Alternatives and similar repositories for HiC-Reg

Users that are interested in HiC-Reg are comparing it to the libraries listed below

• ma-compbio / CTCF-MP
  ☆12Updated 4 years ago
• liulab-dfci / lisa
  epigenome analysis to rank transcription factors
  ☆13Updated 5 years ago
• khodosevichlab / CellAnnotatoR
  Automated marker-based annotation of cell types
  ☆13Updated 3 years ago
• huishenlab / compartmap
  Reconstruction of higher order chromatin from scRNA-seq and scATAC-seq
  ☆14Updated this week
• klarman-cell-observatory / perturbseq
  Perturb-seq analysis package
  ☆14Updated last year
• sinanugur / cellsnake
  Cellsnake tool main repo
  ☆33Updated last year
• FunctionLab / sei-manuscript
  Code for reproducing the Sei manuscript results
  ☆17Updated 3 years ago
• lhqing / ALLCools
  Toolkit for single-cell DNA methylation analysis.
  ☆42Updated last week
• juliaolivieri / SpliZ_pipeline
  Code to calculate the Splicing Z Score (SpliZ) for single cell RNA-seq splicing analysis
  ☆34Updated 3 years ago
• jingshuw / SAVERX
  R package for transfer learning of single-cell RNA-seq denoising
  ☆30Updated 3 years ago
• broadinstitute / single_cell_classification
  Methods to use SNPs or gene expression to classify single cell RNAseq to reference profiles
  ☆29Updated 5 years ago
• GreenleafLab / ChrAccR
  Analyzing chromatin accessibility data in R
  ☆18Updated 2 years ago
• lhqing / mouse_brain_2020
  Jupyter notebook repository for reproducing analysis in "DNA Methylation Landscape of the Mouse Brain at Single-Cell Resolution"
  ☆14Updated 5 years ago
• SchulzLab / STARE
  TF analysis from epigenetic and Hi-C data
  ☆18Updated 5 months ago
• aertslab / PUMATAC
  Pipeline for Universal Mapping of ATAC-seq
  ☆25Updated last year
• kjgaulton / pipelines
  Analytical tools and pipelines for bulk and single cell epigenomic and human genetic data
  ☆27Updated 4 years ago
• veltenlab / mitoClone
  ☆12Updated 4 years ago
• weng-lab / BENGI
  ☆18Updated 3 years ago
• bioinfo-biols / Code_for_circSC
  Analysis pipeline for our circSC manuscript
  ☆14Updated 3 years ago
• caleblareau / maegatk
  Mitochondrial Alteration Enrichment and Genome Analysis Toolkit
  ☆21Updated last year
• satijalab / scChromHMM
  🧬 🦀 A fast and efficient tool to perform a genome wide Single cell Chromatin State Analysis using multimodal histone modification data.…
  ☆29Updated 4 years ago
• EngreitzLab / ABC-GWAS-Paper
  Code to reproduce analyses in Nasser, Bergman, Fulco, Guckelberger, Doughty et al Nature 2021
  ☆15Updated 4 years ago
• SpatialTranscriptomicsResearch / std-nb
  Negative binomial regression for Spatial Transcriptomics data as described in Maaskola et al. 2018
  ☆22Updated 6 years ago
• dibbelab / gficf
  An R implementation of the Gene Frequency - Inverse Cell Frequency method for single cell data normalization
  ☆15Updated 2 years ago
• r3fang / snATAC
  <<------ Use SnapATAC!!
  ☆25Updated 6 years ago
• cxzhu / Paired-seq
  Paired-seq
  ☆14Updated last year
• PoolLab / ReferenceEnhancer
  ☆20Updated 2 years ago
• dbrg77 / scATAC_snakemake
  Snakemake pipeline for plate scATAC-seq processing
  ☆26Updated last year
• buenrostrolab / dscATAC_analysis_code
  Analysis repository for "Droplet-based combinatorial indexing for massive scale single-cell epigenomics"
  ☆11Updated 5 years ago
• tianshilu / QBRC-Neoantigen-Pipeline
  QBRC Neoantigen calling pipeline with CSiN calculation embedded
  ☆24Updated 3 years ago