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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://bionotate.sourceforge.net/
An open source annotation tool for the distributed creation of a large corpus.
Proper citation: Bionotate (RRID:SCR_012098) Copy
http://sourceforge.net/projects/rdpframebot/
A frameshift correction and nearest neighbor classification tool for use with high-throughput amplicon sequencing. It uses a dynamic programming algorithm to align each query DNA sequence against a set of target protein sequences, produces frameshift-corrected protein and DNA sequences and an optimal global or local protein alignment. It also helps filter out non-target reads. The online version of FrameBot is available on http://fungene.cme.msu.edu/FunGenePipeline.
Proper citation: RDP FrameBot (RRID:SCR_013083) Copy
http://fmatoolbox.sourceforge.net
Matlab toolbox used to help analyze electrophysiological and behavioral data recorded from freely moving animals.
Proper citation: FMAToolbox (RRID:SCR_015533) Copy
http://sourceforge.net/projects/metavar/
Software package that enables detection of sequence variation between metagenomic samples.
Proper citation: MaryGold (RRID:SCR_000528) Copy
http://hanalyzer.sourceforge.net/
An open-source data integration system designed to assist biologists in explaining the results observed in genome-scale experiments as well as generating new hypotheses. It combines information extraction techniques, semantic data integration, and reasoning and facilitates network visualization. The Hanalyzer source code and binaries are available for download.
Proper citation: Hanalyzer (RRID:SCR_000923) Copy
https://www.ebi.ac.uk/chebi/beta/
Collection of chemical compounds and other small molecular entities that incorporates an ontological classification of chemical compounds of biological relevance, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.
Proper citation: CHEBI (RRID:SCR_002088) Copy
Software toolbox to facilitate quick and easy import, visualization and measurement for Event Related Potential (ERP) data. The toolbox can open and visualise ERP averaged data (Neuroscan, ascii formats), 2D/3D electrode coordinates and 3D cerebral tissue tesselations (meshes). All the features can be explored quickly and easily using the example data provided in the toolbox. The GUI interface is simple and intuitive.
Proper citation: Bioelectromagnetism Matlab Toolbox (RRID:SCR_006090) Copy
http://marsbar.sourceforge.net/
A toolbox for SPM which provides routines for region of interest analysis. Features include region of interest definition, combination of regions of interest with simple algebra, extraction of data for regions with and without SPM preprocessing (scaling, filtering), and statistical analyses of ROI data using the SPM statistics machinery.
Proper citation: MarsBaR region of interest toolbox for SPM (RRID:SCR_009605) Copy
http://genevenn.sourceforge.net/
A web application creating Venn diagrams from two or three gene lists.
Proper citation: GeneVenn (RRID:SCR_012117) Copy
Standard specification for the information required to report a genotyping experiment, covering: study and experiment design, subject information, genotyping procedure, and data analysis methods. The goal is to set a reporting standard for adoption by the research community to facilitate consistent data interpretation and independent validation/reproduction, and to serve as guidance for database design for storing genotyping experiment data. MIGen is being developed as a collaborative project involving international domain experts and is a registered project under MIBBI: Minimum Information for Biological and Biomedical Investigations.
Proper citation: MIGen (RRID:SCR_006959) Copy
http://samtools.sourceforge.net/
A generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms.
Proper citation: SAM format (RRID:SCR_012093) Copy
http://sourceforge.net/tracker/?group_id=76834&atid=835555
Open Biomedical Ontologies Tracker that allows users to browse the Plant Ontology (PO) term requests and view their status. Details include a summary, ID, status, Date opened, assignee, submitter, resolution and assigned priority. New requests are accepted from logged in users.
Proper citation: OBO Tracker: Plant Ontology (PO) TERM requests (RRID:SCR_006497) Copy
https://sourceforge.net/projects/bva-io/
Software package for interfacing the Brain Vision Analyser data files (load/save) for ongoing development of Matlab routines . This package is also compatible with the EEGLAB software, and may be uncompressed in the plugin folder of this software.
Proper citation: BVA import/export EEGLAB plugin (RRID:SCR_016333) Copy
http://bowtie-bio.sourceforge.net/recount/
RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, they combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward.
Proper citation: ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets (RRID:SCR_001774) Copy
Ratings or validation data are available for this resource
http://broadinstitute.github.io/picard/
Java toolset for working with next generation sequencing data in the BAM format.
Proper citation: Picard (RRID:SCR_006525) Copy
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