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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BuildIndices Resource Report Resource Website 1+ mentions |
BuildIndices (RRID:SCR_027630) | software resource, software toolkit | 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). | check inputs, modify reference files, create STAR index, calculate chromosome sizes, |
has parent organization: Broad Institute is organization facet of: BICCN is organization facet of: BRAIN Initiative Cell Atlas Network |
Free, Available for download, Freely available | SCR_027630 | SciCrunch Registry | 2026-10-31 12:24:36 | 1 | ||||||||||
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Cellarium Resource Report Resource Website 1+ mentions |
Cellarium (RRID:SCR_025438) | software resource | Software platform to annotate cell types. | machine learning open source software, infrastructure, annotate cell types, |
is used by: BRAIN Initiative Cell Atlas Network has parent organization: Broad Institute |
NIH | Free, Freely available | https://github.com/10XGenomics/cell-annotation-service-client | SCR_025438 | SciCrunch Registry | 2026-10-31 12:23:34 | 1 | ||||||||
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ATAC Pipeline Resource Report Resource Website |
ATAC Pipeline (RRID:SCR_024656) | data analysis software, data processing software, software application, software resource | 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. | data processing, 10x Genomics Multiome ATAC-seq assay data, single-cell data, single-cell chromatin accessibility assay data |
is related to: BICCN is related to: SCORCH has parent organization: Broad Institute is organization facet of: BRAIN Initiative Cell Atlas Network |
Free, Available for download, Freely available | https://github.com/broadinstitute/warp/blob/master/pipelines/skylab/multiome/atac.wdl | SCR_024656 | SciCrunch Registry | ATAC, atac, atac pipeline | 2026-10-31 12:19:02 | 0 | ||||||||
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Terra Resource Report Resource Website 50+ mentions |
Terra (RRID:SCR_021648) | data or information resource, portal | 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. | Biomedical researcher platform, access data, run analysis tools, collaborate, access controlled datasets, cloud repositories |
is used by: BRAIN Initiative Cell Atlas Network lists: Cumulus lists: Pegasus lists: Broad Terra cloud commons for pathogen surveillance has parent organization: Broad Institute has organization facet: scATAC Pipeline has organization facet: Smart-seq2 Single Nucleus Multi Sample Pipeline has organization facet: CEMBA MethylC Seq Pipeline has organization facet: Smart-seq2 Multi-Sample Pipeline is organization facet of: BICCN is organization facet of: Single Cell Portal |
NIMH U24 MH130968 | Free, Freely available | SCR_021648 | SciCrunch Registry | Terra Cloud Native Platform, BCDC cloud computing environment | 2026-10-31 12:18:13 | 90 | ||||||||
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SlideTags.wdl Resource Report Resource Website 1+ mentions |
SlideTags.wdl (RRID:SCR_027567) | data analysis software, data processing software, software application, software resource | 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. | Spatial transcriptomics data, single-cell data, Slide-tags technology data, spatial barcode processing pipeline, spatial gene expression quantification, reads alignment, genome, spatial positioning, human tissue data analysis, 5 alpha-SR2 |
has parent organization: Broad Institute is organization facet of: BRAIN Initiative Cell Atlas Network |
Free, Available for download, Freely available | SCR_027567 | SciCrunch Registry | Slide-tags | 2026-10-31 12:24:29 | 2 |
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