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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
A collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms.
Proper citation: USeq (RRID:SCR_004753) Copy
http://svmerge.sourceforge.net/
Software pipeline to detect structural variants (SVs) by integrating calls from several existing SV callers, which are then validated and the breakpoints refined using local de novo assembly. The output is in BED format allowing for easy downstream analysis or viewing in a genome browser. It is modular and extensible allowing new callers to be incorporated as they become available.
Proper citation: SVMerge (RRID:SCR_004777) Copy
http://sourceforge.net/projects/dna-bison/
Allows users with access to a computer cluster to rapidly align whole-genome bisulfite sequencing or RRBS reads.
Proper citation: dna-bison (RRID:SCR_005913) Copy
A web-based software tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context.
Proper citation: GEPAT (RRID:SCR_003597) 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/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
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