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    40 repositories

    • MOCHA

      Public template
      R package for single-cell Open Chromatin Identification & Downstream Analysis
      R
      •
      GNU General Public License v3.0
      •0•2•13•3•Updated Jan 7, 2025Jan 7, 2025

    • IHA-Figure

      Public
      Jupyter Notebook
      •
      Other
      •0•0•0•0•Updated Jan 6, 2025Jan 6, 2025

    • aifi-healthy-pbmc-reference

      Public
      Assembly and Annotation of the Human Immune Health Atlas
      Jupyter Notebook
      •
      Other
      •1•2•0•0•Updated Jan 4, 2025Jan 4, 2025

    • ArchR

      Public
      ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
      R
      •
      MIT License
      •140•1•0•1•Updated Dec 10, 2024Dec 10, 2024

    • SPARROW

      Public
      Jupyter Notebook
      •2•0•0•0•Updated Dec 3, 2024Dec 3, 2024

    • batchreporter

      Public
      HTML
      •
      Other
      •0•0•0•0•Updated Nov 15, 2024Nov 15, 2024

    • H5weaver

      Public
      R functions for reading, rearranging, and writing HDF5 files with 10x-compatible structure
      rrmarkdownhdf5transcriptomics
      R
      •
      Other
      •0•0•2•0•Updated Nov 13, 2024Nov 13, 2024

    • cell-hashing-pipeline

      Public
      Processing of scRNA-seq cell hashing data
      dockerwrapperrpipelinetranscriptomicscell-hashing
      R
      •
      Other
      •0•0•0•0•Updated Oct 29, 2024Oct 29, 2024

    • ALTRA-manuscript

      Public
      repository for codes to generate figures for ALTRA manuscript
      Jupyter Notebook
      •0•1•0•0•Updated Oct 29, 2024Oct 29, 2024

    • CryoSCAPE

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Sep 5, 2024Sep 5, 2024

    • sound-life-scrna-analysis

      Public
      Annotation and Analysis of 13M cells from the Sound Life Cohort
      Jupyter Notebook
      •
      Other
      •0•0•0•0•Updated Aug 20, 2024Aug 20, 2024

    • ATAComb

      Public
      Functions for QC and analysis of ATAC-seq data
      ratac-seq
      R
      •
      Other
      •0•0•0•0•Updated Aug 17, 2024Aug 17, 2024

    • SeuratLabeler

      Public
      R package for bundling Seurat Label Transfer objects, markdowns, and functions
      rlabelingtranscriptomicsseurat
      R
      •
      Other
      •0•0•0•1•Updated Aug 9, 2024Aug 9, 2024

    • HTOparser

      Public
      R functions for parsing cell hashing data
      rrmarkdowntranscriptomicscell-hashing
      R
      •
      Other
      •0•0•0•0•Updated Aug 9, 2024Aug 9, 2024

    • tenx-rnaseq-pipeline

      Public
      Pipeline scripts for processing 10x Genomics scRNA-seq data
      metadatawrapperrtranscriptomicstenxgenomics
      R
      •
      Other
      •0•0•0•0•Updated Aug 9, 2024Aug 9, 2024

    • epiAneufinder

      Public
      R package to detect breakpoints and assign somies to scATAC-seq data
      HTML
      •
      GNU General Public License v3.0
      •9•0•0•0•Updated Aug 2, 2024Aug 2, 2024

    • certpro-workflow-demos

      Public
      Demonstration notebooks for HISE Certificate of Reproducibility workflows
      Jupyter Notebook
      •
      Other
      •0•0•0•0•Updated Jul 11, 2024Jul 11, 2024

    • MOCHA_Manuscript

      Public
      Repository to include Figure Generations for MOCHA
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 21, 2024Jun 21, 2024

    • repro-vrd-tea-seq-common

      Public
      Common files used for analysis of VRd TEA-seq data
      0•0•0•0•Updated Apr 29, 2024Apr 29, 2024

    • repro-vrd-tea-seq

      Public
      Reproducible analysis of T cell VRd treatment TEA-seq
      Jupyter Notebook
      •
      Other
      •0•1•0•0•Updated Apr 29, 2024Apr 29, 2024

    • serverless-registry-proxy

      Public
      Serverless reverse proxy for exposing container registries (GCR, Docker Hub, Artifact Registry etc) on custom domains.
      Go
      •
      Apache License 2.0
      •59•0•0•1•Updated Mar 13, 2024Mar 13, 2024

    • multicelltypist

      Public
      A tool for semi-automatic cell type classification
      Python
      •
      MIT License
      •46•0•0•0•Updated Mar 8, 2024Mar 8, 2024

    • fake_hisepy

      Public
      placeholder project for HISE Python SDK
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 11, 2024Feb 11, 2024

    • scrubleta

      Public
      A fork of Scrublet that uses Actual cell-hashing-derived doublets
      Jupyter Notebook
      •
      MIT License
      •73•0•0•0•Updated Jan 27, 2024Jan 27, 2024

    • repro-vrd-tea-seq-deg-app

      Public
      Jupyter Notebook
      •
      Other
      •0•0•0•0•Updated Jan 5, 2024Jan 5, 2024

    • gke-shift-left-cost

      Public
      Fork of google's costing lib
      Go
      •
      Apache License 2.0
      •10•0•0•0•Updated Dec 14, 2023Dec 14, 2023

    • DietArchR

      Public
      A function for cleaning up an ArchR project
      R
      •
      Apache License 2.0
      •0•0•0•0•Updated Sep 13, 2023Sep 13, 2023

    • Aging_Tcell_TEA-seq

      Public
      Tri-modal single cell profiling reveals a novel pediatric CD8aa T cell subset and broad age-related molecular reprogramming across the T cell compartment.
      Jupyter Notebook
      •1•2•1•0•Updated Sep 1, 2023Sep 1, 2023

    • PALMO

      Public
      Identify Intra-, Inter-donor variations in bulk or single cell longitudinal dataset
      R
      •
      Other
      •4•18•4•2•Updated Jul 31, 2023Jul 31, 2023

    • conda-pack

      Public
      AIFI Fork of Package conda environments for redistribution
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •94•0•0•0•Updated Jul 19, 2023Jul 19, 2023