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Combinatorial single-cell profiling of all major chromatin types with MAbID

Thank you for your interest in MAbID.

This is the developmental branch: see https://github.com/KindLab/MAbID for the stable version!!!

Table of contents

  1. mabid_pipeline
  • manual.html, containing the complete instructions to map raw MAbID data
  • bin, containing all scripts used to map raw MAbID data
  1. MAbIDR_1.0.0
  • an R package to analyse MAbID data in R
  • contains help-pages for each tool
  • installation time: 3 minutes on a 2020 Macbook
  1. demo
  • test datasets
  • Rmd and html example-code and results

Requirements

R (4.1) Cutadapt (3.0) Bowtie2 (2.2.9) samtools (1.10) scDamAndTools (1.0)

Installation

To install MAbIDR, run install.packages("MAbIDR_1.0.0.tar.gz", type="source"). This should take less then 5 minutes.

To use the mapping pipeline, run one of the file starting with mab-id_pipeline_