Alternatives and similar repositories for ENCODE-cCREs

Users that are interested in ENCODE-cCREs are comparing it to the libraries listed below

• yezhengSTAT / CUTTag_tutorial
  Tutorial Website
  ☆61Updated 4 years ago
• gerstung-lab / MutationTimeR
  An R package to time somatic mutations
  ☆64Updated 4 years ago
• stjude / ROSE
  ROSE: RANK ORDERING OF SUPER-ENHANCERS
  ☆53Updated last year
• databio / pepatac
  A modular, containerized pipeline for ATAC-seq data processing
  ☆59Updated 3 weeks ago
• gxiaolab / REDITs
  RNA editing tests
  ☆17Updated 5 years ago
• VCCRI / Sierra
  Discover differential transcript usage from polyA-captured single cell RNA-seq data
  ☆51Updated 2 years ago
• francois-a / fastqtl
  Enhanced version of the FastQTL QTL mapper
  ☆68Updated 2 years ago
• ay-lab / ATACProc
  ATAC-seq processing pipeline
  ☆34Updated 3 years ago
• ratschlab / pancanatlas_code_public
  Public repository containing research code for the TCGA PanCanAtlas Splicing project
  ☆42Updated 4 years ago
• ParkerLab / ataqv
  A toolkit for QC and visualization of ATAC-seq results.
  ☆71Updated 9 months ago
• ElkonLab / scAPA
  This is a package and a shell script for alternative polyadenylation (APA) analysis of 3' tag single-cell RNA-seq data.
  ☆23Updated 3 years ago
• markowetzlab / Drews2022_CIN_Compendium
  Main repository for Drews et al. (Nature, 2022)
  ☆42Updated 2 years ago
• wenweixiong / MARVEL
  ☆51Updated last year
• huangyh09 / brie
  BRIE: Bayesian Regression for Isoform Estimate in Single Cells
  ☆42Updated last year
• chung-lab / SCAFE
  Single Cell Analysis of Five'Ends
  ☆50Updated last year
• morrislab / qapa
  RNA-seq Quantification of Alternative Polyadenylation
  ☆49Updated 3 months ago
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆40Updated 3 years ago
• wbaopaul / scATAC-pro
  A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
  ☆79Updated 7 months ago
• Xinglab / CLAM
  CLIP-seq Analysis of Multi-mapped reads
  ☆31Updated 4 years ago
• sandberg-lab / Smart-seq3
  Code and analysis pipeline for Smart-seq3 (Hagemann-Jensen et al. 2020).
  ☆54Updated 4 years ago
• fmicompbio / monaLisa
  binned motif enrichment analysis and visualisation
  ☆41Updated last month
• GoekeLab / proActiv
  Estimation of Promoter Activity from RNA-Seq data
  ☆56Updated 3 months ago
• natsuhiko / rasqual
  Robust Allele Specific Quantification and quality controL
  ☆40Updated 3 years ago
• cxzhu / Paired-Tag
  Analysis of Paired-Tag datasets
  ☆43Updated last year
• nskvir / RepEnrich
  RepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆28Updated 3 years ago
• McGranahanLab / TcellExTRECT
  ☆47Updated 9 months ago
• fhormoz / caviar
  ☆63Updated 3 years ago
• single-cell-genetics / cellSNP
  Pileup biallelic SNPs from single-cell and bulk RNA-seq data
  ☆80Updated 3 years ago
• cole-trapnell-lab / cicero-release
  ☆58Updated last year
• shengxin321 / HumanKidney_eQTL_and_snATAC-seq
  codes used in the human kidney eQTL(cf) and eQTL(ci) and snATAC-seq data
  ☆19Updated 4 years ago