Alternatives and similar repositories for cellsnp-lite:

Users that are interested in cellsnp-lite are comparing it to the libraries listed below

• cortes-ciriano-lab / SComatic
  A tool for detecting somatic variants in single cell data
  ☆183Updated 4 months ago
• timoast / sinto
  Tools for single-cell data processing
  ☆122Updated 8 months ago
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆162Updated 6 months ago
• vib-singlecell-nf / vsn-pipelines
  A repository of pipelines for single-cell data in Nextflow DSL2
  ☆75Updated last year
• KChen-lab / Monopogen
  SNV calling from single cell sequencing
  ☆91Updated 2 months ago
• JiekaiLab / scTE
  ☆104Updated 9 months ago
• BorchLab / escape
  Easy single cell analysis platform for enrichment
  ☆158Updated this week
• caleblareau / mgatk
  mgatk: mitochondrial genome analysis toolkit
  ☆105Updated last week
• single-cell-genetics / vireo
  Demultiplexing pooled scRNA-seq data with or without genotype reference
  ☆80Updated 8 months ago
• pachterlab / kallistobustools
  kallisto | bustools workflow for pre-processing single-cell RNA-seq data
  ☆117Updated 2 years ago
• wheaton5 / souporcell
  Clustering scRNAseq by genotypes
  ☆174Updated 2 months ago
• aertslab / AUCell
  AUCell: score single cells with gene regulatory networks
  ☆140Updated 10 months ago
• BaderLab / CellAnnotationTutorial
  Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods
  ☆89Updated last year
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆106Updated 2 years ago
• chris-mcginnis-ucsf / MULTI-seq
  R implementation of MULTI-seq sample classification workflow
  ☆61Updated last year
• CebolaLab / ATAC-seq
  Analysis pipeline for ATAC-seq data
  ☆44Updated last year
• AntonioDeFalco / SCEVAN
  R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the …
  ☆95Updated 7 months ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆157Updated last year
• GreenleafLab / 10x-scATAC-2019
  Publication Page for Satpathy*, Granja* et al 2019
  ☆92Updated 4 years ago
• rpolicastro / scProportionTest
  ☆60Updated last year
• tavareshugo / tutorial_DESeq2_contrasts
  ☆57Updated 8 months ago
• snakemake-workflows / single-cell-rna-seq
  A single cell RNA-seq workflow, including highly variable gene analysis, cell type assignment and differential expression analysis.
  ☆101Updated 2 years ago
• CahanLab / singleCellNet
  SingleCellNet: classify single cells across species and platforms
  ☆134Updated last year
• kharchenkolab / numbat
  Haplotype-aware CNV analysis from single-cell RNA-seq
  ☆175Updated last month
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆142Updated 11 months ago
• rnabioco / clustifyr
  Infer cell types in scRNA-seq data using bulk RNA-seq or gene sets
  ☆116Updated 5 months ago
• reskejak / ATAC-seq
  Basic workflow for ATAC-seq analysis
  ☆72Updated 11 months ago
• MarioniLab / EmbryoTimecourse2018
  Data and analysis scripts for our Embryo Timecourse paper.
  ☆66Updated 5 years ago
• sandberg-lab / Smart-seq3
  Code and analysis pipeline for Smart-seq3 (Hagemann-Jensen et al. 2020).
  ☆50Updated 3 years ago
• carmonalab / scGate
  marker-based purification of cell types from single-cell RNA-seq datasets
  ☆100Updated 7 months ago