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HiS-NET-seq_paper_code/README.md
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Developer: Annnkatrin Bressin (bressin@molgen.mpg.de) | |
Date: 3.2.2023 | |
Code was developed for UNIX systems and must be executed via the command line. | |
Software requirements are listed below. All paths to the listed applicatipons must be part of the $PATH variable. | |
For more information see https://wiki.archlinux.org/title/Bash#Configuration_files. | |
Software and Versions: | |
standard unix command line utilities such as paste, cut, join, awk, ln, mkdir , dirname, ... | |
Rscript (R) version 4.2.2 (2022-10-31) (default) | |
* required R libraries will be installed automatically | |
Rscript-4.0.5 (R) version 4.0.5 | |
* required for DiffBind | |
Python 3.10.8 | |
* required libraries: | |
- pyBigWig 0.3.18 (https://github.com/dpryan79/pyBigWig) | |
- numpy 1.23.4 (1.23.4) | |
gunzip (gzip) 1.12 | |
bedGraphToBigWig v 4 | |
bigWigToBedGraph | |
bedtools v2.30.0 | |
deeptools 3.2.1 | |
* computeMatrix, plotHeatmap, computeMatrixOperations,... | |
samtools 1.16.1 | |
STAR 2.7.3a | |
* please call executable file STAR_2.7.3a | |
FastQC v0.11.9 | |
cutadapt 4.1 | |
starcode-v1.1 | |
chromHMM 1.19 (http://compbio.mit.edu/ChromHMM/) | |