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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.
https://code.google.com/p/bsmap/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18,2023. Short reads mapping software for bisulfite sequencing reads.
Proper citation: BSMAP (RRID:SCR_005671) Copy
http://biostat.mc.vanderbilt.edu/wiki/Main/ASAP
Software developed to provide a framework for building and executing a pipeline to preprocess next generation sequence data and variant calls.
Proper citation: Advanced Sequence Automated Pipeline (RRID:SCR_005578) Copy
http://samtools.sourceforge.net/tview.shtml
Text alignment viewer software based on the GNU ncurses library that works with short indels and shows MAQ consensus. It uses different colors to display mapping quality or base quality, subjected to users' choice.
Proper citation: SAMtools Text Alignment Viewer (RRID:SCR_005611) Copy
http://rafalab.jhsph.edu/bsmooth/
A pipeline for analyzing whole genome bisulfite sequencing (WGBS) data.
Proper citation: BSmooth (RRID:SCR_005693) Copy
http://www.ridom.de/traceedit/
A cross-platform graphical DNA trace viewer and editor that displays the chromatogram files from Applied Biosystems automated sequencers and files in the Staden SCF format. Incorrect base calls can be edited and saved. TraceEdit is freely available and designed to operate on Windows and UNIX platforms.
Proper citation: Ridom TraceEdit (RRID:SCR_005568) Copy
http://www.bioinformatics.babraham.ac.uk/projects/hicup/
A tool for mapping and performing quality control on Hi-C data.
Proper citation: HiCUP (RRID:SCR_005569) Copy
https://medicine.yale.edu/lab/rimm/research/software/
Software tool for biomarker assessment and outcome based cut point optimization.
Proper citation: X-Tile (RRID:SCR_005602) Copy
http://sourceforge.net/projects/cancergrid-tma/
A web-based application for the management and storage of tissue microarray (TMA) images and the associated metadata. The application enables the user to navigate a grid of TMA core images within a slide, zoom and pan around an image, and enter a score constrained to a specific scoring system. The submitted scores are scored in the eXist open source database, in an XML format, which is compatible with existing TMA standards, and thus allow the data to be archived and re-used in future analysis.
Proper citation: cancergrid-tma (RRID:SCR_005595) Copy
http://www.sanger.ac.uk/resources/software/lookseq/
A web-based application for alignment visualization, browsing and analysis of genome sequence data.
Proper citation: LookSeq (RRID:SCR_005625) Copy
http://zhanglab.c2b2.columbia.edu/index.php/OLego
A program specifically designed for de novo spliced mapping of mRNA-seq reads. It adopts a multiple-seed-and-extend scheme, and does not rely on a separate external mapper.
Proper citation: OLego (RRID:SCR_005811) Copy
https://code.google.com/p/pepr-chip-seq/
A ChIP-Seq peak calling or differential binding analysis tool that is primarily designed for data with biological replicates. It uses a negative binomial distribution to model the read counts among the samples in the same group, and look for consistent differences between ChIP and control group or two ChIP groups run under different conditions.
Proper citation: PePr (RRID:SCR_005759) 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
http://www.bioinf.uni-freiburg.de/Software/GraphProt/
Software for modeling binding preferences of RNA-binding proteins from high-throughput experiments such as CLIP-seq and RNAcompete.
Proper citation: GraphProt (RRID:SCR_005842) Copy
http://apps.cytoscape.org/apps/jepetto
A Cytoscape plugin that performs integrated gene set analysis using information from interaction, pathways and processes databases. The plugin integrates information from three separate web servers specializing in enrichment analysis, pathways expansion and topological matching. It uses the TopoGSA server to identify topological analogies between the user selected gene set and the known pathways and processes. TopoGSA finds the most similar biological mechanism using the topological features of the interaction network of a user selected gene set. It is also able to suggest genes related to the query gene set using two pathway analysis servers EnrichNet and PathExpand. Both these servers are using a different topological matching algorithms that extends the query gene set with genes from the pathway databases. This integration substantially simplifies the analysis of user gene sets and the interpretation of the results.
Proper citation: JEPETTO (RRID:SCR_005909) Copy
A pattern growth algorithm based pileline for splice site detection in paired-end RNA-Seq data.
Proper citation: PASSion (RRID:SCR_005867) Copy
http://www-math.u-strasbg.fr/genpred/spip.php?article3
R software package to study, predict and simulate the diffusion of a signal through a temporal gene network. It predicts changes in gene expressions after a biological perturbation in the network and provides graphical outputs that allow monitoring the spread of a signal through the network., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Cascade (RRID:SCR_005861) Copy
http://www.cisd.ethz.ch/software/openBIS
Software for an open, distributed system for managing biological information that supports biological research data workflows from the source (i.e. the measurement instruments) to facilitate the process of answering biological questions by means of cross-domain queries against raw data, processed data, knowledge resources and its corresponding metadata. The openBIS software framework can be easily extended and has been customized for the following technologies: * High Content Screening * Proteomics * Deep Sequencing * Metabolomics
Proper citation: openBIS (RRID:SCR_011815) Copy
http://bioen-compbio.bioen.illinois.edu/PSAR-Align/
Software for improving multiple sequence alignment using probabilistic sampling.
Proper citation: PSAR-Align (RRID:SCR_011814) Copy
http://gaggle.systemsbiology.net/docs/geese/genomebrowser/
An open source software tool for visualizing high-density data plotted against coordinates on the genome.
Proper citation: Gaggle (RRID:SCR_011780) Copy
http://www.csd.uwo.ca/~ilie/HiTEC/
Accurate error correction in high-throughput sequencing data.
Proper citation: HiTEC (RRID:SCR_011826) Copy
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