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    65 repositories

    • Genes2Genes

      Public
      Aligning gene expression trajectories of single-cell reference and query systems
      pythonscrna-seqdynamic-programmingbayesian-inferencesingle-cellhuman-cell-atlaspseudotime-trajectorytrajectory-alignmentminimum-message-length
      Jupyter Notebook
      •
      MIT License
      •5•42•1•2•Updated Oct 14, 2024Oct 14, 2024

    • snp2cell

      Public
      cell type specific, trait-associated gene regulation
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•6•0•0•Updated Oct 13, 2024Oct 13, 2024

    • vascular_atlas

      Public
      Repo with analysis code for the vascular atlas paper
      Jupyter Notebook
      •0•0•0•0•Updated Oct 11, 2024Oct 11, 2024

    • TissueTag

      Public
      Python package to interactively annotate histological images within a jupyter notebook
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •3•8•1•0•Updated Oct 11, 2024Oct 11, 2024

    • PanGIAtlas

      Public
      Integration of gut cell atlases
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 10, 2024Oct 10, 2024

    • thymus_spatial_atlas

      Public
      general repo that holds all analysis and figures for the thymus spatial atlas by Yayon, Kedlian, Boehme, Radtke and many more!
      genomicshumanimmunologysingle-cellthymusbioinformatics-toolspatial-transcriptomicscommon-coordinate-framwork
      Jupyter Notebook
      •0•5•0•0•Updated Oct 8, 2024Oct 8, 2024

    • G2G_notebooks

      Public
      Analysis notebooks for G2G MS
      Jupyter Notebook
      •0•5•0•0•Updated Oct 7, 2024Oct 7, 2024

    • bin2cell

      Public
      Join subcellular Visium HD bins into cells
      Jupyter Notebook
      •
      MIT License
      •1•47•5•0•Updated Oct 4, 2024Oct 4, 2024

    • sctk

      Public
      Python
      •
      GNU General Public License v3.0
      •4•21•1•1•Updated Sep 27, 2024Sep 27, 2024

    • cell2tcr

      Public
      Inference of TCR motifs
      Jupyter Notebook
      •
      Other
      •3•26•1•0•Updated Sep 24, 2024Sep 24, 2024

    • limbcellatlas

      Public
      This repository contains codes used for the human fetal limb cell atlas.
      Jupyter Notebook
      •2•12•0•0•Updated Sep 18, 2024Sep 18, 2024

    • gene2probe

      Public
      Pipeline for designing custom probes against human genes
      Jupyter Notebook
      •
      MIT License
      •3•11•1•1•Updated Sep 12, 2024Sep 12, 2024

    • scg_lib_structs

      Public
      Collections of library structure and sequence of popular single cell genomic methods
      HTML
      •88•424•2•0•Updated Sep 11, 2024Sep 11, 2024

    • celltypist_wiki

      Public
      Materials and scripts for building cell type encyclopedia table
      Python
      •3•15•0•0•Updated Sep 5, 2024Sep 5, 2024

    • bracer

      Public
      BraCeR - reconstruction of B cell receptor sequences from single-cell RNAseq data
      Python
      •
      Other
      •22•41•17•2•Updated Sep 4, 2024Sep 4, 2024

    • skeletal_dev_atlas

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Aug 28, 2024Aug 28, 2024

    • ALI_COVID19

      Public
      Repo with analysis code for the ALI_COVID19 paper
      Jupyter Notebook
      •1•4•1•0•Updated Aug 2, 2024Aug 2, 2024

    • drug2cell

      Public
      Gene group activity utility functions for Scanpy
      Jupyter Notebook
      •
      Other
      •3•54•6•0•Updated Jul 29, 2024Jul 29, 2024

    • GeneDistFinder

      Public
      Alignment tests for reference and query single cell datasets
      Jupyter Notebook
      •0•1•0•0•Updated Jul 1, 2024Jul 1, 2024

    • COVID-19_Challenge_Study

      Public
      HTML
      •
      MIT License
      •1•4•1•0•Updated Jun 24, 2024Jun 24, 2024

    • celltypist

      Public
      A tool for semi-automatic cell type classification
      pythonmachine-learningscrna-seqsingle-cellcell-type-classificationlabel-transfer
      Python
      •
      MIT License
      •45•288•25•1•Updated Jun 6, 2024Jun 6, 2024

    • COVID-19paed

      Public
      R
      •2•2•2•0•Updated May 22, 2024May 22, 2024

    • multi-view-atlas

      Public
      Multi-view objects for annotation and mapping to single-cell atlases
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•13•2•Updated May 21, 2024May 21, 2024

    • SpatialDE

      Public
      Test genes for Spatial Variation
      Jupyter Notebook
      •
      MIT License
      •54•143•14•5•Updated May 7, 2024May 7, 2024

    • lung-immune-cell-atlas

      Public
      This is a folder containing information of the human fetal lung leukocyte atlas
      HTML
      •1•1•0•0•Updated Apr 23, 2024Apr 23, 2024

    • SKM_ageing_atlas

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •5•7•1•0•Updated Apr 11, 2024Apr 11, 2024

    • treg-gut-niches

      Public
      Data pre-processing and analysis scripts for the article "Immune microniches shape intestinal Treg function"
      Jupyter Notebook
      •
      MIT License
      •2•3•0•0•Updated Apr 3, 2024Apr 3, 2024

    • cellhint

      Public
      A tool for semi-automatic cell type harmonization and integration
      pythonmachine-learningscrna-seqdata-integrationsingle-cellcell-type-harmonization
      Python
      •
      MIT License
      •11•90•6•0•Updated Jan 20, 2024Jan 20, 2024

    • tracer

      Public
      TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
      Python
      •
      Other
      •48•124•28•4•Updated Nov 28, 2023Nov 28, 2023

    • iss_patcher

      Public
      Approximate missing features from higher dimensionality data neighbours
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Nov 15, 2023Nov 15, 2023