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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.
Chemical 2D structure editor and viewer application/applet based on the Chemistry Development Kit (CDK).
Proper citation: JChemPaint (RRID:SCR_000095) Copy
http://www.bioconductor.org/packages/release/bioc/html/flowCL.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for semantic labelling of flow cytometric cell populations.
Proper citation: flowCL (RRID:SCR_000046) Copy
https://code.google.com/p/cbrowse/
Software providing an AJAX-based web browser for visualizing and analyzing transcriptome assemblies and contigs.
Proper citation: Cbrowse (RRID:SCR_000044) Copy
http://www.bioconductor.org/packages/release/data/annotation/html/RmiR.Hs.miRNA.html
Software package for various databases of microRNA Targets.
Proper citation: RmiR.Hs.miRNA (RRID:SCR_000101) Copy
http://www.bioconductor.org/packages/release/bioc/html/MIMOSA.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for modeling count data using Dirichlet-multinomial and beta-binomial mixtures with applications to single-cell assays.
Proper citation: MIMOSA (RRID:SCR_000184) Copy
http://www.bioconductor.org/packages/release/bioc/html/iASeq.html
Software that uses a Bayesian hierarchical mixture model to learn correlation patterns of allele-specificity among multiple proteins.
Proper citation: iASeq (RRID:SCR_000420) Copy
http://www.bioconductor.org/packages/release/bioc/html/rTANDEM.html
An R/Bioconductor package that interfaces the X!Tandem protein identification algorithm.
Proper citation: rTANDEM (RRID:SCR_000409) Copy
https://github.com/yongchao/flowPeaks
Software for fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.
Proper citation: flowPeaks (RRID:SCR_000407) Copy
http://www.bioconductor.org/packages/release/bioc/html/QUALIFIER.html
Software that provides quality control and quality assessment tools for gated flow cytometry data.
Proper citation: QUALIFIER (RRID:SCR_000389) Copy
http://bioconductor.org/packages/release/bioc/html/Rdisop.html
Software for identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists.
Proper citation: Rdisop (RRID:SCR_000453) Copy
http://bioconductor.org/packages/release/bioc/html/flipflop.html
Software that discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data.
Proper citation: FlipFlop (RRID:SCR_000625) Copy
http://www.psb.ugent.be/esb/PiNGO/
A Java-based tool to easily find unknown genes in a network that are significantly associated with user-defined target Gene Ontology (GO) categories. PiNGO is implemented as a plugin for Cytoscape, a popular open source software platform for visualizing and integrating molecular interaction networks. PiNGO predicts the categorization of a gene based on the annotations of its neighbors, using the enrichment statistics of its sister tool BiNGO. Networks can either be selected from the Cytoscape interface or uploaded from file. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Proper citation: PiNGO (RRID:SCR_000692) Copy
https://code.google.com/p/jmzml/
A Java application programming interface (API) for the Proteomics Standards Initiative mzML data standard.
Proper citation: jmzML (RRID:SCR_001119) Copy
http://bioconductor.org/packages/devel/bioc/html/massiR.html
Software that predicts the sex of samples in gene expression microarray datasets.
Proper citation: massiR (RRID:SCR_001157) Copy
https://github.com/nolanlab/cytospade
Cytoscape plugin that provides a high-performance implementation of an interface for the Spanning-tree Progression Analysis of Density-normalized Events (SPADE) algorithm for tree-based analysis and visualization of high-dimensional cytometry data.
Proper citation: CytoSPADE (RRID:SCR_001457) Copy
https://github.com/CollasLab/edd
A ChIP-seq peak caller for detection of megabase domains of enrichment.
Proper citation: Enriched Domain Detector (RRID:SCR_001693) Copy
http://www.bioconductor.org/packages/devel/bioc/html/CNVrd2.html
A software package that uses next-generation sequencing data to measure human gene copy number for multiple samples, indentify SNPs tagging copy number variants and detect copy number polymorphic genomic regions.
Proper citation: CNVrd2 (RRID:SCR_001723) Copy
An open source data warehouse system built for the integration and analysis of complex biological data that enables the creation of biological databases accessed by sophisticated web query tools. Parsers are provided for integrating data from many common biological data sources and formats, and there is a framework for adding data. InterMine includes a user-friendly web interface that works "out of the box" and can be easily customized for specific needs, as well as a powerful, scriptable web-service API to allow programmatic access to data.
Proper citation: InterMine (RRID:SCR_001772) Copy
http://www.bioconductor.org/packages/release/bioc/html/unifiedWMWqPCR.html
Software package that implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data.
Proper citation: unifiedWMWqPCR (RRID:SCR_001706) Copy
http://www.bioconductor.org/packages/release/bioc/html/RSVSim.html
A software package for the simulation of deletions, insertions, inversions, tandem duplications and translocations of various sizes in any genome available as FASTA-file or data package in R. SV breakpoints can be placed uniformly accross the whole genome, with a bias towards repeat regions and regions of high homology (for hg19) or at user-supplied coordinates.
Proper citation: RSVSim (RRID:SCR_001777) Copy
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