GenePattern 3.9.11 – Genomic Analysis Platform

GenePattern 3.9.11

:: DESCRIPTION

GenePattern is a powerful genomic analysis platform that provides access to more than 125 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.

GenePattern provides access to a broad array of computational methods used to analyze genomic data. Its extendable architecture makes it easy for computational biologists to add analysis and visualization modules, which ensures that GenePattern users have access to new computational methods on a regular basis.

::DEVELOPER

The GenePattern team

:: SCREENSHOTS

:: REQUIREMENTS

  • Java VM
  • MacOSX/Windows/Linux
  • Other Java-enabled Platforms

:: DOWNLOAD

GenePattern

:: MORE INFORMATION

Citation

ATARiS: computational quantification of gene suppression phenotypes from multisample RNAi screens.
Shao DD, Tsherniak A, Gopal S, Weir BA, Tamayo P, Stransky N, Schumacher SE, Zack TI, Beroukhim R, Garraway LA, Margolin AA, Root DE, Hahn WC, Mesirov JP.
Genome Res. 2013 Apr;23(4):665-78. doi: 10.1101/gr.143586.112.

Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP
GenePattern 2.0
Nature Genetics 38 no. 5 (2006): pp500-501

X-CYT 1.3 – User-guided Automated Flow Cytometric Data Analysis

X-CYT 1.3

:: DESCRIPTION

X-Cyt follows a user-designed scheme and template to partition cytometric data in two or more dimensions for identifying cell populations of interest. In a small subset of samples, the user may try out several different partitioning schemes, and select one “optimal” partitioning to use as the template to guide the batch analysis of all samples.

::DEVELOPER

The Raychaudhuri Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R package

:: DOWNLOAD

 X-CYT

 :: MORE INFORMATION

Citation

Proc Natl Acad Sci U S A. 2013 Nov 19;110(47):19030-5. doi: 10.1073/pnas.1318322110. Epub 2013 Nov 4.
Application of user-guided automated cytometric data analysis to large-scale immunoprofiling of invariant natural killer T cells.
Hu X1, Kim H, Brennan PJ, Han B, Baecher-Allan CM, De Jager PL, Brenner MB, Raychaudhuri S.

SNP2HLA 1.0.3 – Imputation of Amino Acid Polymorphisms in Human Leukocyte Antigens

SNP2HLA 1.0.3

:: DESCRIPTION

SNP2HLA is a tool to impute amino acid polymorphisms and single nucleotide polymorphisms in human luekocyte antigenes (HLA) within the major histocompatibility complex (MHC) region in chromosome 6.

::DEVELOPER

The Raychaudhuri Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SNP2HLA

:: MORE INFORMATION

Citation

PLoS One. 2013 Jun 6;8(6):e64683. doi: 10.1371/journal.pone.0064683.
Imputing amino acid polymorphisms in human leukocyte antigens.
Jia X, Han B, Onengut-Gumuscu S, Chen WM, Concannon PJ, Rich SS, Raychaudhuri S, de Bakker PI.

GRAIL / VIZ-GRAIL – Gene Relationships Across Implicated Loci

GRAIL / VIZ-GRAIL

:: DESCRIPTION

GRAIL is a tool to examine relationships between genes in different disease associated loci. Given several genomic regions or SNPs associated with a particular phenotype or disease, GRAIL looks for similarities in the published scientific text among the associated genes.

GRAIL Online Version

The VIZ-GRAIL software allows users to create informative circle plots of genetic loci that visualizes the functional similarites between genes in an intuitive manner. Code that interact with the online site is available here for download. VIZ-grail is implemented as two separate perl scripts.

::DEVELOPER

The Raychaudhuri Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Perl

:: DOWNLOAD

 VIZ-GRAIL

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jun 1;27(11):1589-90. doi: 10.1093/bioinformatics/btr185.
VIZ-GRAIL: visualizing functional connections across disease loci.
Raychaudhuri S.

Raychaudhuri, S., Plenge, R.M., Rossin, E.J., Ng, A.C.Y., International Schizophrenia Consortium, Purcell, S.M., Sklar, P., Scolnick, E.M., Xavier, R.J., Altshuler, D., and Daly, M.J.
Identifying Relationships Among Genomic Disease Regions: Predicting Genes at Pathogenic SNP Associations and Rare Deletions.
PLOS Genetics, 2009. 5(6):e1000534.

SNPsea 1.0.3 – Identify Cell Types and Pathways Affected by Risk Loci

SNPsea 1.0.3

:: DESCRIPTION

SNPsea is an algorithm to identify cell types and pathways likely to be affected by risk loci. It requires a list of SNP identifiers and a matrix of genes and conditions.

::DEVELOPER

The Raychaudhuri Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 SNPsea

 :: MORE INFORMATION

Citation

Bioinformatics. 2014 May 10. [Epub ahead of print]
SNPsea: an algorithm to identify cell types, tissues, and pathways affected by risk loci.
Slowikowski K1, Hu X, Raychaudhuri S.

Haploview 4.2 – Analysis & Visualization of LD & Haplotype Maps

Haploview 4.2

:: DESCRIPTION

Haploview is designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses.

::DEVELOPER

The Analytic and Translational Genetics Unit(AUGT),The Broad Institute,

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

Haploview

:: MORE INFORMATION

Citation

Barrett JC, Fry B, Maller J, Daly MJ.
Haploview: analysis and visualization of LD and haplotype maps.
Bioinformatics. 2005 Jan 15 [PubMed ID: 15297300]

PLINK 1.90 b – Whole Genome Association Analysis Toolset

PLINK 1.90 b

:: DESCRIPTION

PLINK is a comprehensive toolset for statistical analysis in whole-genome association studies, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

::DEVELOPER

Purcell Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows

:: DOWNLOAD

PLINK

:: MORE INFORMATION

Citation

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC (2007)
PLINK: a toolset for whole-genome association and population-based linkage analysis.
American Journal of Human Genetics, 81.

XHMM 20140711 – eXome-Hidden Markov Model

XHMM 20140711

:: DESCRIPTION

The XHMM C++ software suite was written to call copy number variation (CNV) from next-generation sequencing projects, where exome capture was used (or targeted sequencing, more generally).

::DEVELOPER

Purcell Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 XHMM

:: MORE INFORMATION

Citation

Using XHMM Software to Detect Copy Number Variation in Whole-Exome Sequencing Data.
Fromer M, Purcell SM.
Curr Protoc Hum Genet. 2014 Apr 24;81:7.23.1-7.23.21. doi: 10.1002/0471142905.hg0723s81.

sTarPicker – Global Target Prediction for Bacterial small non-coding RNAs

sTarPicker

:: DESCRIPTION

sTarPicker is a novel method for sRNA target prediction which was based on a two-step model for hybridization between an sRNA and an mRNA target.

::DEVELOPER

Prof. Wuju Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 sTarPicker

:: MORE INFORMATION

Citation:

PLoS One. 2011;6(7):e22705. doi: 10.1371/journal.pone.0022705. Epub 2011 Jul 22.
sTarPicker: a method for efficient prediction of bacterial sRNA targets based on a two-step model for hybridization.
Ying X1, Cao Y, Wu J, Liu Q, Cha L, Li W.

INRICH 1.1 – Interval-based Enrichment Analysis Tool for Genome Wide Association Studies

INRICH 1.1

:: DESCRIPTION

INRICH is a pathway analysis tool for genome wide association studies, designed for detecting enriched association signals of LD-independent genomic regions within biologically relevant gene sets.

::DEVELOPER

Purcell Lab

:: SCREENSHOTS

INRICH

:: REQUIREMENTS

  • Linux/Windows/ MacOsX

:: DOWNLOAD

 INRICH

:: MORE INFORMATION

Citation

INRICH: interval-based enrichment analysis for genome-wide association studies.
Lee PH, O’Dushlaine C, Thomas B, Purcell SM.
Bioinformatics. 2012 Jul 1;28(13):1797-9. doi: 10.1093/bioinformatics/bts191.