Alternatives and similar repositories for scATAC-benchmarking:

Users that are interested in scATAC-benchmarking are comparing it to the libraries listed below

• cortes-ciriano-lab / SComatic
  A tool for detecting somatic variants in single cell data
  ☆193Updated 6 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…
  ☆209Updated 2 months ago
• aertslab / cisTopic
  cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
  ☆137Updated 11 months ago
• aertslab / SCENICprotocol
  A scalable SCENIC workflow for single-cell gene regulatory network analysis
  ☆151Updated 2 years ago
• tabdelaal / scRNAseq_Benchmark
  Bench-marking classification tools for scRNA-seq data
  ☆185Updated 2 years ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆161Updated last year
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆142Updated last year
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆142Updated 3 months ago
• LewisLabUCSD / Ligand-Receptor-Pairs
  Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
  ☆129Updated 2 years ago
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆156Updated 8 months ago
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆197Updated 11 months ago
• mdozmorov / scATAC-seq_notes
  scATAC-seq data analysis tools and papers
  ☆104Updated last year
• basilkhuder / Seurat-to-RNA-Velocity
  A guide to using a Seurat object in conjunction with RNA Velocity
  ☆137Updated 3 years ago
• JiekaiLab / scDIOR
  scDIOR: Single cell data IO softwaRe
  ☆140Updated 3 years ago
• czbiohub-sf / tabula-muris
  Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
  ☆190Updated 2 years ago
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆314Updated last year
• crazyhottommy / scATACseq-analysis-notes
  my notes for scATACseq analysis
  ☆122Updated 11 months ago
• interactivereport / cellxgene_VIP
  Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey a…
  ☆144Updated last week
• zktuong / dandelion
  dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
  ☆112Updated this week
• kaizhang / SnapATAC2
  Single-cell epigenomics analysis tools
  ☆247Updated last week
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆143Updated 4 years ago
• dviraran / xCell
  Cell types enrichment analysis
  ☆194Updated 9 months ago
• wheaton5 / souporcell
  Clustering scRNAseq by genotypes
  ☆175Updated 4 months ago
• yelabucsf / scrna-parameter-estimation
  Direct estimation of mean and covariance from single cell RNA seq experiments
  ☆100Updated last month
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆161Updated 10 months ago
• kundajelab / chrombpnet
  Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
  ☆147Updated last month
• changwn / scFEA
  single cell Flux Estimation Analysis (scFEA) Try the below web server!
  ☆118Updated last year
• liulab-dfci / MAESTRO
  Single-cell Transcriptome and Regulome Analysis Pipeline
  ☆278Updated 2 years ago
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆266Updated 2 years ago
• sunduanchen / Scissor
  Scissor package
  ☆211Updated 10 months ago