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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.
Software platform to annotate cell types.
Proper citation: Cellarium (RRID:SCR_025438) Copy
https://broadinstitute.github.io/warp/docs/Pipelines/SlideSeq_Pipeline/README/
Software pipeline developed in collaboration with BRAIN Initiative Cell Census Network and BRAIN Initiative Cell Atlas Network. Supports processing of spatial transcriptomic data generated with Slide-seq commercialized as Curio Seeker assay.
Proper citation: Slide-seq Pipeline (RRID:SCR_023379) Copy
Open ecosystem of data repositories hosted by various partner organizations, who work together to ensure that their data can be federated across participating platforms. Open source platform for biomedical researchers to access data, run analysis tools, and collaborate. Terra powers important scientific projects including AnVIL, BioData Catalyst, Human Cell Atlas, BICCN, and many others. Easily access both open and access-controlled datasets hosted in cloud repositories. Explore, analyze, and visualize data using Jupyter Notebooks, RStudio, RShinyApps, and Galaxy.
Proper citation: Terra (RRID:SCR_021648) Copy
Web application that allows users to view and explore brain cell data. Composed of three, interlinked tabs. GeneExp allows users to plot expression of one or two genes in Slide-seq atlas. SingleCell allows users to plot gene expression in snRNA-seq atlas. CellSpatial shows spatial localization of snRNA-seq cell types in Slide-seq dataset. Used to visualize, interact with, and download data.
Proper citation: Brain Cell Data Viewer (RRID:SCR_023321) Copy
https://broadinstitute.github.io/warp/docs/Pipelines/ATAC/README
Software open-source, cloud-optimized pipeline developed in collaboration with members of the BRAIN Initiative (BICCN and BICAN Sequencing Working Group) and SCORCH. It supports the processing of 10x single-nucleus data generated with 10x Multiome ATAC-seq (Assay for Transposase-Accessible Chromatin), a technique used in molecular biology to assess genome-wide chromatin accessibility.
Proper citation: ATAC Pipeline (RRID:SCR_024656) 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
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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