Alternatives and similar repositories for leafcutter:

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

• jsh58 / Genrich
  Detecting sites of genomic enrichment
  ☆189Updated last year
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆136Updated 4 years ago
• ENCODE-DCC / chip-seq-pipeline
  ENCODE Uniform processing pipeline for ChIP-seq
  ☆123Updated 5 years ago
• VanLoo-lab / ascat
  ASCAT R package
  ☆179Updated 3 weeks ago
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆246Updated 2 months ago
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆296Updated 3 years ago
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆109Updated 2 years ago
• ENCODE-DCC / long-rna-seq-pipeline
  STAR based ENCODE Long RNA-Seq processing pipeline
  ☆94Updated 3 years ago
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆121Updated 2 years ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆217Updated last week
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆273Updated 9 months ago
• ENCODE-DCC / rna-seq-pipeline
  ☆148Updated 2 years ago
• harvardinformatics / ATAC-seq
  ☆131Updated 6 years ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆251Updated last year
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆172Updated 9 months ago
• zhxiaokang / RASflow
  RNA-Seq analysis workflow
  ☆104Updated 3 years ago
• im3sanger / dndscv
  dN/dS methods to quantify selection in cancer and somatic evolution
  ☆220Updated 2 weeks ago
• haowenz / chromap
  Fast alignment and preprocessing of chromatin profiles
  ☆198Updated 4 months ago
• PoisonAlien / trackplot
  Generate IGV style locus tracks from bigWig files in R
  ☆158Updated 5 months ago
• bmvdgeijn / WASP
  WASP: allele-specific pipeline for unbiased read mapping and molecular QTL discovery
  ☆103Updated 3 years ago
• lima1 / PureCN
  Copy number calling and variant classification using targeted short read sequencing
  ☆133Updated 2 weeks ago
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆208Updated 2 months ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆215Updated 9 months ago
• shenlab-sinai / ngsplot
  Quick mining and visualization of NGS data by integrating genomic databases
  ☆264Updated last year
• RabadanLab / arcasHLA
  Fast and accurate in silico inference of HLA genotypes from RNA-seq
  ☆127Updated 7 months ago
• yupenghe / methylpy
  WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
  ☆140Updated last year
• kundajelab / chipseq_pipeline
  AQUAS TF and histone ChIP-seq pipeline
  ☆108Updated 2 years ago
• akdemirlab / HiCPlotter
  “When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau
  ☆185Updated 4 years ago
• 10XGenomics / vartrix
  Single-Cell Genotyping Tool
  ☆203Updated last year
• TrinityCTAT / Trinity_CTAT
  ☆116Updated last year