Tag: Phenotype

CRaVe 0.0.2 – Association Tests between sets of SNPs and a Phenotype

CRaVe 0.0.2

:: DESCRIPTION

CRaVe is a free, open source, software package designed to perform a range of association tests between sets of SNPs and a phenotype.

::DEVELOPER

 DCEG

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R package

:: DOWNLOAD

 CRaVe

:: MORE INFORMATION

Citation

Eur J Hum Genet. 2013 Jun;21(6):680-6. doi: 10.1038/ejhg.2012.220. Epub 2012 Oct 24.
Statistical tests for detecting associations with groups of genetic variants: generalization, evaluation, and implementation.
Ferguson J, Wheeler W, Fu Y, Prokunina-Olsson L, Zhao H, Sampson J.

CPAG 0.2 – Cross-Phenotype Analysis of GWAS

CPAG 0.2

:: DESCRIPTION

CPAG can estimate disease and trait similarity, identify informative disease clusters, and carry out pathway enrichment analysis. It also provides visualization of these results in the form of hierarchical clustering trees, heatmaps, and networks.

::DEVELOPER

Rawls Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOS

:: DOWNLOAD

 CPAG

:: MORE INFORMATION

Citation:

CPAG: software for leveraging pleiotropy in GWAS to reveal similarity between human traits links plasma fatty acids and intestinal inflammation.
Wang L, Oehlers SH, Espenschied ST, Rawls JF, Tobin DM, Ko DC.
Genome Biol. 2015 Sep 15;16:190. doi: 10.1186/s13059-015-0722-1.

JEPEG 0.2.0 / JEPEGMIX 0.1.0 – Joint Effect on Phenotype of eQTLs/functional SNPs associated with a Gene

JEPEG 0.2.0 /JEPEGMIX 0.1.0

:: DESCRIPTION

JEPEG is a novel software which uses only summary statistics and correlation structures estimated from a reference popluation, to i) impute the summary statistics at unmeasured eQTLs and ii) test for the joint effect of measured and imputed all eQTLs affecting a gene function/expression on a phenotype.

JEPEGMIX is a JEPEG extension for gene-level joint testing of functional variants.

::DEVELOPER

dleelab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 JEPEG , JEPEGMIX

:: MORE INFORMATION

Citation

JEPEGMIX: gene-level joint analysis of functional SNPs in cosmopolitan cohorts.
Lee D, Williamson VS, Bigdeli TB, Riley BP, Webb BT, Fanous AH, Kendler KS, Vladimirov VI, Bacanu SA.
Bioinformatics. 2015 Oct 1. pii: btv567

JEPEG: a summary statistics based tool for gene-level joint testing of functional variants.
Lee D, Williamson VS, Bigdeli TB, Riley BP, Fanous AH, Vladimirov VI, Bacanu SA.
Bioinformatics. 2014 Dec 12. pii: btu816

Bubble GUM 1.3.19 – Extraction of Phenotype Molecular Signatures and Comprehensive Visualization

Bubble GUM 1.3.19

:: DESCRIPTION

Bubble GUM (GSEA Unlimited Map) is a computational tool that allows to automatically extract phenotype signatures based on transcriptomic data and to perform easily multiple GSEA runs in a row.

::DEVELOPER

Centre d’Immunologie, de Marseille-Luminy

:: SCREENSHOTS

BubbleGUM

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 Bubble GUM

:: MORE INFORMATION

Citation

BubbleGUM: automatic extraction of phenotype molecular signatures and comprehensive visualization of multiple Gene Set Enrichment Analyses.
Spinelli L, Carpentier S, Montañana Sanchis F, Dalod M, Vu Manh TP.
BMC Genomics. 2015 Oct 19;16(1):814. doi: 10.1186/s12864-015-2012-4.

Phenolyzer 0.4.0 – Phenotype Based Gene Analyzer

Phenolyzer 0.4.0

:: DESCRIPTION

Phenolyzer is a tool focusing on discovering genes based on user-specific disease/phenotype terms.

::DEVELOPER

Wang Genomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Phenolyzer

:: MORE INFORMATION

Citation

Phenolyzer: phenotype-based prioritization of candidate genes for human diseases.
Yang H, Robinson PN, Wang K.
Nat Methods. 2015 Sep;12(9):841-3. doi: 10.1038/nmeth.3484.

img2net – Automated Network-based Analysis of Imaged Phenotypes

img2net

:: DESCRIPTION

Img2net is a software to automatedly analyze such structures by reconstructing the underlying network, computing relevant network properties, and statistically comparing networks of different types or under different conditions.

::DEVELOPER

Systems biology and Mathematical Modelling

:: SCREENSHOTS

img2net

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 Img2net

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jul 26. pii: btu503.
img2net: automated network-based analysis of imaged phenotypes.
Breuer D, Nikoloski Z.

PICA – Genotype-phenotype data Mining software

PICA

:: DESCRIPTION

PICA (Phenotype Investigation with Classification Algorithms) is a Python framework for testing genotype-phenotype association algorithms.

::DEVELOPER

CUBE – Bioinformatics and Computational Systems Biology, University of Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PICA

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 Aug 1;26(15):1834-40. Epub 2010 Jun 6.
Efficient learning of microbial genotype-phenotype association rules.
MacDonald NJ, Beiko RG.

SigniSite 2.1 – Residue level Genotype Phenotype Correlation in Protein Multiple Sequence Alignments

SigniSite 2.1

:: DESCRIPTION

SigniSite performs residue level genotype phenotype correlation in protein multiple sequence alignments by identifying amino acid residues significantly associated with the phenotype of the data set.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W286-91. doi: 10.1093/nar/gkt497. Epub 2013 Jun 12.
SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments.
Jessen LE1, Hoof I, Lund O, Nielsen M.

gespeR 0.99.5 – Gene Specific Phenotype Estimator

gespeR 0.99.5

:: DESCRIPTION

gespeR estimates gene-specific phenotypes from off-target confounded RNAi screens. Observed phenotype for a specfic siRNA is modeled as a linear combination of gene-specific phenotypes from the on- and all off-target genes.

::DEVELOPER

the Computational Biology Group (CBG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R package

:: DOWNLOAD

 gespeR

:: MORE INFORMATION

Citation

Fabian Schmich, Ewa Szczurek, Saskia Kreibich, Sabrina Dilling, Daniel Andritschke, Alain Casanova, Shyan Huey Low, Simone Eicher, Simone Muntwiler, Mario Emmenlauer, Pauli Ramo, Raquel Conde-Alvarez, Christian von Mering, Wolf-Dietrich Hardt, Christoph Dehio and Niko Beerenwinkel.
gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens
Genome Biology, 2015.

PPFS 2 – Add on to kSNP for predicting Phenotypes from SNPs in Microbial Genome

PPFS 2

:: DESCRIPTION

The PPFS (Predict Phenotypes From SNPs) package is an add-on to kSNP , a program that can identify SNPs in a data set of hundreds of microbial genomes.

::DEVELOPER

Barry G. Hall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

PPFS

:: MORE INFORMATION

Citation

PLoS One. 2014 Feb 28;9(2):e90490. doi: 10.1371/journal.pone.0090490. eCollection 2014.
SNP-associations and phenotype predictions from hundreds of microbial genomes without genome alignments.
Hall BG1.