human-cell-atlas

There are 5 repositories under human-cell-atlas topic.

• satijalab / seurat

  R toolkit for single cell genomics

  human-cell-atlassingle-cell-rna-seqsingle-cell-genomicscran
  Language:R 2113

• scverse / scvi-tools

  Deep probabilistic analysis of single-cell and spatial omics data

  scrna-seqvariational-bayesvariational-autoencodercite-seqsingle-cell-genomicssingle-cell-rna-seqdeep-generative-modelhuman-cell-atlasscversedeep-learning
  Language:Python 1120

• theislab / scarches

  Reference mapping for single-cell genomics

  single-celldeep-learningrna-seq-analysisdata-integrationbatch-correctionmultimodal-deep-learningmultiomicssingle-cell-genomicsscrna-seqhuman-cell-atlas
  Language:Jupyter Notebook 309

• spacetx / starfish

  starfish: unified pipelines for image-based transcriptomics

  transcriptomicsimaginghuman-cell-atlaspython
  Language:Python 220

• iSEE / iSEE

  R/shiny interface for interactive visualization of data in SummarizedExperiment objects

  visualizationguidimension-reductionfeature-extractionclusteringtranscriptomicssingle-cellgene-expressionshinyhuman-cell-atlashacktoberfest
  Language:R 218

• hemberg-lab / SC3

  A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments

  bioconductor-packagehuman-cell-atlassingle-cell-rna-seq
  Language:R 115

• hemberg-lab / scmap

  A tool for unsupervised projection of single cell RNA-seq data

  single-cell-rna-seqprojection-mappingrbioconductor-packagehuman-cell-atlas
  Language:R 87

• LuyiTian / sc_mixology

  This contains the dataset for comparing scRNA-seq analysis methods

  benchmarkingdatasethuman-cell-atlas
  Language:HTML 87

• stemangiola / CuratedAtlasQueryR

  Tidy R query API for the harmonised and curated CELLxGENE single-cell atlas.

  single-celltidyversedatabasehuman-cell-atlasduckdbhdf5singlecellexperiment
  Language:R 73

• theislab / cpa

  The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.

  single-cell-genomicssingle-cell-rna-seqscrna-seqhuman-cell-atlas
  Language:Python 73

• drisso / SingleCellExperiment

  Clone of the Bioconductor repository for the SingleCellExperiment package, see https://bioconductor.org/packages/devel/bioc/html/SingleCellExperiment.html for the official development version.

  human-cell-atlasbioconductorsingle-cell-rna-seqbioconductor-package
  Language:R 61

• broadinstitute / single_cell_portal_core

  Rails/Docker application for the Broad Institute's single cell RNA-seq data portal

  single-cell-genomicsrna-seq-analysishuman-cell-atlas
  Language:Ruby 59

• MarioniLab / DropletUtils

  Clone of the Bioconductor repository for the DropletUtils package.

  bioconductor-packagehuman-cell-atlassingle-cell-rna-seq
  Language:R 53
• CoGAPS

  FertigLab / CoGAPS

  Bayesian MCMC matrix factorization algorithm

  bayesian-inferencebioinformaticshuman-cell-atlasmachine-learningnon-negative-matrix-factorizationsingle-cell-rna-seq
  Language:C++ 52

• broadinstitute / single_cell_portal

  Tutorials, workflows, and convenience scripts for Single Cell Portal

  single-cell-genomicsrna-seq-analysishuman-cell-atlas
  Language:HTML 44

• MarioniLab / scran

  Clone of the Bioconductor repository for the scran package.

  human-cell-atlassingle-cell-rna-seqbioconductor-package
  Language:R 37

• quon-titative-biology / scAlign

  A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches

  human-cell-atlassingle-cellscrna-seqscrna-seq-analysissingle-cell-genomics
  Language:R 33

• tallulandrews / M3Drop

  human-cell-atlassingle-cellrna-seqsingle-cell-rna-seq
  Language:R 28

• morris-lab / BiddyetalWorkflow

  This repository contains our CellTag workflow, as deployed in our 2018 Biddy et al., Nature paper.

  human-cell-atlas
  Language:R 27

• hemberg-lab / D3E

  Discrete Distributional Differential Expression

  differential-expressionsingle-cell-rna-seqhuman-cell-atlas
  Language:Python 22

• showteeth / scfetch

  Access and Format Single-cell RNA-seq Datasets from Public Resources

  geosingle-cell-rna-seqzenodopanglaodbucsc-cell-browserbamfastqformat-conversion-toolhuman-cell-atlassracellxgene
  Language:R 22
• batchelor

  LTLA / batchelor

  Clone of the Bioconductor repository for the batchelor package.

  human-cell-atlassingle-cell-rna-seqbatch-correctionbioconductor-package
  Language:R 18

• MarioniLab / EmptyDrops2017

  Code for the empty droplet and cell detection project from the HCA Hackathon.

  human-cell-atlasmanuscriptsimulationssingle-cell-rna-seq
  Language:TeX 18

• morris-lab / CellTagR

  This repository contains the CellTag data analysis R package to support clone calling and lineage reconstruction.

  human-cell-atlas
  Language:R 18

• lasersonlab / ndarray.scala

  N-dimensional arrays, with Zarr and HDF5 integrations

  ndarrayscalahdf5netcdfzarrhuman-cell-atlas
  Language:Scala 14

• lasersonlab / single-cell-experiments

  Experiments to run single cell analyses efficiently at scale using Zarr, anndata, Scanpy, and Apache Spark

  single-cellbioinformaticsgenomicshuman-cell-atlas
  Language:Jupyter Notebook 13

• drisso / mbkmeans

  K-means clustering for large single-cell datasets

  clusteringhuman-cell-atlas
  Language:R 9

• lasersonlab / zappy

  Distributed processing with NumPy and Zarr

  beamdaskdistributed-computinghuman-cell-atlasnumpypywrensparkzarr
  Language:Python 9

• Bioconductor / HCABrowser

  Browse the Human Cell Atlas data portal

  human-cell-atlasbioconductor
  Language:R 8

• LTLA / MoeDCPLogo

  Making the DCP logo moe-r.

  human-cell-atlas
  8

• federicomarini / HCAData

  Access data from the Human Cell Atlas project, directly via R/Bioconductor

  rna-seqexperimenthubdatasethuman-cell-atlasbioconductorsingle-cell-rna-seq
  Language:R 7

• chanzuckerberg / ontology-ui

  Ontology visualizer

  ontologysingle-cellsingle-cell-rna-seqhuman-cell-atlas
  Language:TypeScript 6

• iSEE / iSEE_custom

  Examples of custom panels for the iSEE package

  human-cell-atlassingle-cellvisualizationtranscriptomicsgene-expressionshinyisee
  Language:R 6
• BiocNeighbors

  LTLA / BiocNeighbors

  Clone of the Bioconductor repository for the BiocNeighbors package.

  human-cell-atlasbioconductor-packagenearest-neighbor-search
  Language:C++ 6
• BiocSingular

  LTLA / BiocSingular

  Clone of the Bioconductor repository for the BiocSingular package.

  human-cell-atlassingular-value-decompositionbioconductor-package
  Language:R 6

• morris-lab / PreviousCloneHunter

  This repository contains our CellTag CloneHunter R package for clone-calling.

  human-cell-atlas
  Language:R 6