Alternatives and similar repositories for SCAFE

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

• single-cell-genetics / cellSNP
  Pileup biallelic SNPs from single-cell and bulk RNA-seq data
  ☆79Updated 3 years ago
• VCCRI / Sierra
  Discover differential transcript usage from polyA-captured single cell RNA-seq data
  ☆51Updated 2 years ago
• MarioniLab / EmbryoTimecourse2018
  Data and analysis scripts for our Embryo Timecourse paper.
  ☆69Updated 5 years ago
• sridnona / cb_sniffer
  mutation(barcode) caller for 10x single cell data
  ☆45Updated 5 years ago
• cole-trapnell-lab / cicero-release
  ☆59Updated 11 months ago
• dbrg77 / plate_scATAC-seq
  A rapid and robust plate-based single cell ATAC-seq (scATAC-seq) method
  ☆43Updated 4 years ago
• statgen / popscle
  A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and au…
  ☆56Updated 4 years ago
• wbaopaul / scATAC-pro
  A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
  ☆76Updated 5 months ago
• CFeregrino / scWGCNA
  scWGCNA
  ☆61Updated 2 years ago
• EDePasquale / DoubletDecon
  A tool for removing doublets from single-cell RNA-seq data
  ☆74Updated 4 years ago
• lhe17 / nebula
  ☆41Updated 2 months ago
• chris-mcginnis-ucsf / MULTI-seq
  R implementation of MULTI-seq sample classification workflow
  ☆64Updated last year
• timoast / sinto
  Tools for single-cell data processing
  ☆126Updated last year
• JunyueC / sci-RNA-seq3_pipeline
  Processing pipeline scripts for sci-RNA-seq3 (bash, R, python)
  ☆43Updated 4 years ago
• nghiavtr / SCmut
  ☆33Updated 6 years ago
• MarioniLab / DropletUtils
  Clone of the Bioconductor repository for the DropletUtils package.
  ☆60Updated last week
• alexisvdb / singleCellHaystack
  Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
  ☆84Updated 11 months ago
• Hoohm / CITE-seq-Count
  A tool that allows to get UMI counts from a single cell protein assay
  ☆82Updated 4 months ago
• Mayrlab / scUTRquant
  Bioinformatics pipeline for single-cell 3' UTR isoform quantification
  ☆24Updated 9 months 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
• immunogenomics / SCENT
  Single-Cell ENhancer Target gene mapping using multimodal data with ATAC + RNA
  ☆77Updated 4 months ago
• lanagarmire / SSrGE
  ☆34Updated 6 years ago
• huangyh09 / brie
  BRIE: Bayesian Regression for Isoform Estimate in Single Cells
  ☆42Updated last year
• hemberg-lab / scmap
  A tool for unsupervised projection of single cell RNA-seq data
  ☆95Updated 4 years ago
• stjude / ROSE
  ROSE: RANK ORDERING OF SUPER-ENHANCERS
  ☆51Updated last year
• jdekanter / CHETAH
  scRNA-seq cell type identification
  ☆43Updated 5 years ago
• kharchenkolab / dropEst
  Pipeline for initial analysis of droplet-based single-cell RNA-seq data
  ☆92Updated 3 years ago
• GreenleafLab / 10x-scATAC-2019
  Publication Page for Satpathy*, Granja* et al 2019
  ☆95Updated 5 years ago
• bvieth / scRNA-seq-pipelines
  Compendium to "A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines"
  ☆54Updated 4 years ago
• prabhakarlab / RCAv2
  R package for robust clustering of single cell RNA sequencing data
  ☆35Updated last year