TEAM 1.2.0 – Design and Management of Panels of Genes for Targeted Enrichment and Massive Sequencing

TEAM 1.2.0

:: DESCRIPTION

TEAM (Targeted Enrichment Analysis and Management) is an open web-based tool for the design and management of panels of genes for targeted enrichment and massive sequencing for diagnostic applications.

::DEVELOPER

Bioinformatics and Genomics Department at CIPF

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
Java

:: DOWNLOAD

TEAM

:: MORE INFORMATION

Citation

A web tool for the design and management of panels of genes for targeted enrichment and massive sequencing for clinical applications.
Alemán A, Garcia-Garcia F, Medina I, Dopazo J.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W83-7. doi: 10.1093/nar/gku472.

PyClone 0.13.1 – Infer Clonal Frequency Estimates of a Panel of deeply Sequenced Mutations

PyClone 0.13.1

:: DESCRIPTION

pyClone is a software used to infer clonal frequency estimates of a panel of deeply sequenced mutations. The software is a Bayesian hierachical model for inferring the frequency of cells with a given mutation from allelic count data generated by next generation sequencing experiments. PyClone makes use of prior information about genotype as well as jointly analysing all mutations in a sample.

postpy is a set of tools to help with post-processing PyClone results.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows
Python

:: DOWNLOAD

PyClone, postpy

:: MORE INFORMATION

Citation

Sohrab P. Shah et al.
“The clonal and mutational evolution spectrum of primary triple-negative breast cancers”.
Nature 486, 395–399 (21 June 2012)
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SoftPanel – Grouping Disorders for Generation of customized Panels

SoftPanel

:: DESCRIPTION

SoftPanel provides a convenient and powerful tool for creating a targeted panel of potential disease genes while supporting different forms of input.

::DEVELOPER

SoftPanel team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

SoftPanel

:: MORE INFORMATION

Citation

SoftPanel: a website for grouping diseases and related disorders for generation of customized panels.
Wang L, Zhang C, Watkins J, Jin Y, McNutt M, Yin Y.
BMC Bioinformatics. 2016 Apr 5;17(1):153. doi: 10.1186/s12859-016-0998-5.

SPIA 1.1.0 – SNP Panel Identification Assay

SPIA 1.1.0

:: DESCRIPTION

SPIA is a genetic-based assay for the identification of cell lines

::DEVELOPER

Demichelis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux /Windows / MacOSX
R

:: DOWNLOAD

SPIA

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2008 Apr;36(7):2446-56. doi: 10.1093/nar/gkn089. Epub 2008 Feb 27.
SNP panel identification assay (SPIA): a genetic-based assay for the identification of cell lines.
Demichelis F1, Greulich H, Macoska JA, Beroukhim R, Sellers WR, Garraway L, Rubin MA.

GeneTerrain – Next-generation Panel Biomarker Discovery and Validation software

GeneTerrain

:: DESCRIPTION

GeneTerrain is a next-generation panel biomarker discovery and validation software.

::DEVELOPER

Discovery Informatics and Computing Laboratory@ Indiana University School of Informatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows

:: DOWNLOAD

Please join the mailing group to obtain instructions for downloading a pre-release version of the software.

:: MORE INFORMATION

Citation

You Qian, Shiaofen Fang, and Jake Y. Chen (2008)
GeneTerrain: Visual Exploration of Differential Gene Expression Profiles Organized in Native Biomolecular Interaction Networks
Information Visualization, doi: 10.1057/palgrave.ivs.9500169