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http://sourceforge.net/projects/cgap-align/
A time efficient read alignment tool built on the top of BWA.
Proper citation: CGAP-Align (RRID:SCR_000350) Copy
http://cutenmr.sourceforge.net/
A multi-platform NMR processing application.
Proper citation: cuteNMR (RRID:SCR_000347) Copy
http://sourceforge.net/projects/jmoldraw/
2-D chemical structure drawing software program.
Proper citation: JMolDraw (RRID:SCR_000349) Copy
http://sourceforge.net/projects/as-peak/
A software that utilizes a peak detection algorithm to identify RNA-protein binding sites.
Proper citation: AS-Peak (RRID:SCR_000380) Copy
http://open2dprot.sourceforge.net/Flicker/
An open-source stand-alone computer program for visually comparing 2D gel images.
Proper citation: Flicker (RRID:SCR_000288) Copy
http://sourceforge.net/projects/omssapercolator/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software tool which interfaces OMSSA with Percolator, a post search machine learning method for rescoring database search results.
Proper citation: OMSSAPercolator (RRID:SCR_000287) Copy
http://sourceforge.net/projects/arrayplex/
Open source software that integrates various forms of microarray data from diverse annotation and primary data sources. This software provides a programmatic framework (API set) that will be used for collaborative development and deploys an easy to maintain client-server architecture.
Proper citation: ArrayPlex (RRID:SCR_000312) Copy
http://sourceforge.net/projects/microanalyzer/
Java tool that performs the preprocessing of Expression and SNPs microarray Affymetrix. The software allows the automatic download and the use of the clustering and visualization software as the Mev 4.0. The tool is equipped by a graphical interface (Swing) that allows to the user to: Create the workspace (files .cel, preferred algorithms , output, libraries to use); Run/save analysis and workspace settings (xml); Efficient download of the libraries (http, ftp, MD5); Customize basic and graphical settings (objects serialization and deserialization). Type of SNPs: Mapping 500k or preceding chips, SNP 5.0, SNP 6.0. Available for 32 or 64 bit systems, and for Windows and Linux Systems.
Proper citation: Micro-Analyzer (RRID:SCR_000394) Copy
http://functsnp.sourceforge.net/
An R package for linking SNPs (Single Nucleotide Polymorphisms) to functional knowledge.
Proper citation: FunctSNP (RRID:SCR_000393) Copy
http://sourceforge.net/projects/foursig/
A suite of software programs for analyzing and visualizing 4C-seq data.
Proper citation: fourSig (RRID:SCR_000516) Copy
http://open-ms.sourceforge.net/documentation/knime-integration/
A graphical user interface (GUI) for rapid composition of HPLC-MS analysis workflows. Workflow construction is reduced to drag-and-drop of analysis tools and adding connections in between.
Proper citation: TOPPAS (RRID:SCR_000533) Copy
http://ishtar.sourceforge.net/
A program for designing primer pairs that amplify multiple target sequences using DNA thermodynamics and one class support vector machines. Written in Python.
Proper citation: Ishtar (RRID:SCR_000538) Copy
http://sourceforge.net/projects/reprever/?source=directory
Software that identifies (a) the insertion breakpoints where the extra duplicons inserted into the donor genome and (b) the actual sequence of the duplicon for any genomic regions that are increased in copy number.
Proper citation: Reprever (RRID:SCR_000463) Copy
http://sourceforge.net/projects/variantmaster/
Software program that extracts causative variants in familial and sporadic genetic diseases. The algorithm takes into account predicted variants (SNPs and indels) in affected individuals or tumor samples and utilizes the row (BAM) data to robustly estimate the conditional probability of segregation in a family, as well as the probability of it being de novo or somatic. In familial cases, various modes of inheritance are considered: X-linked, autosomal dominant, and recessive (homozygosity or compound heterozygosity). Moreover, it integrates phenotypes and genotypes, and employs Annovar to produce additional information as allelic frequencies in general population and damaging scores.
Proper citation: VariantMaster (RRID:SCR_000569) Copy
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
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
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
http://sourceforge.net/projects/bsmapper/
Sequence mapper for bisulfite sequencing reads for DNA methylation studies.
Proper citation: BSmapper (RRID:SCR_012998) Copy
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
http://sourceforge.net/projects/probeselect/
Software for selecting probes in heterogenous transcriptional sets.
Proper citation: ProbeSelect (RRID:SCR_012965) Copy
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