Alternatives and similar repositories for Drop-seq

Users that are interested in Drop-seq are comparing it to the libraries listed below

• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆182Updated last year
• single-cell-genetics / cellsnp-lite
  Efficient genotyping bi-allelic SNPs on single cells
  ☆154Updated 2 weeks ago
• AllonMKlein / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆86Updated 6 years ago
• wheaton5 / souporcell
  Clustering scRNAseq by genotypes
  ☆190Updated 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.
  ☆103Updated 2 years ago
• TrinityCTAT / Trinity_CTAT
  ☆120Updated 2 years ago
• Teichlab / tracer
  TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
  ☆132Updated last year
• kharchenkolab / numbat
  Haplotype-aware CNV analysis from single-cell RNA-seq
  ☆198Updated 3 weeks ago
• kharchenkolab / dropEst
  Pipeline for initial analysis of droplet-based single-cell RNA-seq data
  ☆95Updated 3 years ago
• dviraran / xCell
  Cell types enrichment analysis
  ☆204Updated last year
• timoast / sinto
  Tools for single-cell data processing
  ☆127Updated last year
• JiekaiLab / scTE
  ☆112Updated last year
• fl-yu / CUT-RUNTools-2.0
  CUT&RUN and CUT&Tag data processing and analysis
  ☆113Updated 8 months ago
• tallulandrews / scRNASeqPipeline
  ☆118Updated 7 years ago
• SingleR-inc / SingleR
  Clone of the Bioconductor repository for the SingleR package.
  ☆197Updated 3 weeks ago
• compbiomed / singleCellTK
  Interactively analyze single cell genomic data
  ☆184Updated last month
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆169Updated last year
• kharchenkolab / pagoda2
  R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
  ☆239Updated 2 months ago
• 10XGenomics / vartrix
  Single-Cell Genotyping Tool
  ☆212Updated 2 years ago
• basilkhuder / Seurat-to-RNA-Velocity
  A guide to using a Seurat object in conjunction with RNA Velocity
  ☆139Updated 3 years ago
• satijalab / azimuth
  A Shiny web app for mapping datasets using Seurat v4
  ☆138Updated last year
• farrellja / URD
  URD - Reconstruction of Branching Developmental Trajectories
  ☆125Updated 4 years ago
• pachterlab / kallistobustools
  kallisto | bustools workflow for pre-processing single-cell RNA-seq data
  ☆118Updated 3 years ago
• cellgeni / STARsolo
  wrapper scripts for convenient STARsolo processing of 10X and other scRNA-seq
  ☆69Updated 5 months ago
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆117Updated 2 years ago
• czbiohub-sf / tabula-muris
  Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
  ☆194Updated 2 years ago
• Hoohm / dropSeqPipe
  A SingleCell RNASeq pre-processing snakemake workflow
  ☆148Updated 2 years ago
• cole-trapnell-lab / garnett
  Automated cell type classification
  ☆114Updated 10 months ago
• aertslab / AUCell
  AUCell: score single cells with gene regulatory networks
  ☆173Updated last year
• BaderLab / CellAnnotationTutorial
  Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods
  ☆97Updated 2 years ago