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
  ☆196Updated 2 years ago
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆139Updated 5 years ago
• im3sanger / dndscv
  dN/dS methods to quantify selection in cancer and somatic evolution
  ☆227Updated 6 months ago
• ENCODE-DCC / chip-seq-pipeline
  ENCODE Uniform processing pipeline for ChIP-seq
  ☆123Updated 5 years ago
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆217Updated last week
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆117Updated 2 years ago
• VanLoo-lab / ascat
  ASCAT R package
  ☆191Updated last month
• PoisonAlien / trackplot
  Generate IGV style locus tracks from bigWig files in R
  ☆173Updated last year
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆127Updated 3 years ago
• yupenghe / methylpy
  WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
  ☆145Updated 2 years ago
• nboley / idr
  IDR
  ☆173Updated 7 years ago
• broadinstitute / ichorCNA
  Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
  ☆191Updated last year
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆284Updated last week
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆267Updated last week
• kundajelab / atac_dnase_pipelines
  ATAC-seq and DNase-seq processing pipeline
  ☆166Updated 3 years ago
• shenlab-sinai / ngsplot
  Quick mining and visualization of NGS data by integrating genomic databases
  ☆268Updated 2 years ago
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆327Updated 4 years ago
• kundajelab / chipseq_pipeline
  AQUAS TF and histone ChIP-seq pipeline
  ☆111Updated 3 years ago
• ENCODE-DCC / rna-seq-pipeline
  ☆157Updated 3 years ago
• ENCODE-DCC / long-rna-seq-pipeline
  STAR based ENCODE Long RNA-Seq processing pipeline
  ☆96Updated 4 years ago
• nloyfer / wgbs_tools
  tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
  ☆172Updated last week
• AlexandrovLab / SigProfilerExtractor
  SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the n…
  ☆166Updated 2 weeks ago
• harvardinformatics / ATAC-seq
  ☆143Updated 6 years ago
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆213Updated this week
• virajbdeshpande / AmpliconArchitect
  AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and …
  ☆155Updated last year
• Xinglab / rmats2sashimiplot
  ☆153Updated 5 months ago
• Hoohm / dropSeqPipe
  A SingleCell RNASeq pre-processing snakemake workflow
  ☆148Updated 2 years ago
• haowenz / chromap
  Fast alignment and preprocessing of chromatin profiles
  ☆206Updated last month
• dpryan79 / ChromosomeMappings
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
  ☆244Updated 2 years ago
• loosolab / TOBIAS
  Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
  ☆230Updated 2 months ago