A flexible framework for nucleosome profiling of cell-free DNA
This repository contains scripts used for analyses in the griffin manuscript: Doebley, et al. Griffin: Framework for clinical cancer subtyping from nucleosome profiling of cell-free DNA. (2021) MedRxiv. doi: https://doi.org/10.1101/2021.08.31.21262867
Versions of packages used in the scripts:
argparse 1.1
pandas 1.3.2
pysam 0.15.4
numpy 1.21.2
scipy 1.7.1
pyyaml 5.3.1
pyBigWig 0.3.17
pybedtools 0.8.0
matplotlib 3.4.1
scikit-learn 0.23.2
pingouin 0.5.1
pybedtools 0.8.0
statsmodels 0.13.2
Other software used for analyses in the manuscript:
Picard (2.18.29)
BWA-MEM (0.7.17)
GATK (4.1.0.0)
samtools (1.9)
IchorCNA (downloaded from https://github.com/GavinHaLab/ichorCNA on 11-20-2020)
liftOver (downloaded from https://genome-store.ucsc.edu/)
bigWigToBedGraph (from UCSC)