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http://sourceforge.net/projects/staden/

A C software implementation of SAM, BAM and CRAM file I/O.

Proper citation: Scramble (RRID:SCR_012036) Copy   

•   Source: SciCrunch Registry

http://mzmatch.sourceforge.net/mzmatch.R/mzmatch.ipeak.align.CowCoda.html

Software that performs retention time alignment on the given set of peaks.

Proper citation: CowCoDA (RRID:SCR_012039) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/open-ms/

An algorithm to align LC-MS samples and to match corresponding ion species across samples.

Proper citation: OpenMS (RRID:SCR_012042) Copy   

•   Source: SciCrunch Registry

http://obi-warp.sourceforge.net/

Software that aligns matrices along a single axis using Dynamic Time Warping (DTW) and a one-to-one (bijective) interpolated warp function.

Proper citation: OBI-Warp (RRID:SCR_012041) Copy   

•   Source: SciCrunch Registry

http://open-ms.sourceforge.net/

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on May 23rd,2023. Software that provides a set of computational tools which can be easily combined into analysis pipelines even by non-experts and can be used in proteomics workflows.

Proper citation: TOPP (RRID:SCR_012044) Copy   

•   Source: SciCrunch Registry

http://open-ms.sourceforge.net/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23rd,2023. Software that combines Lagrangian relaxation for solving an integer linear programming formulation with an adaptation of Yen''s k shortest paths algorithm.

Proper citation: Antilope (RRID:SCR_012046) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/swisspit/

Software for pipelined analysis of mass spectrometry data.

Proper citation: swissPIT (RRID:SCR_012045) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/icplquant/

A proteomics software tool for quantitatively analyzing large mass spectrometric datasets acquired from ICPL based proteomics experiments.

Proper citation: ICPL ESIQuant (RRID:SCR_012047) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mtoolbox/

Software for a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data.

Proper citation: MToolBox (RRID:SCR_012112) Copy   

•   Source: SciCrunch Registry

http://revister.sourceforge.net/

Software for an automated pipeline using a ''local mapping reference reconstruction method'' to revise mismapped or partially misaligned reads at simple tandem repeat loci.

Proper citation: ReviSTER (RRID:SCR_012113) Copy   

•   Source: SciCrunch Registry

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