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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.
https://app.terra.bio/#workspaces/pathogen-genomic-surveillance/COVID-19
Broad Terra cloud workspace for best practices with COVID-19 genomics data. Raw COVID-19 sequencing data from NCBI Sequence Read Archive. Workflows for genome assembly, quality control, metagenomic classification, and aggregate statistics.
Proper citation: Broad Terra cloud commons for pathogen surveillance (RRID:SCR_018278) Copy
https://broadinstitute.github.io/warp/docs/Pipelines/Single_Cell_ATAC_Seq_Pipeline/README
Pipeline developed in collaboration with Bing Ren lab and supports processing of BICCN single-cell/nucleus ATAC-seq datasets. Pipeline uses python module SnapTools to align and process paired reads in form of FASTQ files. Produces hdf5-structured Snap file that includes cell-by-bin count matrix. Final outputs also include GA4GH compliant aligned BAM and QC metrics.
Proper citation: scATAC Pipeline (RRID:SCR_018919) Copy
https://broadinstitute.github.io/warp/docs/Pipelines/CEMBA_MethylC_Seq_Pipeline/README
Software pipeline that supports processing of multiplexed single nuclei bisulfite sequencing data to detect methylated bases. Alignment and methylated base calling pipeline that trims adaptors, attaches cell barcodes, aligns reads to genome, filters reads based on quality and creates both VCF and ALLC file with Emethylation site coverage.
Proper citation: CEMBA MethylC Seq Pipeline (RRID:SCR_021219) Copy
https://proteomics.broadinstitute.org/
Software tool for high throughput processing of MS/MS and MS spectra to provide protein and peptide identifications and relative quantitation.
Proper citation: Spectrum Mill (RRID:SCR_022171) Copy
https://singlecell.broadinstitute.org/single_cell?scpbr=biccn-anatomy-and-morphology-project
Joint effort with Brain Architecture Portal and Single Cell Portal to visually combine anatomic and molecular brain data in. Users can search for neuroscience data using natural language and faceted search, and then this portal retrieves molecular data housed in the Single Cell Portal and anatomical data in the Brain Architecture Portal. Each study includes information on cell types, gene expression, related genes, and spatial transcriptomics. You can also download a study’s data to explore further and build on your science.
Proper citation: BICCN Anatomy and Morphology Project (RRID:SCR_021647) Copy
https://www.broadinstitute.org/imaging
Core to help users turn images into answers by offering assistance and training with open source image analysis tools, creating custom image analysis workflows, and creating custom software for image analysis when needed.
Proper citation: Broad Institute Imaging Platform Core Facility (RRID:SCR_024653) Copy
https://portals.broadinstitute.org/gppx/crispick/public
Web tool for prediction of sgRNAs. Helps to select optimal guide RNA for gene of interest. Support for designing guide libraries. CRISPick ranks and picks candidate CRISPRko sgRNA sequences for targets provided, while attempting to maximize on-target activity and minimizing off-target activity.
Proper citation: CRISPick (RRID:SCR_025148) Copy
https://broadinstitute.github.io/warp/docs/Pipelines/SlideTags_Pipeline/README
Software pipeline as open-source, cloud-optimized workflow for processing spatial transcriptomics data. It supports data derived from spatially barcoded sequencing technologies, including Slide-tags-based single-molecule profiling. The pipeline processes raw sequencing data into spatially resolved gene expression matrices, ensuring accurate alignment, spatial positioning, and quantification.
Proper citation: SlideTags.wdl (RRID:SCR_027567) Copy
https://broadinstitute.github.io/warp/docs/Pipelines/BuildIndices_Pipeline/README
Software workflow is an open-source, cloud-optimized pipeline developed in collaboration with the BRAIN Initiative Cell Census Network (BICCN) and the BRAIN Initiative Cell Atlas Network (BICAN).
Proper citation: BuildIndices (RRID:SCR_027630) Copy
https://gatk.broadinstitute.org/hc/en-us/articles/360042913231-HaplotypeCaller
Software tool for identifying single nucleotide polymorphisms (SNPs) and insertion/deletion (indels) variants, offering high accuracy via local de-novo assembly of reads. It works by identifying "active regions" with potential variation, reassembling those reads, and calculating genotype likelihoods, making it superior for complex variant detection.
Proper citation: GATK HaplotypeCaller (RRID:SCR_028440) Copy
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
