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http://www.mmnt.net/db/0/0/ftp-genome.wi.mit.edu/distribution/GISTIC2.0
Software to identify genes targeted by somatic copy-number alterations (SCNAs) that drive cancer growth. By separating SCNA profiles into underlying arm-level and focal alterations, they improve the estimation of background rates for each category.
Proper citation: GISTIC (RRID:SCR_000151) Copy
http://www.cs.utexas.edu/~bajaj/cvc/software/f2dockclient.shtml
A collection of user interfaces packaged into TexMol that allows a user to interactively submit protein-protein docking jobs to a remote computing cluster, monitor the status of the jobs and retrieve and visually display/compare the results.
Proper citation: F2DockClient (RRID:SCR_000185) Copy
http://www.biosolveit.de/flexx/index.html?ct=1
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software with two main applications: predicting the binding mode of three-dimensional proteins and virtual high-throughput screening (vHTS) which allows screening of compounds at rapid speeds.
Proper citation: FlexX (RRID:SCR_000186) Copy
http://www.cs.toronto.edu/~hilal/rnacontext/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Motif finding software suited for using large-scale RNA-binding affinity datasets to determine the relative binding preferences of RNA-binding proteins (RBPs) for a wide range of RNA sequences and structures. The tool is also implemented in a website.
Proper citation: RNAcontext (RRID:SCR_000179) Copy
http://www.bioconductor.org/packages/release/bioc/html/TransView.html
Software package to generate, access and display read densities of sequencing based data sets such as from RNA-Seq and ChIP-Seq.
Proper citation: TransView (RRID:SCR_000358) Copy
http://www.bioconductor.org/packages/release/bioc/html/pvac.html
Software package that contains the function for filtering genes by the proportion of variation accounted for by the first principal component (PVAC).
Proper citation: pvac (RRID:SCR_000359) Copy
https://code.google.com/p/taps/
A bioinformatic tool for the identification of allele-specific copy numbers in tumor samples using data from Affymetrix SNP arrays.
Proper citation: TAPS (RRID:SCR_000356) Copy
https://code.google.com/p/pyrohmmsnp/
Software using a realignment-based SNP calling method for 454 and Ion Torrent sequencing data.
Proper citation: PyroHMMsnp (RRID:SCR_000357) Copy
http://sourceforge.net/projects/cgap-align/
A time efficient read alignment tool built on the top of BWA.
Proper citation: CGAP-Align (RRID:SCR_000350) Copy
http://cutenmr.sourceforge.net/
A multi-platform NMR processing application.
Proper citation: cuteNMR (RRID:SCR_000347) Copy
http://sourceforge.net/projects/jmoldraw/
2-D chemical structure drawing software program.
Proper citation: JMolDraw (RRID:SCR_000349) Copy
http://bioinformatics.research.nicta.com.au/software/is-rsnp/
Software tool that predicts whether a single nucleotide polymorphism (SNP) is a regulatory SNP (rSNP). For a given SNP, and using a statistical framework, it can successfully predict the set of transcription factors (TFs) for which binding is affected. The algorithm provides the statistical power to scan large numbers of SNPs, making it suitable to use to screen all associated SNPs output by a typical genome-wide association studies (GWAS).
Proper citation: is-rSNP (RRID:SCR_000387) Copy
http://sourceforge.net/projects/as-peak/
A software that utilizes a peak detection algorithm to identify RNA-protein binding sites.
Proper citation: AS-Peak (RRID:SCR_000380) Copy
http://cellnet.cecad.uni-koeln.de/15763.html
R software package for transcription factor (TF) target gene prediction based on ChIP-seq data. Version 0.4 contains code to compute FDR-corrected q-values via permutations of the peak-to-gene assignments (ClosestGene only).
Proper citation: TargetCaller (RRID:SCR_000414) Copy
http://sourceforge.net/projects/genseng/
Software for detecting copy number variations from next generation sequencing data. Used to identify regions of discrete copy number changes while simultaneously accounting for effects of multiple confounders.
Proper citation: GENSENG (RRID:SCR_000378) Copy
A data compressor for files. This software is freely available, patent free, and is organized as a library with a programming interface.
Proper citation: bzip2 (RRID:SCR_000376) Copy
http://www.bioconductor.org/packages/release/bioc/html/flowFlowJo.html
A Bioconductor package that can import gates defined by the commercial package FlowJo and work with them in a manner consistent with the other flow packages in Bioconductor. FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the FlowJo Workspace. This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm.
Proper citation: flowFlowJo (RRID:SCR_000410) Copy
http://www.bioconductor.org/packages/release/bioc/html/OLINgui.html
Software package providing a graphical user interface for the OLIN package.
Proper citation: OLINgui (RRID:SCR_000435) Copy
http://sourceforge.net/projects/arrayplex/
Open source software that integrates various forms of microarray data from diverse annotation and primary data sources. This software provides a programmatic framework (API set) that will be used for collaborative development and deploys an easy to maintain client-server architecture.
Proper citation: ArrayPlex (RRID:SCR_000312) Copy
http://life.tongji.edu.cn/meqa/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2022. Software for pre-processing, quality assessment, read distribution and methylation estimation for MeDIP-sequence datasets. It has the ability to quickly analyze sequence data for DNA methylation. This software integrates customized scripting and existing utilities tools that work on both paired end and single end data.
Proper citation: MeQA (RRID:SCR_000317) Copy
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