Alternatives and similar repositories for scarches

Users that are interested in scarches are comparing it to the libraries listed below

• theislab / scib
  Benchmarking analysis of data integration tools
  ☆399Updated 3 months ago
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆404Updated 11 months ago
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆230Updated last week
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆440Updated this week
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆254Updated 2 weeks ago
• scverse / decoupler
  Python package to perform enrichment analysis from omics data.
  ☆245Updated last week
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆395Updated 4 months ago
• theislab / cellrank
  CellRank: dynamics from multi-view single-cell data
  ☆411Updated last month
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆454Updated 6 months ago
• Genentech / scimilarity
  A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to repr…
  ☆230Updated 6 months ago
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆450Updated last year
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆408Updated 3 weeks ago
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆368Updated 5 months ago
• scverse / pertpy
  Single-cell perturbation analysis
  ☆225Updated this week
• brianhie / scanorama
  Panoramic stitching of single cell data
  ☆293Updated 5 months ago
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆481Updated last week
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆205Updated 2 months ago
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆424Updated 5 months ago
• aertslab / scenicplus
  SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…
  ☆240Updated 11 months ago
• openproblems-bio / openproblems
  Formalizing and benchmarking open problems in single-cell genomics
  ☆414Updated last month
• crazyhottommy / awesome_spatial_omics
  tools and notes for spatial omics
  ☆333Updated 10 months ago
• scverse / SnapATAC2
  Single-cell epigenomics analysis tools
  ☆301Updated this week
• scverse / muon
  muon is a multimodal omics Python framework
  ☆257Updated 3 weeks ago
• aristoteleo / dynamo-release
  Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …
  ☆477Updated last week
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆242Updated last week
• Teichlab / cellphonedb
  ☆359Updated 4 years ago
• crazyhottommy / TCR-BCR-seq-analysis
  T/B cell receptor sequencing analysis notes
  ☆271Updated last year
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆567Updated 6 months ago
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆303Updated 2 months ago
• dynverse / dynbenchmark
  Comparison of methods for trajectory inference on single-cell data 🥇
  ☆218Updated 2 years ago