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https://singlecell.broadinstitute.org/single_cell

Portal specializes in visualizing and disseminating single cell data. Allows you to use natural language and faceted search to discover other scientists’ research and share your own findings. Each study includes information on cell types, singular or multiple gene expression, and spatial transcriptomics. Interactive visualizations allow to explore cell clusters and search for related genes.

Proper citation: Single Cell Portal (RRID:SCR_014816) Copy   

•   Source: SciCrunch Registry
  

https://broadinstitute.github.io/warp/docs/Pipelines/Smart-seq2_Single_Nucleus_Multi_Sample_Pipeline/README

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.

Proper citation: Smart-seq2 Multi-Sample Pipeline (RRID:SCR_018920) Copy   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

https://cumulus.readthedocs.io/en/stable

Software tool as cloud based single cell genomics and spatial transcriptomics data analysis framework that is scalable to massive amounts of data and able to process variety of data types. Consists of cloud analysis workflow, Python analysis package and visualization application. Supports analysis of single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire and spatial transcriptomics data.

Proper citation: Cumulus (RRID:SCR_021644) Copy   

•   Source: SciCrunch Registry
  

https://terra.bio

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   

•   Source: SciCrunch Registry
  

https://pegasus.readthedocs.io/en/stable

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.

Proper citation: Pegasus (RRID:SCR_021645) Copy   

•   Source: SciCrunch Registry
  

https://cirrocumulus.readthedocs.io/en/stable/

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.

Proper citation: Cirrocumulus (RRID:SCR_021646) Copy   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry