Alternatives and similar repositories for sctools

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

• meuleman / epilogos
  Methods for summarizing and visualizing multi-biosample functional genomic annotations
  ☆46Updated 9 months ago
• aertslab / single_cell_toolkit
  Tools for correcting single cell barcodes for various scATAC-seq techniques and creating fragment files and spltting BAM files per cluste…
  ☆29Updated 2 weeks ago
• HumanCellAtlas / data-consumer-vignettes
  Simple walk-throughs of interacting with the DCP as a downstream data consumer.
  ☆17Updated 3 weeks ago
• pachterlab / sircel
  Identify cell barcodes from single-cell genomics sequencing experiments
  ☆43Updated 4 years ago
• complextissue / pytximport
  Feature-rich Python implementation of the tximport package for gene count estimation.
  ☆41Updated 2 months ago
• ebi-gene-expression-group / scanpy-scripts
  Scripts for using scanpy
  ☆38Updated 2 months ago
• czbiohub-sf / cerebra
  A tool for fast and accurate summarizing of variant calling format (VCF) files
  ☆61Updated 3 years ago
• scverse / genomic-features
  Genomic Features in Python from BioConductor's AnnotationHub
  ☆22Updated 2 weeks ago
• cbg-ethz / SCICoNE
  Single-cell copy number calling and event history reconstruction.
  ☆27Updated last year
• open2c / quaich
  snakemake pipeline for Hi-C post-processing
  ☆22Updated last year
• BUStools / bustools
  Tools for working with BUS files
  ☆102Updated 7 months ago
• dozmorovlab / excluderanges
  Genomic coordinates of problematic genomic regions as GRanges
  ☆49Updated 3 weeks ago
• rajewsky-lab / spacemake
  ☆48Updated last week
• dpeerlab / Harmony
  Harmony framework for connecting scRNA-seq data from discrete time points
  ☆53Updated last month
• MarioniLab / EmptyDrops2017
  Code for the empty droplet and cell detection project from the HCA Hackathon.
  ☆21Updated 6 years ago
• lcmmichielsen / scHPL
  ☆37Updated 10 months ago
• nvictus / pybbi
  Python bindings to UCSC BigWig and BigBed library
  ☆35Updated 3 weeks ago
• higlass / higlass-docker
  Builds a docker container wrapping higlass-server and higlass-client in nginx
  ☆31Updated 3 years ago
• jmbreda / Sanity
  Filtering of Poison noise on a single-cell RNA-seq UMI count matrix
  ☆78Updated last month
• pachterlab / seqspec
  machine-readable file format for genomic library sequence and structure
  ☆126Updated 4 months ago
• nf-core / spatialvi
  Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcri…
  ☆69Updated last month
• HorvathLab / NGS
  Next-Gen Sequencing tools from the Horvath Lab
  ☆44Updated 3 months ago
• natsuhiko / rasqual
  Robust Allele Specific Quantification and quality controL
  ☆40Updated 4 years ago
• COMBINE-lab / simpleaf
  A rust framework to make using alevin-fry even simpler
  ☆60Updated 8 months ago
• YeoLab / outrigger
  Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
  ☆67Updated 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…
  ☆58Updated 4 years ago
• broadinstitute / single_cell_portal
  Tutorials, workflows, and convenience scripts for Single Cell Portal
  ☆50Updated last year
• vaquerizaslab / chess
  Comparison of Hi-C Experiments using Structural Similarity.
  ☆28Updated 2 years ago
• hemberg-lab / MicroExonator
  Snakemake pipeline for microexon discovery and quantification
  ☆20Updated 11 months ago
• pachterlab / scRNA-Seq-TCC-prep
  Preprocessing of single-cell RNA-Seq (deprecated)
  ☆62Updated 6 years ago