Alternatives and similar repositories for conga

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

• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆148Updated last year
• zktuong / dandelion
  dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
  ☆115Updated this week
• ncborcherding / utility
  Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR
  ☆88Updated 11 months ago
• yelabucsf / scrna-parameter-estimation
  Direct estimation of mean and covariance from single cell RNA seq experiments
  ☆110Updated last month
• timoast / sinto
  Tools for single-cell data processing
  ☆125Updated last year
• YosefLab / popV
  ☆78Updated 2 weeks ago
• BorchLab / Trex
  Using TCR and expression for sequence embedding
  ☆56Updated 4 months ago
• GregorySchwartz / too-many-cells
  Cluster single cells and analyze cell clade relationships with colorful visualizations.
  ☆112Updated 7 months ago
• rnakato / ShortCake
  A docker image for single-cell analysis
  ☆88Updated 4 months ago
• JEFworks-Lab / STdeconvolve
  Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
  ☆131Updated last week
• saezlab / progeny
  R package for Pathway RespOnsive GENe activity inference
  ☆106Updated 2 years ago
• PierreBSC / Viral-Track
  ☆57Updated 4 years ago
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆73Updated 5 months ago
• changwn / scFEA
  single cell Flux Estimation Analysis (scFEA) Try the below web server!
  ☆124Updated last year
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆162Updated 2 months ago
• carmonalab / STACAS
  R package for semi-supervised single-cell data integration
  ☆82Updated last month
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆71Updated 4 months ago
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆165Updated 2 years ago
• immunoengineer / gliph
  Grouping of Lymphocyte Interactions by Paratope Hotspots
  ☆93Updated 4 years ago
• Single-Cell-Genomics-Group-CNAG-CRG / Tumor-Immune-Cell-Atlas
  Code repository for the Tumor Immune Cell Atlas (TICA) project
  ☆62Updated 3 years ago
• carmonalab / scGate
  marker-based purification of cell types from single-cell RNA-seq datasets
  ☆112Updated last month
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆102Updated 9 months ago
• bioinfo-ibms-pumc / SCSA
  SCSA: cell type annotation for single-cell RNA-seq data
  ☆90Updated 2 years ago
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆110Updated 8 months ago
• noamteyssier / adpbulk
  pseudobulking on an AnnData object
  ☆32Updated 3 months ago
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆101Updated last year
• tanaylab / metacells
  Metacells - Single-cell RNA Sequencing Analysis
  ☆107Updated 8 months ago
• Teichlab / cellhint
  A tool for semi-automatic cell type harmonization and integration
  ☆107Updated 3 months ago
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆144Updated 6 months ago
• JiekaiLab / scDIOR
  scDIOR: Single cell data IO softwaRe
  ☆141Updated 3 years ago