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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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/dhacdist/

Software for clustering time-evolving networks.

Proper citation: DHAC (RRID:SCR_012139) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/LVSmiRNA.html

Software for normalization of Agilent miRNA arrays.

Proper citation: LVSmiRNA (RRID:SCR_012752) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/sequencing

Whole genome secondary analysis on Illumina sequencing platforms.

Proper citation: Isaac (RRID:SCR_012772) Copy   

•   Source: SciCrunch Registry

https://github.com/torognes/swipe

A software tool for performing rapid local alignment searches in amino acid or nucleotide sequence databases.

Proper citation: SWIPE (RRID:SCR_012771) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/lumi.html

Software that provides an integrated solution for the Illumina microarray data analysis.

Proper citation: lumi (RRID:SCR_012781) Copy   

•   Source: SciCrunch Registry

http://bioinf.comav.upv.es/ngs_backbone/index.html

A bioinformatic application created to work on sequence analysis by using NGS (Next Generation Sequencing) and sanger sequences.

Proper citation: Ngs backbone (RRID:SCR_012907) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/rqubic.html

This software package implements the QUBIC algorithm for the qualitative biclustering with gene expression data.

Proper citation: rqubic (RRID:SCR_012869) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/DiffBind.html

Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.

Proper citation: DiffBind (RRID:SCR_012918) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/iBBiG.html

A bi-clustering algorithm which is optimizes for binary data analysis.

Proper citation: iBBiG (RRID:SCR_012882) Copy   

•   Source: SciCrunch Registry