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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://drive5.com/usearch/manual/uchime_algo.html
An algorithm for detecting chimeric sequences.
Proper citation: UCHIME (RRID:SCR_008057) Copy
http://cran.r-project.org/web/packages/RJaCGH/index.html
Software for Bayesian analysis of CGH microarrays fitting Hidden Markov Chain models.
Proper citation: RJaCGH (RRID:SCR_008381) Copy
http://www.cerc.utexas.edu/OnlineCall/
A fast basecalling scheme for Illumina''s Next Generation sequencing machines, specifically designed for GAII.
Proper citation: OnlineCall (RRID:SCR_008263) Copy
http://bioinfo.cipf.es/isacghtrac
Software to analyze CNV that will now normalize arrays CGH and it will visually integrate different genome annotations.
Proper citation: IsaCGH (RRID:SCR_008375) Copy
http://seqpig.sourceforge.net/
A software library for Apache Pig for the distributed analysis of large sequencing datasets on Hadoop clusters.
Proper citation: SeqPig (RRID:SCR_008548) Copy
http://mothra.ornl.gov/cgi-bin/cat/cat.cgi
A repository of tools for analysis and annotation of CAZYmes (Carbohydrate Active enZYmes)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CAT (RRID:SCR_008421) Copy
http://www.broadinstitute.org/scientific-community/science/programs/cancer/ultrasome
An efficient methodology for detecting and delineating gains and losses of chromosomal material in DNA copy-number data.
Proper citation: Ultrasome (RRID:SCR_008465) Copy
http://pga.mgh.harvard.edu/oligopicker/
Software to help selecting up to five oligo probes for each of the DNA sequences you provided for microarray spotting.
Proper citation: OligoPicker (RRID:SCR_008720) Copy
http://dc.crs4.it/projects/biodoop
A suite of parallel bioinformatics applications based upon a popular open-source Java implementation of MapReduce, Hadoop.
Proper citation: Biodoop (RRID:SCR_008711) Copy
http://code.google.com/p/drgap/
Designed to identify Driver Genes and Pathways in cancer genome sequencing studies.
Proper citation: DrGaP (RRID:SCR_008670) Copy
http://www.broadinstitute.org/cancer/cga/invex/
A permutation-based method (written in Python) for ascertaining genes with a somatic mutation distribution showing evidence of positive selection for non-silent mutations.
Proper citation: InVEx (RRID:SCR_008734) Copy
http://www.bioconductor.org/packages/devel/bioc/html/MBASED.html
Software package containing functions for allele-specific gene expression (ASE) analysis using meta-analysis based allele-specific expression detection.
Proper citation: MBASED (RRID:SCR_002584) Copy
Python module to parse mzML data in Python based on cElementTree. It is an extension to Python that offers (i) an easy access to mass spectrometry (MS) data that allows the rapid development of tools, (ii) a very fast parser for mzML data and (iii) a set of functions to compare or handle spectra., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: pymzML (RRID:SCR_002500) Copy
https://code.google.com/p/peptide-shaker/
Software providing a search engine independent platform for visualization of peptide and protein identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot and mzIdentML. By combining the results from multiple search engines, while re-calculating PTM localization scores and redoing the protein inference, PeptideShaker attempts to give you the best possible understanding of your proteomics data.
Proper citation: PeptideShaker (RRID:SCR_002520) Copy
http://www.nitrc.org/projects/penncnv
A free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays. PennCNV implements a hidden Markov model (HMM) that integrates multiple sources of information to infer CNV calls for individual genotyped samples. It differs form segmentation-based algorithm in that it considered SNP allelic ratio distribution as well as other factors, in addition to signal intensity alone. In addition, PennCNV can optionally utilize family information to generate family-based CNV calls by several different algorithms. Furthermore, PennCNV can generate CNV calls given a specific set of candidate CNV regions, through a validation-calling algorithm.
Proper citation: PennCNV (RRID:SCR_002518) Copy
http://liulab.dfci.harvard.edu/BINOCh/
Software that infers the identity of transcription factors used to regulate cell response to stimulus or determine a program of differentiation. It uses genome wide information on enhancer proximal nucleosome occupancy, acquired using ChIP-seq targeting enhancer related histone modifications., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.
Proper citation: BINOCh (RRID:SCR_002778) Copy
http://bioconductor.org/packages/release/bioc/html/sapFinder.html
An R software package, for detection of the variant peptides based on tandem mass spectrometry (MS/MS)-based proteomics data. It automates (1) variation-associated database construction, (2) database searching, (3) post-processing, (4) HTML-based report generation in shotgun proteomics.
Proper citation: sapFinder (RRID:SCR_002685) Copy
https://github.com/grenaud/leeHom
Software program for the Bayesian reconstruction of ancient DNA fragments. The algorithm removes the adaptors and reconstructs the original DNA sequences using a Bayesian maximum a posteriori probability approach.
Proper citation: leeHom (RRID:SCR_002710) Copy
http://www.bioconductor.org/packages/release/bioc/html/pathview.html
A tool set for pathway-based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.
Proper citation: Pathview (RRID:SCR_002732) Copy
http://sourceforge.net/projects/glprobs/
Software implementing a simple and effective approach to improve the accuracy of multiple sequence alignment.
Proper citation: GLProbs (RRID:SCR_002739) Copy
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