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
• shendurelab / mouse-atac
  Repo for website and other code for mouse sci-ATAC-seq project
  ☆28Updated 5 years ago
• dbrg77 / plate_scATAC-seq
  A rapid and robust plate-based single cell ATAC-seq (scATAC-seq) method
  ☆43Updated 4 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
• 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
• VCCRI / Sierra
  Discover differential transcript usage from polyA-captured single cell RNA-seq data
  ☆53Updated 2 years ago
• caleblareau / gchromVAR
  Cell type specific enrichments using finemapped variants and quantitative epigenetic data
  ☆47Updated 2 years ago
• ggjlab / scHCL
  ☆47Updated 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…
  ☆58Updated 4 years ago
• jdekanter / CHETAH
  scRNA-seq cell type identification
  ☆43Updated 6 years ago
• seasoncloud / Alleloscope
  Alleloscope is a method for allele-specific copy number estimation that can be applied to single cell DNA and ATAC sequencing data (separ…
  ☆31Updated 2 years ago
• lanagarmire / SSrGE
  ☆34Updated 6 years ago
• nghiavtr / SCmut
  ☆34Updated 6 years ago
• saezlab / footprints
  Analysis code for "Perturbation-response genes reveal signaling footprints in cancer gene expression"
  ☆20Updated 7 years ago
• huangyh09 / brie
  BRIE: Bayesian Regression for Isoform Estimate in Single Cells
  ☆42Updated last year
• sridnona / cb_sniffer
  mutation(barcode) caller for 10x single cell data
  ☆44Updated 5 years ago
• lambdamoses / novoSpaRc
  Reconstruction of spatial context of gene expression with optimal transport
  ☆11Updated 6 years ago
• single-cell-genetics / cardelino
  Clone identification from single-cell data
  ☆61Updated 3 years ago
• jon-xu / scSplit
  Genotype-free demultiplexing of pooled single-cell RNA-Seq, using a hidden state model for identifying genetically distinct samples withi…
  ☆41Updated 2 years ago
• satijalab / Integration2019
  ☆17Updated 6 years ago
• YeoLab / singlecell_pnm
  Code and figures accompanying the paper, "Single-cell alternative splicing analysis with Expedition reveals splicing dynamics during neu…
  ☆20Updated 8 years ago
• WeiqiangZhou / BIRD
  Big data Regression for predicting DNase I hypersensitivity
  ☆31Updated last year
• McGranahanLab / TcellExTRECT
  ☆48Updated last year
• cole-trapnell-lab / cicero-release
  ☆59Updated last year
• caleblareau / bap
  Bead-based single-cell atac processing
  ☆33Updated 4 years ago
• fmicompbio / monaLisa
  binned motif enrichment analysis and visualisation
  ☆43Updated 2 months ago
• wenweixiong / MARVEL
  ☆53Updated last year
• NKI-GCF / XenofilteR
  Filtering of PDX samples for mouse derived reads
  ☆28Updated this week
• JunyueC / sci-RNA-seq3_pipeline
  Processing pipeline scripts for sci-RNA-seq3 (bash, R, python)
  ☆45Updated 4 years ago
• Neurosurgery-Brain-Tumor-Center-DiazLab / CONICS
  CONICS: COpy-Number analysis In single-Cell RNA-Sequencing
  ☆75Updated 2 years ago