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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.
http://sourceforge.net/projects/snptools/
A suite of software tools that enables integrative SNP analysis in next generation sequencing data with large cohorts.
Proper citation: SNPTools (RRID:SCR_013052) Copy
http://sourceforge.net/projects/swiftng/
An open source package for primary data analysis on next-gen sequence data from images to basecalls. Currently Swift is targeted toward Solexa/Illumina sequencing, but is designed to be platform agnostic.
Proper citation: Swift (RRID:SCR_013018) Copy
http://sourceforge.net/projects/cloudaligner/
A map/reduce based application for mapping short reads generated by the next-generation sequencing machines.
Proper citation: CloudAligner (RRID:SCR_012962) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/Rolexa.html
Software that provides probabilistic base calling, quality checks and diagnostic plots for Solexa sequencing data.
Proper citation: Rolexa (RRID:SCR_013017) Copy
http://www.ra.cs.uni-tuebingen.de/software/InCroMAP/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5,2023. Integrated analysis of cross-platform microarray and pathway data.
Proper citation: InCroMAP (RRID:SCR_012964) Copy
http://sourceforge.net/projects/tracetuner/
Software tool for base and quality calling of trace files from DNA sequencing instruments.
Proper citation: TraceTuner (RRID:SCR_013019) Copy
http://sourceforge.net/projects/seqminer/
Software for a genome wide mapping data interpretation platform for NGS (ChIPSeq).
Proper citation: seqMINER (RRID:SCR_013020) Copy
http://sourceforge.net/projects/mireap/
A software tool which can be used to identify both known and novel microRNAs from small RNA libraries deeply sequenced by Solexa/454/Solid technology.
Proper citation: MIREAP (RRID:SCR_013025) Copy
http://www.lgm.upmc.fr/mirena/index.html
A software tool to find microRNAs with high accuracy and no learning at genome scale and from deep sequencing data.
Proper citation: MIReNA (RRID:SCR_013024) Copy
https://mig.molbiol.ox.ac.uk/mig/
Allows the user to conveniently compare data from many loci., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MIG (RRID:SCR_012972) Copy
http://sourceforge.net/projects/msa-edna/
Software for Multiple Sequence Alignment for Transcription Factor Binding Sites using Di nucleotides dependencies and relying on Free Interaction energies between neighbouring DNA bases to stabilise substitution energy of the alignment.
Proper citation: EDNA (RRID:SCR_012981) Copy
http://bioconductor.org/packages/2.12/bioc/html/cn.mops.html
A data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data.
Proper citation: cn.mops (RRID:SCR_013036) Copy
http://sourceforge.net/projects/samzip/
An encoding and decoding tool for Sequence Alignment/Map (SAM) files.
Proper citation: SAMZIP (RRID:SCR_012980) Copy
http://sammate.sourceforge.net/
An open source GUI software suite to process RNA-Seq data. It is composed of two modules: assemblySAM and SAMMate.
Proper citation: SAMMate (RRID:SCR_013037) Copy
http://sourceforge.net/projects/flexbar/
Flexible barcode and adapter removal for sequencing platforms.
Proper citation: Flexbar (RRID:SCR_013001) Copy
http://www.cochrane.org/reviews/clibintro.htm
Contains data to inform healthcare decision-making from Cochrane and other systematic reviews, clinical trials, and more. Cochrane reviews bring you the combined results of the worlds best medical research studies, and are recognized as the gold standard in evidence-based health care. Consists of a regularly updated collection of evidence-based medicine databases, including The Cochrane Database of Systematic Reviews. This database includes systematic reviews of healthcare interventions that are produced and disseminated by The Cochrane Collaboration. It is published on a monthly basis and made available both on CD-ROM and the Internet. The review abstracts are available to browse and search free of charge on this website. The Cochrane Library Users'' Group (CLUG) provides a forum for discussion of usability, readability, searchability, and formatting issues related to the use of The Cochrane Library. The Cochrane Collaboration is an international not-for-profit and independent organization, dedicated to making up-to-date, accurate information about the effects of healthcare readily available worldwide. Funded by John Wiley and Sons Limited. The individual entities of The Cochrane Collaboration are funded by a large variety of governmental, institutional and private funding sources, and are bound by organisation-wide policy limiting uses of funds from corporate sponsors.
Proper citation: Cochrane Library (RRID:SCR_013000) Copy
http://sourceforge.net/projects/shrec-ec/
A bioinformatics tool for error correction of HTS read data.
Proper citation: SHREC (RRID:SCR_013009) Copy
http://sourceforge.net/projects/hictools/
This collection of tools stream-lines the processing of HiC data from raw sequence to contact matrices and beyond.
Proper citation: hiCtools (RRID:SCR_013010) Copy
http://sourceforge.net/projects/locas/
A software to assemble short reads of next generation sequencing technologies at low coverage.
Proper citation: LOCAS (RRID:SCR_013064) Copy
http://sourceforge.net/projects/vdjfasta/?source=navbar
Bioinformatics Perl extension for the analysis of antibody variable domain repertoires.
Proper citation: VDJFasta (RRID:SCR_013069) Copy
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