Alternatives and similar repositories for scib-pipeline:

Users that are interested in scib-pipeline are comparing it to the libraries listed below

• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆66Updated this week
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆64Updated last month
• carmonalab / STACAS
  R package for semi-supervised single-cell data integration
  ☆81Updated 2 weeks ago
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆61Updated 11 months ago
• cellgeni / batchbench
  ☆46Updated 2 years ago
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆71Updated 3 weeks ago
• immunogenomics / symphony
  Efficient and precise single-cell reference atlas mapping with Symphony
  ☆103Updated 2 years ago
• vib-singlecell-nf / vsn-pipelines
  A repository of pipelines for single-cell data in Nextflow DSL2
  ☆75Updated last year
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆59Updated 10 months ago
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆100Updated 7 months ago
• Single-Cell-Genomics-Group-CNAG-CRG / Tumor-Immune-Cell-Atlas
  Code repository for the Tumor Immune Cell Atlas (TICA) project
  ☆61Updated 3 years ago
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆51Updated last month
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆99Updated last year
• ShobiStassen / VIA
  trajectory inference
  ☆96Updated 2 months ago
• immunogenomics / LISI
  Methods to compute Local Inverse Simpson's Index (LISI)
  ☆61Updated 3 years ago
• jackbibby1 / SCPA
  R package for pathway analysis in scRNA-seq data
  ☆72Updated 7 months ago
• KlugerLab / GeneTrajectory
  R implementation of GeneTrajectory
  ☆58Updated last year
• cailab-tamu / scTenifoldKnk
  R/MATLAB package to perform virtual knockout experiments on single-cell gene regulatory networks.
  ☆44Updated 3 months ago
• ncborcherding / utility
  Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR
  ☆84Updated 9 months ago
• buenrostrolab / FigR
  Functional Inference of Gene Regulation
  ☆41Updated 9 months ago
• crazyhottommy / scclusteval
  Single Cell Cluster Evaluation
  ☆94Updated 3 years ago
• saezlab / CollecTRI
  Gene regulatory network containing signed transcription factor-target gene interactions
  ☆73Updated 11 months ago
• rargelaguet / mouse_organogenesis_10x_multiome_publication
  Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""
  ☆40Updated 2 years ago
• theislab / AutoGeneS
  ☆59Updated 3 years ago
• GfellerLab / SuperCell
  Coarse-graining of large single-cell RNA-seq data into metacells
  ☆77Updated 7 months ago
• msraredon / NICHES
  Niche Interactions and Cellular Heterogeneity in Extracellular Signaling
  ☆52Updated 6 months ago
• icbi-lab / luca
  Single-cell Lung Cancer Atlas with 1.2M cells
  ☆61Updated 2 months ago
• RausellLab / CelliD
  Gene signature extraction and cell-identity recognition at individual cell level from single-cell RNA-seq.
  ☆93Updated last year
• JEFworks-Lab / MERINGUE
  characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…
  ☆72Updated 2 years ago
• carmonalab / scGate
  marker-based purification of cell types from single-cell RNA-seq datasets
  ☆106Updated 2 months ago