Alternatives and similar repositories for cellsnp-lite:

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

• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆172Updated 9 months ago
• KChen-lab / Monopogen
  SNV calling from single cell sequencing
  ☆97Updated 5 months ago
• timoast / sinto
  Tools for single-cell data processing
  ☆123Updated 11 months ago
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆109Updated 2 years ago
• cortes-ciriano-lab / SComatic
  A tool for detecting somatic variants in single cell data
  ☆199Updated 7 months ago
• JiekaiLab / scTE
  ☆105Updated last year
• TrinityCTAT / Trinity_CTAT
  ☆116Updated last year
• caleblareau / mgatk
  mgatk: mitochondrial genome analysis toolkit
  ☆108Updated 3 months ago
• CebolaLab / ATAC-seq
  Analysis pipeline for ATAC-seq data
  ☆59Updated last year
• MGI-tech-bioinformatics / DNBelab_C_Series_HT_scRNA-analysis-software
  An open source and flexible pipeline to analysis high-throughput DNBelab C Series single-cell RNA datasets
  ☆90Updated last week
• 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
• vib-singlecell-nf / vsn-pipelines
  A repository of pipelines for single-cell data in Nextflow DSL2
  ☆75Updated 2 years ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆162Updated last year
• VanLoo-lab / ascat
  ASCAT R package
  ☆180Updated last month
• pachterlab / kallistobustools
  kallisto | bustools workflow for pre-processing single-cell RNA-seq data
  ☆118Updated 2 years ago
• reskejak / ATAC-seq
  Basic workflow for ATAC-seq analysis
  ☆77Updated last year
• single-cell-genetics / vireo
  Demultiplexing pooled scRNA-seq data with or without genotype reference
  ☆83Updated 2 weeks ago
• AntonioDeFalco / SCEVAN
  R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the …
  ☆103Updated 3 weeks ago
• singleron-RD / CeleScope
  Single Cell Analysis Pipelines
  ☆100Updated 2 weeks ago
• wheaton5 / souporcell
  Clustering scRNAseq by genotypes
  ☆178Updated 5 months ago
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆162Updated last year
• aertslab / AUCell
  AUCell: score single cells with gene regulatory networks
  ☆152Updated last year
• Hoohm / CITE-seq-Count
  A tool that allows to get UMI counts from a single cell protein assay
  ☆82Updated this week
• RabadanLab / arcasHLA
  Fast and accurate in silico inference of HLA genotypes from RNA-seq
  ☆127Updated 8 months ago
• kharchenkolab / numbat
  Haplotype-aware CNV analysis from single-cell RNA-seq
  ☆181Updated last month
• 10XGenomics / vartrix
  Single-Cell Genotyping Tool
  ☆205Updated last year
• harvardinformatics / ATAC-seq
  ☆131Updated 6 years ago
• tobiasrausch / ATACseq
  Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
  ☆75Updated last year
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆144Updated last year
• Teichlab / tracer
  TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
  ☆128Updated last year