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
  ☆149Updated last year
• zktuong / dandelion
  dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
  ☆117Updated 3 weeks ago
• interactivereport / cellxgene_VIP
  Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey a…
  ☆155Updated this week
• CahanLab / singleCellNet
  SingleCellNet: classify single cells across species and platforms
  ☆138Updated last year
• yelabucsf / scrna-parameter-estimation
  Direct estimation of mean and covariance from single cell RNA seq experiments
  ☆112Updated 2 months ago
• YosefLab / popV
  ☆80Updated last week
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆75Updated 6 months ago
• Hoohm / CITE-seq-Count
  A tool that allows to get UMI counts from a single cell protein assay
  ☆82Updated 3 months ago
• timoast / sinto
  Tools for single-cell data processing
  ☆125Updated last year
• ncborcherding / utility
  Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR
  ☆90Updated last year
• pachterlab / kallistobustools
  kallisto | bustools workflow for pre-processing single-cell RNA-seq data
  ☆118Updated 3 years ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆165Updated last year
• saezlab / progeny
  R package for Pathway RespOnsive GENe activity inference
  ☆106Updated 2 years ago
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆105Updated last year
• BorchLab / Trex
  Using TCR and expression for sequence embedding
  ☆57Updated 6 months ago
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆170Updated 2 years ago
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆145Updated 7 months ago
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆103Updated 10 months ago
• immunogenomics / LISI
  Methods to compute Local Inverse Simpson's Index (LISI)
  ☆67Updated 3 years ago
• aertslab / cisTopic
  cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
  ☆140Updated last year
• calico / solo
  software to detect doublets
  ☆93Updated 7 months ago
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆164Updated 4 months ago
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆110Updated 9 months ago
• immunogenomics / symphony
  Efficient and precise single-cell reference atlas mapping with Symphony
  ☆105Updated 2 years ago
• rnakato / ShortCake
  A docker image for single-cell analysis
  ☆88Updated 6 months ago
• asncd / MIMOSCA
  A repository for the design and analysis of pooled single cell RNA-seq perturbation experiments.
  ☆92Updated 6 years ago
• mohuangx / SAVER
  Single-cell RNA-seq Gene Expression Recovery
  ☆111Updated 8 months ago
• YosefLab / Compass
  In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes
  ☆109Updated 6 months ago
• JEFworks-Lab / STdeconvolve
  Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
  ☆138Updated last month
• cellgeni / batchbench
  ☆47Updated 3 years ago