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http://sourceforge.net/projects/virtools/
Software for a low frequency Virus Variant detection pipeline for Illumina data.
Proper citation: VirVarSeq (RRID:SCR_012116) Copy
http://sourceforge.net/projects/pegasus-fus/
Software that annotates biologically functional gene fusion candidates.
Proper citation: Pegasus-fus (RRID:SCR_012118) Copy
Cancer specific CNV caller for Next Generation sequence.
Proper citation: WaveCNV (RRID:SCR_012244) Copy
https://github.com/BEETL/BEETL
Software tool as data transformation algorithm that restructures data in such a way that the transformed message is more compressible. Used for large scale compression of genomic sequence databases.
Proper citation: Burrows-Wheeler transform (RRID:SCR_012304) Copy
http://code.google.com/p/npstat/
Software that implements some population genetics tests and estimators that can be applied to pooled sequences from Next Generation Sequencing experiments.
Proper citation: npstat (RRID:SCR_012128) Copy
http://sourceforge.net/projects/nailsystemsbiology/
A set of software tools to simplify the range of computational activities involved in regulatory network inference. It is technology-independent and includes an interface layer to allow easy integration of components into other applications. It is implemented in MATLAB and is available for all researchers to use.
Proper citation: NAIL (RRID:SCR_012134) Copy
http://sourceforge.net/projects/imsat/
A python program that uses the polymorphism data obtained from mapping individual Illumina sequence reads onto a reference genome to identify polymorphic STRs.
Proper citation: iMSAT (RRID:SCR_012135) Copy
http://sourceforge.net/projects/nesmapper/
A computational software tool to predict leucine-rich nuclear export signals (NESs) by using profiles that had been further optimized by training and combining the amino acid properties of the NES-flanking regions. It is a multiplatform command-line Perl application with activity-based NES profiles.
Proper citation: NESmapper (RRID:SCR_012138) Copy
http://sourceforge.net/projects/dhacdist/
Software for clustering time-evolving networks.
Proper citation: DHAC (RRID:SCR_012139) Copy
https://code.google.com/p/mp-est/
Software that can consistently estimate the topology and branch lengths (in coalescent units) of the species tree. Although the pseudo-likelihood is derived from coalescent theory, and assumes no gene flow or horizontal gene transfer (HGT), the MP-EST method is robust to a small amount of HGT in the dataset. In addition, increasing the number of genes does not increase the computational time substantially. The MP-EST method is fast for analyzing datasets that involve a large number of genes but a moderate number of species.
Proper citation: MP-EST (RRID:SCR_012145) Copy
http://xmsanalyzer.sourceforge.net
A software package of utilities for data extraction, quality control assessment, detection of overlapping and unique metabolites in multiple datasets, and batch annotation of metabolites. xMSanalyzer comprises of utilities that can be classified into five main modules: 1) merging apLCMS or XCMS sample processing results from multiple sets of parameter settings, 2) evaluation of sample quality, feature consistency, and batch-effect, 3) feature matching, and 4) characterization of m/z using KEGG REST; 5) Batch-effect correction using ComBat.
Proper citation: xMSanalyzer (RRID:SCR_012144) Copy
https://code.google.com/p/localali/
A fast and scalable local network alignment software tool for the identification of functionally conserved modules in multiple networks. LocalAli outperforms all existing algorithms in terms of coverage, consistency and scalability, meanwhile retains a high precision in the identification of functionally coherent subnetworks.
Proper citation: LocalAli (RRID:SCR_012147) Copy
https://sites.google.com/site/oncosnpseq/
An analytical tool for characterizing copy number alterations and loss-of-heterozygosity (LOH) events in cancer samples from whole genome sequencing data.
Proper citation: OncoSNP-SEQ (RRID:SCR_012742) Copy
http://www.bioconductor.org/packages/release/bioc/html/LVSmiRNA.html
Software for normalization of Agilent miRNA arrays.
Proper citation: LVSmiRNA (RRID:SCR_012752) Copy
http://bioconductor.org/packages/release/bioc/html/MMDiff.html
Software package that detects statistically significant difference between read enrichment profiles in different ChIP-Seq samples.
Proper citation: MMDiff (RRID:SCR_012692) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/crlmm.html
Genotype Calling and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
Proper citation: CRLMM (RRID:SCR_012580) Copy
http://www.bioconductor.org/packages/release/bioc/html/baySeq.html
Software package that identifies differential expression in high-throughput ''count'' data, such as that derived from next-generation sequencing machines.
Proper citation: baySeq (RRID:SCR_012795) Copy
http://sourceforge.net/projects/excavatortool/
A software package for the detection of copy number variants (CNVs) from whole-exome sequencing data.
Proper citation: EXCAVATOR-tool (RRID:SCR_012766) Copy
http://bioconductor.org/packages/devel/bioc/html/RPA.html
A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases.
Proper citation: RPA (RRID:SCR_012768) Copy
Whole genome secondary analysis on Illumina sequencing platforms.
Proper citation: Isaac (RRID:SCR_012772) Copy
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