Alternatives and similar repositories for SnapATAC2

Users that are interested in SnapATAC2 are comparing it to the libraries listed below

• aertslab / scenicplus
  SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…
  ☆233Updated 7 months ago
• cortes-ciriano-lab / SComatic
  A tool for detecting somatic variants in single cell data
  ☆212Updated last year
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆404Updated this week
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆155Updated 4 years ago
• pinellolab / scATAC-benchmarking
  Benchmarking computational single cell ATAC-seq methods
  ☆184Updated 4 years ago
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆210Updated last year
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆204Updated 6 months ago
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆291Updated 2 years ago
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆318Updated 2 years ago
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆439Updated last year
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆354Updated last month
• navinlabcode / copykat
  ☆251Updated last year
• mdozmorov / scATAC-seq_notes
  scATAC-seq data analysis tools and papers
  ☆120Updated 2 months ago
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆220Updated last week
• IanevskiAleksandr / sc-type
  ☆275Updated 10 months ago
• brianhie / scanorama
  Panoramic stitching of single cell data
  ☆289Updated 2 months ago
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆231Updated 2 months ago
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆378Updated 8 months ago
• STOmics / Stereopy
  A toolkit of spatial transcriptomic analysis.
  ☆258Updated this week
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆167Updated last year
• liulab-dfci / MAESTRO
  Single-cell Transcriptome and Regulome Analysis Pipeline
  ☆291Updated 2 years ago
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆237Updated this week
• aertslab / SCENICprotocol
  A scalable SCENIC workflow for single-cell gene regulatory network analysis
  ☆166Updated 2 years ago
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆231Updated 2 years ago
• liulab-dfci / TRUST4
  TCR and BCR assembly from RNA-seq data
  ☆324Updated 2 weeks ago
• tabdelaal / scRNAseq_Benchmark
  Bench-marking classification tools for scRNA-seq data
  ☆188Updated 3 years ago
• STOmics / SAW
  ☆170Updated last year
• JiekaiLab / scDIOR
  scDIOR: Single cell data IO softwaRe
  ☆146Updated 3 years ago
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆394Updated last month
• icbi-lab / infercnvpy
  Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
  ☆168Updated last week