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http://kimlab.io/brain-map/atlas/
Website to visualize and share anatomical labels. Franklin and Paxinos (FP) based anatomical labels in Allen Common Coordinate Framework (CCF). Cell type specific transgenic mice and MRI atlas were used to adjust and further segment labels. New segmentations were created in dorsal striatum using cortico-striatal connectivity data. Anatomical labels were digitized based on Allen ontology, and web-interface was created for easy visualization. These labels provide resource to isolate and identify mouse brain anatomical structures. Open source data sharing will facilitate further refinement of anatomical labels and integration of data interpretation within single anatomical platform.
Proper citation: Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas (RRID:SCR_019267) Copy
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.
Proper citation: Allen Institute for Brain Science (RRID:SCR_006491) 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://github.com/BICCN/cell-locator/
Open source and multi-platform pinning software tool to facilitate mapping samples into common 3D spaces. Desktop application based on 3D Slicer that displays Allen Institute for Brain Science CCF or MNI atlas, color segmented by structure of brain, and allows user to create planar polyline annotation to facilitate mapping samples into corresponding atlas.
Proper citation: CellLocator (RRID:SCR_019264) Copy
https://broadinstitute.github.io/warp/docs/Pipelines/PairedTag_Pipeline/README
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.
Proper citation: Paired-Tag Pipeline (RRID:SCR_025042) Copy
https://broadinstitute.github.io/warp/docs/Pipelines/Multiome_Pipeline/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 3' single-cell and single-nucleus gene expression (GEX) and chromatin accessibility (ATAC) data generated with the 10x Genomics Multiome assay.
Proper citation: Multiome Pipeline (RRID:SCR_024217) 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/snm3C/README
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.
Proper citation: snm3C Pipeline (RRID:SCR_025041) 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
https://chanzuckerberg.com/science/programs-resources/single-cell-biology/cellxgene/
Software tool as interactive explorer for single cell transcriptomics datasets. Used to explore and visualize high dimensional single cell datasets in interactive way. Can visualize gene expression at level of entire dataset or particular subset of cells to help identify cell types, which can in turn help identify diseases. Enables plotting gene expression level against another gene to compare how these different genes are expressed across dataset. Open source cell visualization tool integrates with tools like SciPy and Jupyter.
Proper citation: cellxgene (RRID:SCR_021059) Copy
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