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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.
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.Platform provides free software and data services to international scientific community in order to foster scientific collaboration and facilitate scientific discovery process. Project adheres to open source philosophy that promotes collaboration and code reuse.
Proper citation: BioMart Project (RRID:SCR_002987) Copy
https://github.com/muxingu/rnamut
Software package for robust identification of somatic mutations in acute myeloid leukemia using RNA-sequencing. Detects clinically important somatic mutations from RNA-seq data on relatively small gene panel (typically less than 100 genes).
Proper citation: RNAmut (RRID:SCR_026965) Copy
https://github.com/williamslab/ped-sim
Software tool to simulate pedigree structures. Used for simulating relatives that can utilize either sex-specific or sex averaged genetic maps and also either model of crossover interference or traditional Poisson model for inter-crossover distances.
Proper citation: ped-sim (RRID:SCR_026957) Copy
https://github.com/wershofe/TWOMBLI
Software pipeline includes metrics of matrix alignment, length, branching, end points, gaps, fractal dimension, curvature, and the distribution of fibre thickness. FIJI macro for quantifying pattern in extracellular matrix.
Proper citation: TWOMBLI (RRID:SCR_027217) Copy
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BIANCA
Software tool for automated segmentation of white matter hyperintensities. Classifies image’s voxels based on their intensity and spatial features, and the output image represents the probability per voxel of being WMH. Flexible in terms of MRI modalities to use and offers different options for weighting spatial information, local spatial intensity averaging, and different options for choice of number and location of training points.
Proper citation: Brain Intensity AbNormality Classification Algorithm (RRID:SCR_024928) Copy
https://github.com/single-cell-genetics/vireo
Software tool for Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference.
Proper citation: Vireo (RRID:SCR_027463) Copy
https://cellmodelpassports.sanger.ac.uk/
Hub for clinical, genetic and functional datasets of preclinical cancer models.Provides details of cell model relationships, patient and clinical information, as well as access to associated genetic and functional datasets. Passports database contains curated details and standardized annotation for cell models, including cancer organoid cultures. Users can navigate database via tissue, cancer-type, genetic feature and data availability to select model. REST-API provides programmatic data access and exploration.
Proper citation: Cell Model Passports (RRID:SCR_027682) Copy
https://tritrypdb.org/tritrypdb/app
Free online resource for data mining of genomic and functional data from these kinetoplastid parasites and is part of the VEuPathDB Bioinformatics Resource Center. Integrates functional genome scale datasets (e.g. transcript expression, protein expression, genetic variation data) and information predicted from automated bioinformatics pipelines and from manual curation. Provides a user friendly web interface and a number of tools and functions for users to conduct in silico experiments to ask questions and generate hypotheses. Researchers can also contribute their expertise via the User Comments form and Apollo annotation platform, and utilize cloud-based workspace to analyze their own data.
Proper citation: TryTripDB (RRID:SCR_028607) Copy
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
