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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://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
https://bitbucket.org/nsegata/graphlan/wiki/Home
Software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. Used for concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation as a high-resolution microbial tree of life with taxonomic annotations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: GraPhlAn (RRID:SCR_016130) Copy
Software as set of commandline tools with GUI frontend that performs data reconstruction and fiber tracking on diffusion MR images. It does preparation work for TrackVis. Software Package for diffusion imaging data processing and tractography.
Proper citation: Diffusion Toolkit (RRID:SCR_017345) Copy
Database of Drosophila genetic and genomic information with information about stock collections and fly genetic tools. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. Additionally, FlyBase accepts data submissions. FlyBase can be searched for genes, alleles, aberrations and other genetic objects, phenotypes, sequences, stocks, images and movies, controlled terms, and Drosophila researchers using the tools available from the "Tools" drop-down menu in the Navigation bar.
Proper citation: FlyBase (RRID:SCR_006549) Copy
http://compbio.mit.edu/cummeRbund/index.html
Software R package used for simplifying and analyzing Cufflink RNA-Seq output. This program takes various output files from a cuffdiff run and creates a SQLite database of the results that will describe the appropriate relationships between the genes, transcripts, transcription start sites and CDS regions.
Proper citation: CummeRbund (RRID:SCR_014568) Copy
http://genetics.bwh.harvard.edu/pph2/
Software tool which predicts possible impact of amino acid substitution on structure and function of human protein using straightforward physical and comparative considerations. PolyPhen-2 is new development of PolyPhen tool for annotating coding nonsynonymous SNPs.
Proper citation: PolyPhen: Polymorphism Phenotyping (RRID:SCR_013189) Copy
Web based integrative platform for transcriptional regulation studies.
Proper citation: Cistrome (RRID:SCR_000242) Copy
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