chanzuckerberg / cellxgene-census

Related projects ⓘ

Alternatives and complementary repositories for cellxgene-census

• Genentech / scimilarity
  A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to repr…
  ☆93Updated this week
• saezlab / decoupler-py
  Python package to perform enrichment analysis from omics data.
  ☆166Updated 2 months ago
• icbi-lab / infercnvpy
  Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
  ☆137Updated this week
• scverse / mudata
  Multimodal Data (.h5mu) implementation for Python
  ☆78Updated last month
• tanaylab / metacells
  Metacells - Single-cell RNA Sequencing Analysis
  ☆96Updated last month
• chanzuckerberg / single-cell-curation
  Code and documentation for the curation of cellxgene datasets
  ☆38Updated this week
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆93Updated last year
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆60Updated last year
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆141Updated last week
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆66Updated last year
• parashardhapola / scarf
  Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with mill…
  ☆98Updated 3 weeks ago
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆167Updated 2 months ago
• theislab / anndata2ri
  Convert between AnnData and SingleCellExperiment
  ☆129Updated this week
• Novartis / cellxgene-gateway
  Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cel…
  ☆56Updated 8 months ago
• zktuong / dandelion
  dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
  ☆109Updated this week
• livnatje / DIALOGUE
  DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…
  ☆105Updated 9 months ago
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆92Updated last week
• Teichlab / bbknn
  Batch balanced KNN
  ☆149Updated last year
• yelabucsf / scrna-parameter-estimation
  Direct estimation of mean and covariance from single cell RNA seq experiments
  ☆75Updated 5 months ago
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆107Updated 3 weeks ago
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆147Updated 4 months ago
• mousepixels / sanbomics
  bioinformatics plotting and tools
  ☆53Updated 5 months ago
• YosefLab / scib-metrics
  Accelerated, Python-only, single-cell integration benchmarking metrics
  ☆49Updated this week
• scverse / pytometry
  Flow & mass cytometry analytics.
  ☆42Updated this week
• scverse / pertpy
  Perturbation Analysis in the scverse ecosystem.
  ☆141Updated 3 weeks ago
• DendrouLab / panpipes
  Multi-modal single cell analysis pipelines
  ☆55Updated last week
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆48Updated 2 months ago
• changwn / scFEA
  single cell Flux Estimation Analysis (scFEA) Try the below web server!
  ☆102Updated last year
• dpeerlab / spectra
  Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
  ☆158Updated 3 months ago
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆111Updated 2 months ago