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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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BICCN Resource Report Resource Website 100+ mentions |
BICCN (RRID:SCR_015820) | BICCN | consortium, data or information resource, organization portal, portal | Consortium for the cell census in the brain. Integrated network of data generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate brains. | cell census, neuroscience, brain, brain initiative cell census network, whole mouse brain, |
uses: QuickNII uses: HistoloZee uses: CellLocator uses: Semi-Manual Alignment to Reference Templates uses: LoomPy uses: Cytosplore Viewer uses: Allen Human Brain Atlas: BrainSpan (Atlas of the Developing Brain) uses: Blue Brain Cell Atlas uses: Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas uses: Hippocampome.org uses: Neuron Phenotype Ontology uses: Brain Image Library uses: Distributed Archives for Neurophysiology Data Integration uses: NeuroMorpho.Org uses: Azimuth uses: Brain Observatory Storage Service and Database (BossDB) uses: Optimus Pipeline uses: scATAC Pipeline uses: Smart-seq2 Single Nucleus Multi Sample Pipeline uses: CEMBA MethylC Seq Pipeline uses: Brain Architecture Project uses: Single Cell Portal uses: MorphoHub uses: Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas uses: Mouse Connectome Project uses: Allen Mouse Brain Reference Atlas uses: Allen Mouse Brain Common Coordinate Framework uses: Allen Human Reference Atlas, 3D, 2020 uses: NeMO Analytics uses: ANTS - Advanced Normalization ToolS uses: CloudReg uses: Brainome portal uses: CATlas uses: MetaNeighbor uses: Cell Annotation Platform uses: cellxgene uses: Neuroglancer uses: Vaa3D uses: QuickNII and VisuAlign uses: Hi5App uses: CloudVolume uses: neuroXiv uses: Brain Data Standards Ontology uses: Pittsburgh Supercomputing Center uses: Molecular Biosensor and Imaging Center uses: Generative Diffeomorphic Mapping uses: NIH NeuroBioBank uses: NeMOarchive lists: ccf_streamlines is related to: Mouse Connectome Project is related to: BarensLab Mini-Atlas is related to: Cumulus is related to: Pegasus is related to: Cirrocumulus is related to: Gene functional conservation across cell types and species is related to: BRAIN Initiative Cell Atlas Network is related to: ATAC Pipeline is related to: Slide-seq Pipeline is related to: Brain Knowledge Platform has parent organization: Allen Institute has parent organization: Allen Institute for Brain Science provides: mBrainAligner provides: BICCN Cell Registry provides: Cell Type Knowledge Explorer provides: Epiviz has organization facet: BICCN Anatomy and Morphology Project has organization facet: Cell Type Knowledge Explorer has organization facet: mBrainAligner has organization facet: Terra has organization facet: Allen Brain Cell Atlas has organization facet: Multiome Pipeline has organization facet: Allen Software Development Kit has organization facet: BICCN Imaging and analysis Techniques to Construct Cell Census Atlas of Human Brain has organization facet: Allen Brain Map BICCN Data Catalog has organization facet: snm3C Pipeline has organization facet: Paired-Tag Pipeline has organization facet: BuildIndices has organization facet: MapMyCells has organization facet: Smart-seq2 Multi-Sample Pipeline |
NIMH U19 MH114821; NIMH U19 MH114830; NIMH U19 MH114831 |
PMID:37390046 | Restricted | SCR_017266 | SCR_015820 | SciCrunch Registry | BICCN 2.0, BRAIN Initiative Cell Census Network, BRAIN Initiative Cell Census Network (BICCN) | 2026-10-24 12:47:31 | 234 | |||||
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BICCN Imaging and analysis Techniques to Construct Cell Census Atlas of Human Brain Resource Report Resource Website 1+ mentions |
BICCN Imaging and analysis Techniques to Construct Cell Census Atlas of Human Brain (RRID:SCR_023000) | consortium, data or information resource, organization portal, portal, project portal | Project to develop and utilize imaging infrastructure to create human brain cell census and instantiate it in coordinate system that will enable immediate impact of all in vivo MRI studies of human brain. Consortium for creating cellular census of human cerebral cortex. | BRAIN Initiative Cell Census Network, imaging and analysis, construct cell census of human brain, creating cellular census, human cerebral cortex | is organization facet of: BICCN | DOI:10.1101/2021.10.20.464979 | Free, Freely available | SCR_023000 | SciCrunch Registry | 2026-10-24 12:49:24 | 2 | |||||||||
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MapMyCells Resource Report Resource Website 50+ mentions |
MapMyCells (RRID:SCR_024672) | algorithm resource, software application, software resource, web application | MapMyCells maps single cell and spatial transcriptomics data sets to massive, high-quality, and high-resolution cell type taxonomies. It enables speeding up the creation of brain reference atlases by facilitating the integration of datasets from the scientific community with a shared reference. MapMyCells is part of the growing Brain Knowledge Platform. Its key advantage is scale: researchers can provide up to 327 million cell-gene pairs from their own data, a huge leap forward for working with whole-brain datasets. Allen Institute and its collaborators continue to add new reference taxonomies and algorithms to MapMyCells. | mapping of single cell and spatial transcriptomics data, mapping to whole mouse brain taxonomy, mapping to human brain taxonomy, correlation mapping, hierarchical mapping, label transfer |
has parent organization: Allen Institute is organization facet of: BICCN |
NIMH U24MH130918; Paul G. Allen Foundation |
Free, Freely available | https://knowledge.brain-map.org/mapmycells/process/, https://portal.brain-map.org/atlases-and-data/bkp/mapmycells/mapmycells-use-case-single-cell-genomics | SCR_024672 | SciCrunch Registry | Map My Cells, Allen MapMyCells | 2026-10-24 12:49:44 | 60 | |||||||
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Smart-seq2 Multi-Sample Pipeline Resource Report Resource Website 1+ mentions |
Smart-seq2 Multi-Sample Pipeline (RRID:SCR_018920) | data processing software, software application, software resource, software toolkit | Software pipeline for single-nucleus RNAseq data generated by Smart-seq2 assays. Developed in collaboration with the BRAIN Initiative Cell Census Network (BICCN) to process single-nucleus RNAseq (snRNAseq) data generated by Smart-seq2 assays. Used to simultaneously process multiple libraries of single nuclei Smart-seq2 and Smart-seq4 data. For each library (nucleus), the pipeline trims paired FASTQ files, aligns trimmed reads to the genome, counts intronic and exonic reads, and calculates quality control metrics. Counts and metrics for all libraries are combined into merged Loom formatted count matrix. | snRNAseq data, Smart-seq2 assays, single nucleus, multi sample, WARP repository |
is related to: Human Cell Atlas has parent organization: University of California at San Diego; California; USA has parent organization: Allen Institute has parent organization: Broad Institute is organization facet of: Terra is organization facet of: BICCN |
Free, Available for download, Freely available | SCR_021312 | https://app.terra.bio/#workspaces/warp-pipelines/Smart-seq2_Single_Nucleus_Muti-Sample | https://github.com/broadinstitute/warp/tree/master/pipelines/skylab/smartseq2_multisample | SCR_018920 | SciCrunch Registry | Multi-snSS2, Smart-seq2 Single Nucleus Multi-Sample (Multi-snSS2) | 2026-10-24 12:50:05 | 4 | ||||||
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Cell Type Knowledge Explorer Resource Report Resource Website 1+ mentions |
Cell Type Knowledge Explorer (RRID:SCR_022793) | software application, software resource | Software application to examine multimodal data from thousands of cells across 3 mammalian species. | Allen Brain Map, Cell Type Taxonomies, examine multimodal data, cells across mammalian species |
is related to: Common Cell Type Nomenclature is provided by: BICCN is organization facet of: BICCN |
Free, Freely available | SCR_022793 | SciCrunch Registry | Allen Brain Map Cell Type Knowledge Explorer | 2026-10-24 12:51:54 | 4 | |||||||||
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mBrainAligner Resource Report Resource Website 1+ mentions |
mBrainAligner (RRID:SCR_022791) | software resource, software toolkit | Software package provides cross modality image registration pipeline to support whole brain mapping projects. Contains three modules: (1) image preprocessing and global registration, (2) Coherent Landmark Mapping (CLM) based automatic registration, and (3) optional semi-automatic refinement. | cross modality image registration, whole brain mapping, image registration |
is provided by: BICCN is organization facet of: BICCN |
Fundamental Research Funds ; NSFC-Guangdong Joint Fund ; NSFC ; Southeast University ; University Synergy Innovation Program of Anhui Province |
PMID:34887551 | Free, Available for download, Freely available | SCR_022791 | SciCrunch Registry | 2026-10-24 12:51:54 | 3 | ||||||||
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snm3C Pipeline Resource Report Resource Website 1+ mentions |
snm3C Pipeline (RRID:SCR_025041) | snM3C | data processing software, software application, software resource | Software open-source, cloud-optimized computational workflow for processing single-nucleus methylome and chromatin contact (snm3C) sequencing data. The workflow is designed to demultiplex and align raw sequencing reads, call chromatin contacts, and generate summary metrics. | data processing, single-nucleus methylome data, single-cell data, chromatin contact data, single-cell methylome and chromatin contact sequencing data, |
is organization facet of: BICCN is organization facet of: BRAIN Initiative Cell Atlas Network |
Free, Freely available | https://github.com/broadinstitute/warp/tree/master/pipelines/skylab/snM3C | SCR_025041 | SciCrunch Registry | , Single Nucleus Methly-Seq and Chromatin Capture, single-nucleus Methylome and Chromatin Contact, Single Nucleus Methly-Seq and Chromatin Capture (snM3C) | 2026-10-24 12:53:29 | 2 | |||||||
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Pegasus Resource Report Resource Website 50+ mentions |
Pegasus (RRID:SCR_021645) | data analysis software, data processing software, software application, software resource, software toolkit | Software package for massive single cell data processing. Enables analysis of million scale single cell RNA-seq data and is functionally comparable to Seurat and SCANPY. Command line tool, Python package and base for Cloud based analysis workflows. Supports variety of analysis tasks, such as cell and gene level quality control, highly variable gene selection, dimension reduction, kNN graph building, data integration, clustering, differential expression analysis and putative cell type annotation. | massive single cell data processing, million scale single cell RNA-seq data, gene level quality control, highly variable gene selection, dimension reduction |
is used by: Cumulus is listed by: Terra is related to: BICCN has parent organization: Broad Institute |
Free, Available for download, Freely available | https://app.terra.bio/#workspaces/kco-tech/Cumulus/notebooks | SCR_021645 | SciCrunch Registry | Pegasus for Single Cell Analysis, Pegasus tool for massive single cell data processing | 2026-10-24 12:48:57 | 53 | ||||||||
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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 | 2026-10-24 12:49:43 | 0 | ||||||||
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Cirrocumulus Resource Report Resource Website |
Cirrocumulus (RRID:SCR_021646) | software resource, web application | Web interactive visualization tool for large scale single cell genomics data.Interactive web application for exploring million scale single cell datasets. Can be hosted on Google App Engine application for collaborative use or can be run in standalone mode on personal computer. Consists of client side component implemented in JavaScript and server component implemented in Python. Client uses React to manage state and WebGL to visualize variables on 2D/3D embeddings in performant manner. Server component consists of functions to manage datasets, slice variables from dataset stored in PARQUET, Zarr or H5AD formats. | large scale single cell genomics data, exploring million scale single cell datasets, visualize variables, manage datasets |
is used by: Cumulus is related to: BICCN has parent organization: Broad Institute |
Free, Available for download, Freely available | https://github.com/klarman-cell-observatory/cirrocumulus/blob/413898061f1c48350071d200f043cc43104dd04f/docs/index.rst | SCR_021646 | SciCrunch Registry | 2026-10-24 12:49:28 | 0 | |||||||||
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Allen Institute for Brain Science Resource Report Resource Website 500+ mentions |
Allen Institute for Brain Science (RRID:SCR_006491) | atlas, data or information resource, portal, topical portal | Seattle based independent, nonprofit medical research organization dedicated to accelerating the understanding of how human brain works. Provides free data and tools to researchers and educators and variety of unique online public resources for exploring the nervous system. Integrates gene expression data and neuroanatomy, along with data search and viewing tools, these resources are openly accessible via the Allen Brain Atlas data portal. Provides Allen Mouse Brain, Allen Spinal Cord Atlas, Allen Developing Mouse Brain Atlas, Allen Human Brain Atlas,Allen Mouse Brain Connectivity Atlas, Allen Cell Type Database, The Ivy Glioblastoma Atlas Project (Ivy GAP), The BrainSpan Atlas of the Developing Human Brain. | Institute, embryonic, gene, expression, data, neuroscience, medical, research, neuroanatomy |
is listed by: Brain Architecture Project is related to: VisiGene Image Browser is related to: Recombinase (cre) Activity is related to: Cytosplore Viewer is related to: Mozak is related to: Microns Explorer is related to: CellLocator is related to: Seattle Alzheimer Disease Brain Cell Atlas is related to: Atlasplot is related to: Atlas Ontology Model is related to: Allen Brain Atlas-Driven Visualizations is related to: Brain heatmap is related to: Brainmapr is related to: ABAEnrichment is related to: Hippo-ATESC is related to: AllenDigger is related to: Cocoframer is related to: Process Genes List is related to: AIDAhisto is related to: MeshGen is related to: PET-CT mouse brain toolbox is related to: Multimodal Environment for Neuroimaging and Genomic Analysis is related to: goi2roimapping is related to: Spatiotemporal pattern Exploration of Brain is related to: Allen Mouse Brain ImageLoader is related to: ARA Tools is related to: allenCCF is related to: CutNII is related to: Genomic-and-High-Dimensional-Data is related to: Mouse_abi_tool is related to: Abagen is related to: VoxHunt is related to: ABI-expression-data-generator is related to: GCEA_FalsePositives is related to: Atlas Splitter is related to: ABAnnotate is related to: JuGEx is related to: Alleninf is related to: Atlas Alignment Meter is related to: Pinpoint is related to: Atlas Densities is related to: Atlas Direction Vectors is related to: SageBionetworks Portals is related to: brain-mapping is related to: BrainModules is related to: BrainRegionMarkers is related to: AP-histology is related to: Brainreg-segment is related to: Segmenting Brain Regions is related to: DeepSlice is related to: Cell Type Analysis Toolbox is related to: BrainGlobe Atlas API is related to: QUINT is related to: BRain area Input Output is related to: Brainreg is related to: MorphAPI is related to: Aligning Big Brains and Atlases is related to: Allen Brain Atlas Tools is related to: Brain Gene Expression Analysis toolbox is related to: Blue Brain Cell Atlas is related to: 3DBar is related to: Brainrender is related to: QuickNII is related to: Brain Architecture Project is related to: NeuroInfo is related to: Azimuth is related to: Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas is related to: Integrated Brain Gene Expression is related to: MIRACL is related to: Linked Neuron Data is related to: BrainStars is related to: MouseLight Project is related to: Distributed Archives for Neurophysiology Data Integration is related to: Open Source Brain is related to: VisuAlign is related to: NS-Forest is related to: SHARCQ is related to: ModelDB is related to: Gene Expression Omnibus (GEO) is related to: NCBI database of Genotypes and Phenotypes (dbGap) is related to: CellFinder is related to: Nutil - Neuroimaging utilities is related to: NeuroMorpho.Org is related to: Semi-Manual Alignment to Reference Templates is related to: MeshView is related to: Single Cell Portal is related to: Brain Image Library is related to: UCSC Cell Browser is related to: National Institute on Aging Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS) is related to: cellxgene is related to: Atlas Ontology Model has parent organization: Allen Institute is parent organization of: Allen Mouse Brain Reference Atlas is parent organization of: Allen Institute for Brain Science Sleep Study is parent organization of: Allen Developing Mouse Brain Atlas is parent organization of: Allen Institute for Brain Science Transgenic Mouse Study is parent organization of: Allen Institute Neurowiki is parent organization of: Ivy Glioblastoma Atlas Project is parent organization of: Allen Brain Atlas API is parent organization of: Allen Human Brain Atlas is parent organization of: Allen Mouse Spinal Cord Atlas is parent organization of: Allen Institute Mouse Diversity Study is parent organization of: Allen Human Brain Atlas: BrainSpan (Atlas of the Developing Brain) is parent organization of: Allen Mouse Brain Connectivity Atlas is parent organization of: ABA Adult Mouse Brain Ontology is parent organization of: NIH Blueprint NHP Atlas is parent organization of: Aging Dementia and Traumatic Brain Injury Study is parent organization of: ACQ4 is parent organization of: CellTax vignette is parent organization of: Allen Brain Atlas is parent organization of: BRAIN Cell Data Center is parent organization of: BICCN Cell Registry is parent organization of: ABA Mouse Brain: Atlas is parent organization of: Allen Institute Mouse Whole Cortex and Hippocampus SMART-seq is parent organization of: Allen Mouse Brain Common Coordinate Framework is parent organization of: Allen Mouse Reference Atlas Ontology is parent organization of: BICCN is parent organization of: BRAIN Initiative Cell Atlas Network is parent organization of: Brain Knowledge Platform |
nif-0000-00146 | SCR_006491 | SciCrunch Registry | The Allen Institute for Brain Science, Allen Mouse Brain | 2026-10-24 12:49:07 | 803 | |||||||||
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Allen Software Development Kit Resource Report Resource Website 10+ mentions |
Allen Software Development Kit (RRID:SCR_018183) | AllenSDK | data analysis software, data processing software, software application, software resource | Software tool as code for processing and analyzing data in Allen Brain Atlas. Source code for reading and processing Allen Brain Atlas data. Allen SDK focuses on Allen Brain Observatory, Cell Types Database, and Mouse Brain Connectivity Atlas. | Data analysis, data processing, Allen Brain Atlas, data, brain |
is related to: Allen Brain Atlas is organization facet of: BICCN |
Free, Freely available | SCR_018192 | https://allensdk.readthedocs.io/en/latest/ | SCR_018183 | SciCrunch Registry | 2026-10-24 12:47:54 | 35 | |||||||
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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 | 2026-10-24 12:48:57 | 90 | ||||||||
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Multiome Pipeline Resource Report Resource Website 1+ mentions |
Multiome Pipeline (RRID:SCR_024217) | 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 3' single-cell and single-nucleus gene expression (GEX) and chromatin accessibility (ATAC) data generated with the 10x Genomics Multiome assay. | data processing, 10x Genomics Multiome assay data, single cell data, single nucleus gene expression data, single cell chromatin accessibility data, |
is organization facet of: BRAIN Initiative Cell Atlas Network is organization facet of: BICCN is organization facet of: SCORCH |
Free, Available for download, Freely available | https://github.com/broadinstitute/warp/tree/master/pipelines/skylab/multiome | SCR_024217 | SciCrunch Registry | , Multiome GEX and scATAC Pipeline, Multiome Pipeline | 2026-10-24 12:49:39 | 1 | ||||||||
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Allen Brain Cell Atlas Resource Report Resource Website 50+ mentions |
Allen Brain Cell Atlas (RRID:SCR_024440) | atlas, data or information resource, expression atlas | Provides platform for visualizing multimodal single cell data across mammalian brain and aims to empower researchers to explore and analyze multiple whole brain datasets simultaneously. Allen Institute and its collaborators continue to add new modalities, species, and insights to the ABC Atlas. Atlas as part of Brain Knowledge Platform will enable neuroscience community to identify more cell types in brain; Investigate spatial location of cell types; Investigate gene expression and co-expression patterns in cell types; Refine boundaries and knowledge of brain regions defined by gene expression. | visualizing multimodal single cell data across mammalian brain, explore and analyze multiple whole brain datasets, identify cell types in brain, brain regions defined by gene expression, |
has parent organization: Allen Institute works with: UNRAVEL is organization facet of: BICCN |
NIMH MH130919 | Free, Freely available | SCR_024440 | SciCrunch Registry | Allen Brain Cell (ABC) Atlas, The Allen Brain Cell Atlas, ABC Atlas | 2026-10-24 12:49:41 | 50 | ||||||||
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Allen Brain Map BICCN Data Catalog Resource Report Resource Website 1+ mentions |
Allen Brain Map BICCN Data Catalog (RRID:SCR_022815) | catalog, data or information resource, database | BRAIN Initiative Cell Census Network data catalog. Provides access to all major data sets of the BICCN with descriptions. | BRAIN Initiative, Cell Census Network data catalog, BICCN |
is organization facet of: BICCN is organization facet of: BRAIN Initiative Cell Atlas Network |
Free, Freely available | SCR_022815 | SciCrunch Registry | Allen Brain Map BRAIN Initiative Cell Census Network Data Catalog, BRAIN Initiative Cell Census Network Data Catalog, BICCN Data Inventory Catalog | 2026-10-24 12:49:22 | 2 | |||||||||
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BICCN Anatomy and Morphology Project Resource Report Resource Website |
BICCN Anatomy and Morphology Project (RRID:SCR_021647) | data or information resource, portal, project portal, service resource | 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. | Visually combine brain data, anatomic brain data, molecular brain data, brain data |
is related to: Single Cell Portal is related to: Brain Architecture Project has parent organization: Broad Institute is organization facet of: BICCN |
Free, Available for download, Freely available | SCR_021647 | SciCrunch Registry | SCP - A&M, Anatomy and Morphology Project | 2026-10-24 12:50:07 | 0 | |||||||||
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Paired-Tag Pipeline Resource Report Resource Website 1+ mentions |
Paired-Tag Pipeline (RRID:SCR_025042) | data processing software, software application, software resource | Software open-source, cloud-optimized pipeline developed in collaboration with the BRAIN Initiative Cell Census Network (BICCN) and the BRAIN Initiative Cell Atlas Network (BICAN). It supports the processing of 3' single-nucleus histone modification data (generated with the paired-tag protocol]) and 10x gene expression (GEX) data generated with the 10x Chromium Multiome assay. | data processing, 10x Genomics Multiome assay data, single-cell data, single nucleus gene expression data, single-nucleus histone modification data, |
is organization facet of: BICCN is organization facet of: BRAIN Initiative Cell Atlas Network |
Free, Freely available | https://github.com/broadinstitute/warp/tree/master/pipelines/skylab/paired_tag | SCR_025042 | SciCrunch Registry | Paired-Tag Pipeline, paired_tag, Paired-Tag | 2026-10-24 12:53:29 | 1 | ||||||||
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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 | 2026-10-24 12:54:26 | 1 | ||||||||||
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Allen Institute Resource Report Resource Website 50+ mentions |
Allen Institute (RRID:SCR_005435) | institution | Non profit bioscience research organization in Seattle, Washington dedicated to accelerating research globally and sharing that data within the science community. Allen Institute for Brain Science, Allen Institute for Cell Science, Allen Institute for Immunology, and The Paul G. Allen Frontiers Group are four divisions of this Institute with commitment to open science model within its research institutes. | organization, brain, health, disease, research, human, mouse, dataset, cell, immunology, data, map |
is related to: scrattch taxonomy is related to: UNRAVEL is parent organization of: Allen Institute for Brain Science is parent organization of: Allen Brain Atlas is parent organization of: Allen Human Reference Atlas, 3D, 2020 is parent organization of: Scrattch.Hicat is parent organization of: COVID-19 Open Research Dataset is parent organization of: CORD-19 Explorer is parent organization of: CellLocator is parent organization of: Allen Mouse Brain Common Coordinate Framework is parent organization of: Common Cell Type Nomenclature is parent organization of: Smart-seq2 Single Nucleus Multi Sample Pipeline is parent organization of: BICCN is parent organization of: Allen Cell and Structure Segmenter is parent organization of: Allen Brain Cell Atlas is parent organization of: BRAIN Initiative Cell Atlas Network is parent organization of: MapMyCells is parent organization of: Genetic Tools Atlas is parent organization of: Annotation Comparison Explorer is parent organization of: BioFile Finder is parent organization of: HMBA Adult Human Brain Atlas is parent organization of: Harmonized Ontology of Mammalian Brain Anatomy (HOMBA) is parent organization of: HMBA Adult Rhesus Macaque Brain Atlas is parent organization of: HMBA Adult Cynomolgus Macaque Brain Atlas is parent organization of: Deep SSR is parent organization of: HMBA Adult Marmoset Atlas is parent organization of: Macaque D99 Atlas is parent organization of: SCALPEL is parent organization of: Smart-seq2 Multi-Sample Pipeline |
nlx_144532, Wikidata:Q24191489, grid.507729.e | https://ror.org/03cpe7c52 | SCR_005435 | SciCrunch Registry | The Allen Institute | 2026-10-24 12:45:26 | 61 |
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