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
  ☆81Updated 3 years ago
• VCCRI / Sierra
  Discover differential transcript usage from polyA-captured single cell RNA-seq data
  ☆52Updated 2 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
• MarioniLab / EmbryoTimecourse2018
  Data and analysis scripts for our Embryo Timecourse paper.
  ☆69Updated 5 years ago
• chris-mcginnis-ucsf / MULTI-seq
  R implementation of MULTI-seq sample classification workflow
  ☆64Updated last year
• lhe17 / nebula
  ☆43Updated 5 months ago
• cole-trapnell-lab / cicero-release
  ☆59Updated last year
• CFeregrino / scWGCNA
  scWGCNA
  ☆61Updated 3 years ago
• noush-joglekar / scisorseqr
  scisorseqr is an R-package for processing of single-cell long read data and analyzing differential isoform expression across any two cond…
  ☆43Updated 2 years ago
• dbrg77 / plate_scATAC-seq
  A rapid and robust plate-based single cell ATAC-seq (scATAC-seq) method
  ☆43Updated 4 years ago
• bvieth / scRNA-seq-pipelines
  Compendium to "A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines"
  ☆55Updated 4 years ago
• EDePasquale / DoubletDecon
  A tool for removing doublets from single-cell RNA-seq data
  ☆75Updated 4 years ago
• timoast / sinto
  Tools for single-cell data processing
  ☆127Updated last year
• sandberg-lab / Smart-seq3
  Code and analysis pipeline for Smart-seq3 (Hagemann-Jensen et al. 2020).
  ☆54Updated 4 years ago
• vib-singlecell-nf / vsn-pipelines
  A repository of pipelines for single-cell data in Nextflow DSL2
  ☆77Updated 2 years ago
• wbaopaul / scATAC-pro
  A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
  ☆79Updated 8 months ago
• rpolicastro / scProportionTest
  ☆74Updated 2 years ago
• MarioniLab / DropletUtils
  Clone of the Bioconductor repository for the DropletUtils package.
  ☆62Updated 2 months ago
• alexisvdb / singleCellHaystack
  Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
  ☆85Updated last year
• 10XGenomics / subset-bam
  ☆81Updated last year
• akdess / CaSpER
  ☆88Updated 4 years ago
• Mayrlab / scUTRquant
  Bioinformatics pipeline for single-cell 3' UTR isoform quantification
  ☆26Updated 11 months ago
• wmacnair / psupertime
  psupertime is pseudotime ordering for single cell RNA-seq data with sequential labels
  ☆43Updated 3 years ago
• hemberg-lab / scmap
  A tool for unsupervised projection of single cell RNA-seq data
  ☆95Updated 4 years ago
• KChen-lab / Monopogen
  SNV calling from single cell sequencing
  ☆114Updated last year
• caleblareau / mgatk
  mgatk: mitochondrial genome analysis toolkit
  ☆109Updated 9 months ago
• elimereu / matchSCore2
  ☆55Updated 4 years ago
• wenweixiong / MARVEL
  ☆51Updated last year
• haniffalab / scRNA-seq_analysis
  Single cell RNA-seq analysis bundle
  ☆37Updated 6 years ago