEXA 1.1 – Microarray Design platform for ‘Alternative Expression Analysis’

ALEXA 1.1

:: DESCRIPTION

ALEXA is a microarray design platform for ‘alternative expression analysis’. This platform facilitates the design of gene expression arrays for analysis of mRNA isoforms generated from a single locus by the use of alternative transcription initiation, splicing and polyadenylation sites.

::DEVELOPER

ALEXA-Seq Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Virtual Machines

:: DOWNLOAD

  ALEXA

:: MORE INFORMATION

Citation:

Malachi Griffith,et al.
ALEXA – A microarray design platform for alternative expression analysis.
Nature Methods. Feb 2008. 5(2):118.

ALEXA-Seq 1.17 – Alternative Expression Analysis by massively parallel RNA Sequencing

ALEXA-Seq 1.17

:: DESCRIPTION

ALEXA-Seq is a method for using massively parallel paired-end transcriptome sequencing for ‘alternative expression analysis’.

::DEVELOPER

ALEXA-Seq Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Virtual Machines

:: DOWNLOAD

 ALEXA-Seq

:: MORE INFORMATION

Citation:

Malachi Griffith, et al.
Alternative expression analysis by RNA sequencing.
Nature Methods. 2010 Oct;7(10):843-847.

RNASeqR 1.1 – RNAseq Expression Analysis

RNASeqR 1.1

:: DESCRIPTION

 RNAseqR is designed for expression analysis of RNA-seq data, and is best suited for analysis of multiple, unreplicated libraries.

::DEVELOPER

Thomas Walk (tom.walk@ars.usda.gov) and Scott Geib (scott.geib@ars.usda.gov)

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RNASeqR

:: MORE INFORMATION