Alternatives and similar repositories for reCAT

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

• wzthu / esATAC
  Bioconductor package esATAC: an Easy-to-use Systematic pipeline for ATAC-seq data analysis
  ☆23Updated 3 years ago
• dbrg77 / plate_scATAC-seq
  A rapid and robust plate-based single cell ATAC-seq (scATAC-seq) method
  ☆42Updated 4 years ago
• shendurelab / mouse-atac
  Repo for website and other code for mouse sci-ATAC-seq project
  ☆28Updated 5 years ago
• shendurelab / single-cell-ko-screens
  Repository containing all code for secondary analysis in the manuscript "On the design of CRISPR-based single cell molecular screens", Hi…
  ☆26Updated 3 years ago
• ggjlab / scHCL
  ☆47Updated 5 years ago
• saezlab / footprints
  Analysis code for "Perturbation-response genes reveal signaling footprints in cancer gene expression"
  ☆20Updated 7 years ago
• cole-trapnell-lab / monocle2-rge-paper
  Scripts needed to generate the figures for the Monocle 2 paper (Qiu et al, 2017)
  ☆29Updated 5 years ago
• sridnona / cb_sniffer
  mutation(barcode) caller for 10x single cell data
  ☆45Updated 5 years ago
• statgen / popscle
  A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and au…
  ☆57Updated 4 years ago
• nghiavtr / SCmut
  ☆34Updated 6 years ago
• McGranahanLab / TcellExTRECT
  ☆47Updated 9 months ago
• lanagarmire / SSrGE
  ☆34Updated 6 years ago
• wenweixiong / MARVEL
  ☆51Updated last year
• jdekanter / CHETAH
  scRNA-seq cell type identification
  ☆43Updated 6 years ago
• huangyh09 / brie
  BRIE: Bayesian Regression for Isoform Estimate in Single Cells
  ☆42Updated last year
• VCCRI / Sierra
  Discover differential transcript usage from polyA-captured single cell RNA-seq data
  ☆51Updated 2 years ago
• prabhakarlab / RCAv2
  R package for robust clustering of single cell RNA sequencing data
  ☆35Updated last year
• wbaopaul / scATAC-pro
  A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
  ☆79Updated 7 months ago
• single-cell-genetics / cardelino
  Clone identification from single-cell data
  ☆61Updated 2 years ago
• CFeregrino / scWGCNA
  scWGCNA
  ☆61Updated 2 years ago
• csoneson / rna_velocity_quant
  Evaluation of the effect of quantification choices on RNA velocity estimates
  ☆27Updated 3 years ago
• satijalab / azimuth-references
  ☆25Updated 5 months ago
• caleblareau / gchromVAR
  Cell type specific enrichments using finemapped variants and quantitative epigenetic data
  ☆45Updated 2 years ago
• cole-trapnell-lab / cicero-release
  ☆58Updated last year
• bvieth / scRNA-seq-pipelines
  Compendium to "A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines"
  ☆55Updated 4 years ago
• lambdamoses / novoSpaRc
  Reconstruction of spatial context of gene expression with optimal transport
  ☆11Updated 6 years ago
• satijalab / Integration2019
  ☆17Updated 6 years ago
• caleblareau / bap
  Bead-based single-cell atac processing
  ☆33Updated 3 years ago
• r3fang / snATAC
  <<------ Use SnapATAC!!
  ☆26Updated 6 years ago
• kharchenkolab / cacoa
  Single-cell Case Control Analysis
  ☆52Updated this week