cisMetalysis 1.3 – Meta Analysis of Gene Expression data sets

cisMetalysis 1.3

:: DESCRIPTION

Metalysis is meant for revealing higher level insights from multiple gene expression data sets. In particular, if you have up- and down-regulated gene sets from several different conditions and want to know what might be common to those different gene sets, you can use the Metalysis program.

cis-Metalysis” is an extension to Metalysis specifically designed to use motif target sets as annotation sets. It takes gene target predictions of the transcription factor motifs and then uses the Metalysis framework to identify meta associations between a motif and set of conditions. Because of the general consensus that condition-specific expression of a gene may be determine by combinations of transcription factors, cis-Metalysis also searches for motif combinations associated with expression.

::DEVELOPER

The Sinha Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • C++ Compiler

:: DOWNLOAD

 cisMetalysis

:: MORE INFORMATION

Citation

Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):E1801-10. doi: 10.1073/pnas.1205283109.
New meta-analysis tools reveal common transcriptional regulatory basis for multiple determinants of behavior.
Ament SA, Blatti CA, Alaux C, Wheeler MM, Toth AL, Le Conte Y, Hunt GJ, Guzmán-Novoa E, Degrandi-Hoffman G, Uribe-Rubio JL, Amdam GV, Page RE Jr, Rodriguez-Zas SL, Robinson GE, Sinha S

NCIS – Network-Assisted Co-clustering Algorithm to Discover Cancer Subtypes based on Gene Expression

NCIS

:: DESCRIPTION

NCIS (network-assisted co-clustering for the identification of cancer subtypes) combines molecular interaction network into co-clustering.

::DEVELOPER

Ma Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • MatLab

:: DOWNLOAD

  NCIS

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Feb 4;15:37. doi: 10.1186/1471-2105-15-37.
A network-assisted co-clustering algorithm to discover cancer subtypes based on gene expression.
Liu Y, Gu Q, Hou JP, Han J, Ma J

MIDClass 2 – Gene Expression Classification

MIDClass 2

:: DESCRIPTION

MIDClass (Microarray Interval Discriminant CLASSifier) is a new classification method for expression profiling data based on association rules.

::DEVELOPER

MIDClass team

:: SCREENSHOTS

MIDClass

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • JRE

:: DOWNLOAD

 MIDClass

:: MORE INFORMATION

Citation:

MIDClass: microarray data classification by association rules and gene expression intervals.
Giugno R, Pulvirenti A, Cascione L, Pigola G, Ferro A.
PLoS One. 2013 Aug 6;8(8):e69873. doi: 10.1371/journal.pone.0069873. Print 2013.

EXPANDER 7.2 – Gene Expression Analysis & Visualization

EXPANDER 7.2

:: DESCRIPTION

EXPANDER (EXpression Analyzer and DisplayER) is a java-based tool for analysis of gene expression data.It is capable of (1) preprocessing (2) visualizing (3) clustering (4) biclustering and (5) performing downstream analysis of clusters and biclusters such as functional enrichment and promoter analysis It seamlessly integrates in one package all analysis steps, including:

  • Data preprocessing and normalization
  • Identification of differential genes
  • Clustering and biclustering;
  • Down-stream enrichment analyses of:
    – GO functional categories
    – TF binding sites in promoter regions
    – MicroRNA sites in 3′-UTRs and
    – Chromosomal locations
  • Network-based analysis of the expression data.

EXPANDER provides support for analysis of human, mouse, rat, chicken, fly, zebrafish, C. elegans, yeast (s.cerevisiaeand s. pombe), arabidopsis, tomato, listeria, A. fumigatus and E. coli.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

EXPANDER

:: MORE INFORMATION

Citation

Expander: from expression microarrays to networks and functions.
Ulitsky I, Maron-Katz A, Shavit S, Sagir D, Linhart C, Elkon R, Tanay A, Sharan R, Shiloh Y, Shamir R.
Nat Protoc. 2010 Feb;5(2):303-22. doi: 10.1038/nprot.2009.230.

SPONGE 1.8.0 – Sparse Partial Correlations On Gene Expression

SPONGE 1.8.0

:: DESCRIPTION

SPONGE provides methods to efficiently detect competitive endogeneous RNA interactions between two genes. Such interactions are mediated by one or several miRNAs such that both gene and miRNA expression data for a larger number of samples is needed as input.

::DEVELOPER

Baumbach lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R
  • Bioconductor

:: DOWNLOAD

SPONGE

:: MORE INFORMATION

Citation

Bioinformatics. 2019 Jul 15;35(14):i596-i604. doi: 10.1093/bioinformatics/btz314.
Large-scale inference of competing endogenous RNA networks with sparse partial correlation.
List M, Dehghani Amirabad A, Kostka D, Schulz MH

Bi-Force v2 – Large-scale Bicluster Editing and its application to Gene Expression data Biclustering

Bi-Force v2

:: DESCRIPTION

Bi-Force is a novel way of modeling the problem as combinatorial optimization problem on graphs: Weighted Bi-Cluster Editing. It is a very flexible model that can handle arbitrary kinds of multi-condition data sets (not limited to gene expression).

::DEVELOPER

Baumbach lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

 Bi-Force

:: MORE INFORMATION

Citation

Bi-Force: large-scale bicluster editing and its application to gene expression data biclustering.
Sun P, Speicher NK, Röttger R, Guo J, Baumbach J.
Nucleic Acids Res. 2014 May;42(9):e78. doi: 10.1093/nar/gku201.

tRanslatome 1.24.0 – Comparison between multiple levels of Gene Expression

tRanslatome 1.24.0

:: DESCRIPTION

tRanslatome is a R/Bioconductor package, which is a complete platform for the simultaneous pairwise analysis of transcriptome, translatome and proteome data.

::DEVELOPER

Laboratory of Translational Genomics , CIBIO

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • R/Bioconductor

:: DOWNLOAD

 tRanslatome

:: MORE INFORMATION

Citation

tRanslatome: an R/Bioconductor package to portray translational control.
Tebaldi T, Dassi E, Kostoska G, Viero G, Quattrone A.
Bioinformatics. 2014 Jan 15;30(2):289-91. doi: 10.1093/bioinformatics/btt634.

CAFE 1.22.0 – Detection of Gross Chromosomal Abnormalities from Gene Expression Microarray data

CAFE 1.22.0

:: DESCRIPTION

CAFE (Chromosomal Aberration Finder in Expression data) is an R package for the detection of gross chromosomal gains and losses from expression microarrays, with a resolution up to cytoband level.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ windows/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

  CAFE

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 15;30(10):1484-5. doi: 10.1093/bioinformatics/btu028. Epub 2014 Jan 21.
CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data.
Bollen S1, Leddin M, Andrade-Navarro MA, Mah N.

NetPathMiner 1.22.0 – R package for Network Path Mining through Gene Expression

NetPathMiner 1.22.0

:: DESCRIPTION

NetPathMiner implements a flexible module-based process flow for network path mining and visualization, which can be fully inte-grated with user-customized functions. It supports construction of various types of genome scale networks from three different pathway file formats, enabling its utility to most common pathway databases. In addition, NetPathMiner provides different visualization techniques to facilitate the analysis of even thousands of output paths.

::DEVELOPER

NetPathMiner team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 NetPathMiner 

:: MORE INFORMATION

Citation

NetPathMiner: R/Bioconductor package for network path mining through gene expression.
Mohamed A, Hancock T, Nguyen CH, Mamitsuka H.
Bioinformatics. 2014 Jul 28. pii: btu501.

Allim 1.2 – Measuring Allele Specific Gene Expression

Allim 1.2

:: DESCRIPTION

Allim (Allelic imbalance meter) offers an integrated and user-friendly solution for measuring allele specific gene expression (ASE) within species.

DEVELOPER

Institute of Population Genetics, University of Veterinary Medicine Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python
  • BioPython
  • Java
  • PICARD
  • R
  • SAMTOOLS
  • BedTools

:: DOWNLOAD

 Allim

:: MORE INFORMATION

Citation:

Pandey RV, Franssen SU, Futschik A, Schlötterer C. (2013)
Allelic imbalance metre (Allim), a new tool for measuring allele-specific gene expression with RNA-seq data.
Mol Ecol Resour. 13(4):740-745.