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
  ☆340Updated 2 months ago
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆349Updated last week
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆318Updated 8 months ago
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆343Updated 2 months ago
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆416Updated last year
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆200Updated last month
• Genentech / scimilarity
  A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to repr…
  ☆181Updated last month
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆207Updated last week
• saezlab / decoupler-py
  Python package to perform enrichment analysis from omics data.
  ☆184Updated last month
• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆268Updated last month
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆227Updated this week
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆314Updated last year
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆315Updated last month
• brianhie / scanorama
  Panoramic stitching of single cell data
  ☆278Updated 11 months ago
• theislab / cellrank
  CellRank: dynamics from multi-view single-cell data
  ☆375Updated last month
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆433Updated last month
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆407Updated 2 months ago
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆197Updated last month
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆347Updated 9 months ago
• Teichlab / cellphonedb
  ☆353Updated 3 years ago
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆226Updated last year
• MarioniLab / miloR
  R package implementation of Milo for testing for differential abundance in KNN graphs
  ☆362Updated 4 months ago
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆526Updated last month
• scverse / muon
  muon is a multimodal omics Python framework
  ☆230Updated last month
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆328Updated this week
• dynverse / dynbenchmark
  Comparison of methods for trajectory inference on single-cell data 🥇
  ☆206Updated last year
• pinellolab / scATAC-benchmarking
  Benchmarking computational single cell ATAC-seq methods
  ☆182Updated 4 years 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…
  ☆212Updated 2 months ago
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆196Updated 7 months ago
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆372Updated 2 months ago