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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   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/pegasus-fus/

Software that annotates biologically functional gene fusion candidates.

Proper citation: Pegasus-fus (RRID:SCR_012118) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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

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

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://sourceforge.net/projects/trowel-ec/

An error correction module for Illumina sequencing reads, which is based on the k-mer spectrum approach.

Proper citation: Trowel (RRID:SCR_012890) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/oncosts/

Software for a web-based Laboratory Information Management System for sample and analysis tracking in oncogenomic experiments.

Proper citation: Onco-STS (RRID:SCR_012990) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/nxgview/

A virtual software pipeline that contains several PERL modules for processing next generation sequencing data.

Proper citation: NxGview (RRID:SCR_012994) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bamformatics/

Software that provides a coherent and consistent approach to analysis of high-throughput sequencing data.

Proper citation: Bamformatics (RRID:SCR_013041) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bsmapper/

Sequence mapper for bisulfite sequencing reads for DNA methylation studies.

Proper citation: BSmapper (RRID:SCR_012998) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mendelscan/

A software tool for prioritizing candidate variants in family-based studies of inherited disease.

Proper citation: MendelScan (RRID:SCR_013053) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/probeselect/

Software for selecting probes in heterogenous transcriptional sets.

Proper citation: ProbeSelect (RRID:SCR_012965) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/seqgenomebrowse/

Mini cross-platform local genome browser software designed for visualizing next-generation sequencing data.

Proper citation: SeqGenome Browser (RRID:SCR_012970) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mirdp/

A computational tool for analyzing the microRNA (miRNA) transcriptome in plants.

Proper citation: miRDeep-P (RRID:SCR_013026) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/quicktsaf/

Tool that compresses and decompresses fastq files.

Proper citation: KungFq (RRID:SCR_012979) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ncproseq/

Software that aims to interrogate and perform detailed analysis on small RNAs derived from annotated non-coding regions.

Proper citation: ncPRO-seq (RRID:SCR_013031) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/vcf2msat/

A python software program to identify microsatellite repeat regions based on known polymorphisms identified in a .vcf report after using SAMtools to analyze next-generation sequencing files.

Proper citation: vcf2MSAT (RRID:SCR_013034) Copy   

•   Source: SciCrunch Registry