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
  ☆193Updated 3 years ago
• aertslab / cisTopic
  cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
  ☆143Updated last year
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆169Updated 2 years ago
• czbiohub-sf / tabula-muris
  Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
  ☆197Updated 2 years ago
• aertslab / SCENICprotocol
  A scalable SCENIC workflow for single-cell gene regulatory network analysis
  ☆171Updated 3 years ago
• cortes-ciriano-lab / SComatic
  A tool for detecting somatic variants in single cell data
  ☆215Updated last year
• crazyhottommy / scATACseq-analysis-notes
  my notes for scATACseq analysis
  ☆133Updated last year
• mdozmorov / scATAC-seq_notes
  scATAC-seq data analysis tools and papers
  ☆128Updated 7 months ago
• JiekaiLab / scDIOR
  scDIOR: Single cell data IO softwaRe
  ☆153Updated 3 years ago
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆206Updated 3 months ago
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆155Updated last year
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆182Updated last year
• liulab-dfci / MAESTRO
  Single-cell Transcriptome and Regulome Analysis Pipeline
  ☆300Updated 2 years ago
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆237Updated 2 years ago
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆162Updated 5 years 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…
  ☆245Updated 3 weeks ago
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆322Updated 2 years ago
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆149Updated last year
• brianhie / scanorama
  Panoramic stitching of single cell data
  ☆295Updated 6 months ago
• Irrationone / cellassign
  Automated, probabilistic assignment of cell types in scRNA-seq data
  ☆210Updated 3 years ago
• broadinstitute / ABC-Enhancer-Gene-Prediction
  Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
  ☆246Updated last week
• velocyto-team / velocyto.py
  RNA velocity estimation in Python
  ☆175Updated 4 months ago
• CahanLab / singleCellNet
  SingleCellNet: classify single cells across species and platforms
  ☆140Updated 2 years ago
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆179Updated 10 months ago
• dviraran / xCell
  Cell types enrichment analysis
  ☆207Updated last year
• LewisLabUCSD / Ligand-Receptor-Pairs
  Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
  ☆149Updated 3 years ago
• interactivereport / cellxgene_VIP
  Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey a…
  ☆161Updated 2 weeks ago
• phbradley / conga
  Clonotype Neighbor Graph Analysis
  ☆95Updated 5 months ago
• basilkhuder / Seurat-to-RNA-Velocity
  A guide to using a Seurat object in conjunction with RNA Velocity
  ☆140Updated 4 years ago
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆185Updated last year