Alternatives and similar repositories for scATAC-benchmarking

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

• tabdelaal / scRNAseq_Benchmark
  Bench-marking classification tools for scRNA-seq data
  ☆189Updated 3 years ago
• cortes-ciriano-lab / SComatic
  A tool for detecting somatic variants in single cell data
  ☆215Updated last year
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆168Updated last year
• mdozmorov / scATAC-seq_notes
  scATAC-seq data analysis tools and papers
  ☆124Updated 4 months ago
• aertslab / cisTopic
  cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
  ☆142Updated last year
• crazyhottommy / scATACseq-analysis-notes
  my notes for scATACseq analysis
  ☆131Updated last year
• czbiohub-sf / tabula-muris
  Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
  ☆194Updated 2 years ago
• aertslab / SCENICprotocol
  A scalable SCENIC workflow for single-cell gene regulatory network analysis
  ☆168Updated 2 years ago
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆320Updated 2 years ago
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆175Updated last year
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆153Updated last year
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆148Updated 11 months ago
• JiekaiLab / scDIOR
  scDIOR: Single cell data IO softwaRe
  ☆150Updated 3 years ago
• liulab-dfci / MAESTRO
  Single-cell Transcriptome and Regulome Analysis Pipeline
  ☆293Updated 2 years ago
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆234Updated 2 years ago
• Irrationone / cellassign
  Automated, probabilistic assignment of cell types in scRNA-seq data
  ☆209Updated 2 years ago
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆204Updated 3 weeks ago
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆158Updated 4 years ago
• changwn / scFEA
  single cell Flux Estimation Analysis (scFEA) Try the below web server!
  ☆135Updated 2 years ago
• broadinstitute / ABC-Enhancer-Gene-Prediction
  Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
  ☆239Updated 4 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…
  ☆239Updated 9 months ago
• wheaton5 / souporcell
  Clustering scRNAseq by genotypes
  ☆190Updated this week
• CahanLab / singleCellNet
  SingleCellNet: classify single cells across species and platforms
  ☆139Updated 2 years ago
• kundajelab / chrombpnet
  Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
  ☆186Updated 2 months ago
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆182Updated last year
• scverse / SnapATAC2
  Single-cell epigenomics analysis tools
  ☆298Updated this week
• jsxlei / SCALE
  Single-cell ATAC-seq analysis via Latent feature Extraction
  ☆103Updated 2 years ago
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆218Updated last year
• brianhie / scanorama
  Panoramic stitching of single cell data
  ☆292Updated 4 months ago
• interactivereport / cellxgene_VIP
  Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey a…
  ☆159Updated last week