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http://sourceforge.net/projects/spdesigner/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An open source software program for the design of specific PCR primer pairs from a DNA sequence alignment containing sequences from various taxa.

Proper citation: SP-Designer (RRID:SCR_000031) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mysirna/

Software that integrates several factors in an automated work-flow considering mRNA transcripts variations, siRNA and mRNA target accessibility, and both near-perfect and partial off-target matches.

Proper citation: MysiRNA-designer (RRID:SCR_000102) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/dprimer/

A command line software utility for designing degenerate PCR primers against multiple, aligned sequences. Its primary use case is searching for a family of related pathogens in a host tissue sample.

Proper citation: dprimer (RRID:SCR_000050) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/imethy/

Software for investigation and visualization of DNA methylation by high-throughput bisulfite sequencing.

Proper citation: iMethy (RRID:SCR_000049) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/protms/

A software tool for the proteomics community that may help improving analysis of proteomic experimental data.

Proper citation: Quant (RRID:SCR_000267) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/biogrinder/

An open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms. The tool is available through multiple interfaces like GUI, CLI and API. It is useful for simulating clinical or environmental microbial communities and complements the use of in vitro mock communities.

Proper citation: Grinder (RRID:SCR_000168) Copy   

•   Source: SciCrunch Registry

http://gprox.sourceforge.net/

A freely available complete software platform for comprehensive and integrated analysis and visualization of large proteomics datasets.

Proper citation: GProX (RRID:SCR_000273) Copy   

•   Source: SciCrunch Registry

http://peptideprophet.sourceforge.net/

Software that automatically validates peptide assignments to MS/MS spectra made by database search programs such as SEQUEST.

Proper citation: PeptideProphet (RRID:SCR_000274) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/cohcap/

An algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values.

Proper citation: COHCAP (RRID:SCR_006499) Copy   

•   Source: SciCrunch Registry

http://garm-meta-assem.sourceforge.net/

A new software pipeline to merge and reconcile assemblies from different algorithms or sequencing technologies.

Proper citation: GARM (RRID:SCR_006731) Copy   

•   Source: SciCrunch Registry

http://ebardenovo.sourceforge.net/

Highly accurate de novo assembly of RNA-Seq with efficient chimera-detection.

Proper citation: EBARDenovo (RRID:SCR_011890) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/apps/mediawiki/seqgene/?title=SeqGene

An open-source software for mining next-gen sequencing datasets, focusing on post-alignment quality control, SNP and indel identification and annotation, RNA expression quantification, etc.

Proper citation: SeqGene (RRID:SCR_011861) Copy   

•   Source: SciCrunch Registry

http://bayescall.sourceforge.net/

An efficient model-based base-calling algorithm for high-throughput sequencing.

Proper citation: naiveBayesCall (RRID:SCR_011866) Copy   

•   Source: SciCrunch Registry

http://scalpel.sourceforge.net/

A software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome which has been sequenced with next-generation sequencing technology (e.g., Illumina).

Proper citation: Scalpel (RRID:SCR_012107) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/snpratiotest/

Software to calculate the number of significant SNPs in pathway divided by the number of SNPs in pathway.

Proper citation: SNP ratio test (RRID:SCR_012070) Copy   

•   Source: SciCrunch Registry

http://toxtree.sourceforge.net/

A full-featured and flexible user-friendly open source software application, which is able to estimate toxic hazard by applying a decision tree approach.

Proper citation: Toxtree (RRID:SCR_012086) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/viewmol/

Software providing a graphical front end for computational chemistry programs.

Proper citation: Viewmol (RRID:SCR_012088) Copy   

•   Source: SciCrunch Registry

http://toxmatch.sourceforge.net/

A software tool to facilitate chemical similarity calculations.

Proper citation: Toxmatch (RRID:SCR_012087) Copy   

•   Source: SciCrunch Registry

http://qutemol.sourceforge.net/

Open source (GPL) software providing an interactive, high quality molecular visualization system.

Proper citation: QuteMol (RRID:SCR_012089) Copy   

•   Source: SciCrunch Registry

http://maltcms.sourceforge.net/users/features.html

An application framework mainly suited for developers working in the domain of bioinformatics for metabolomics and proteomics.

Proper citation: Maltcms (RRID:SCR_012057) Copy   

•   Source: SciCrunch Registry