Alternatives and similar repositories for single_cell_toolkit

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

• Mayrlab / scUTRquant
  Bioinformatics pipeline for single-cell 3' UTR isoform quantification
  ☆26Updated 11 months 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
• dozmorovlab / excluderanges
  Genomic coordinates of problematic genomic regions as GRanges
  ☆45Updated 2 months ago
• natsuhiko / rasqual
  Robust Allele Specific Quantification and quality controL
  ☆40Updated 3 years ago
• sridnona / cb_sniffer
  mutation(barcode) caller for 10x single cell data
  ☆45Updated 5 years ago
• lanagarmire / SSrGE
  ☆34Updated 6 years ago
• databio / pepatac
  A modular, containerized pipeline for ATAC-seq data processing
  ☆60Updated last month
• gerstung-lab / MutationTimeR
  An R package to time somatic mutations
  ☆64Updated 4 years ago
• 10XGenomics / scHLAcount
  Count HLA alleles in single-cell RNA-seq data
  ☆62Updated 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
• chung-lab / SCAFE
  Single Cell Analysis of Five'Ends
  ☆50Updated last year
• HorvathLab / NGS
  Next-Gen Sequencing tools from the Horvath Lab
  ☆44Updated last month
• 10XGenomics / subset-bam
  ☆81Updated last year
• open2c / open2c_examples
  ☆17Updated last year
• LuyiTian / FLAMES
  Full-length transcriptome splicing and mutation analysis
  ☆84Updated last year
• broadinstitute / RNA_MUTECT_1.0-1
  ☆39Updated 5 years ago
• ParkerLab / ataqv
  A toolkit for QC and visualization of ATAC-seq results.
  ☆71Updated 9 months ago
• yezhengSTAT / CUTTag_tutorial
  Tutorial Website
  ☆60Updated 4 years ago
• nf-core / spatialvi
  Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcri…
  ☆66Updated last week
• wbaopaul / scATAC-pro
  A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
  ☆79Updated 7 months ago
• single-cell-genetics / cellSNP
  Pileup biallelic SNPs from single-cell and bulk RNA-seq data
  ☆80Updated 3 years ago
• gwlab-ca / scsnv
  scSNV Mapping tool for 10X Single Cell Data
  ☆25Updated last year
• mcvickerlab / varCA
  Use an ensemble of variant callers to call variants from ATAC-seq data
  ☆23Updated 5 months ago
• vivekbhr / Subread_to_DEXSeq
  Scripts to import your FeatureCounts output into DEXSeq
  ☆34Updated 7 years ago
• vib-singlecell-nf / vsn-pipelines
  A repository of pipelines for single-cell data in Nextflow DSL2
  ☆76Updated 2 years ago
• dan-landau / IronThrone-GoT
  processes GoT amplicon data and generates a table of metrics
  ☆32Updated 3 years ago
• cbg-ethz / SCICoNE
  Single-cell copy number calling and event history reconstruction.
  ☆27Updated 10 months ago
• Xinglab / CLAM
  CLIP-seq Analysis of Multi-mapped reads
  ☆31Updated 4 years ago
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆50Updated 6 years ago
• tushiqi / MAnorm2
  MAnorm2 for Normalizing and Comparing ChIP-seq Samples
  ☆32Updated 2 years ago