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http://sourceforge.net/projects/finesplice/
A software pipeline based on TopHat2 combined with a splice junction detection algorithm.
Proper citation: FineSplice (RRID:SCR_000691) Copy
http://sourceforge.net/projects/particlecall/
A base-calling algorithm for Illumina DNA sequencing.
Proper citation: ParticleCall (RRID:SCR_001103) Copy
http://sourceforge.net/projects/cuda-ec/
A fast parallel error correction tool for short reads.
Proper citation: CUDA-EC (RRID:SCR_001090) Copy
http://sourceforge.net/projects/qips/
A software package for analyzing ChIP-seq (Chromatin ImmunoPrecipitation on sequencing) data that finds enriched regions of arbitrary lengths and is therefore especially suited for analyzing ChIP-seq of histone marks or polymerase.
Proper citation: qips (RRID:SCR_001092) Copy
http://sourceforge.net/projects/dtailor/
A fully extendable software framework, for property-based design of synthetic DNA sequences.
Proper citation: D-Tailor (RRID:SCR_000115) Copy
http://sourceforge.net/projects/sirnarules/
An open-source JAVA program that is surprisingly efficient at predicting active siRNAs.
Proper citation: siRNArules (RRID:SCR_000096) Copy
http://sourceforge.net/projects/abmining/
Python scripts to analyze antibody libraries sequenced by next generation sequencing methods (454, Ion Torrent, MiSeq).
Proper citation: AbMining ToolBox (RRID:SCR_000090) Copy
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
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
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
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
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
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
A freely available complete software platform for comprehensive and integrated analysis and visualization of large proteomics datasets.
Proper citation: GProX (RRID:SCR_000273) Copy
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
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
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
http://sourceforge.net/projects/powermap/
Software tool specifically designed for neuroimaging data that implements theoretical power calculation algorithms based on non-central random field theory. It can also calculate power for statistical analyses with FDR (false discovery rate) corrections. This GUI (graphical user interface)-based tool enables neuroimaging researchers without advanced knowledge in imaging statistics to calculate power and sample size in the form of 3D images. This tool is currently under limited release for beta testing. At this time, only users that have been directed to this site by the PowerMap developers will receive support.
Proper citation: PowerMap (RRID:SCR_006721) Copy
http://sourceforge.net/projects/samscope/
A lightweight SAM/BAM file viewer that makes visually exploring next generation sequencing data intuitive and maybe even fun! Quickly and easily generate aggregate statistics from SAM/BAM files like coverage, polarity, and minor allele frequencies, then scroll and explore freely with a simple mouse based interface. Multiple windows can be synchronized for careful comparison across multiple experiments.
Proper citation: Samscope (RRID:SCR_006715) Copy
http://sourceforge.net/projects/dmeas/
A user-friendly DNA methylation analysis tool for DNA methylation pattern extraction, DNA methylation level estimation, DNA methylation entropy analysis and multi-sample comparison. It was developed in order to assess the DNA methylation variations for a given genomic locus or genome-wide methylation data.
Proper citation: DMEAS (RRID:SCR_006679) Copy
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