GBM_SV_anaysis

• Overview
• System Requirements
• Installation Guide
• License

Overview

GBM_SV_anaysis Offering code&commands for Hi-C chromatin structure, SVs and neoloop identifications, CUT&tag and RNA-seq analysis, subtype classfication and circos plot etc.

System Requirements

Software requirements

OS Requirements

This package is supported for Linux. The package has been tested on the following systems:

• Linux: Ubuntu 16.04

software Dependencies

-bwa mem (v0.7.17;https://bio-bwa.sourceforge.net/)
-runHiC (v0.8.4-r1; https://zenodo.org/badge/doi/10.5281/zenodo)
-cooler (v0.8.6;https://cooler.readthedocs.io/en/latest/index.html) 
-EagleC (v0.1.3;https://github.com/XiaoTaoWang/EagleC)
-Neoloopfinder (v0.3.0.post4;https://github.com/XiaoTaoWang/NeoLoopFinder)
-HiCrep (v0.2.3;https://github.com/TaoYang-dev/hicrep)
-cooltools (v0.3.2;https://cooltools.readthedocs.io/en/latest/#)
-peakachu (v1.2.0;https://github.com/open2c/cooltools)
-STAR (v2.6.0c;https://github.com/alexdobin/STAR)
-RSEM (v1.3.3;https://github.com/deweylab/RSEM)
-deepTools2 (v3.5.1;https://github.com/deeptools/deepTools)
-Bowtie2 (v2.3.4.1;https://bowtie-bio.sourceforge.net/bowtie2/manual.shtml)
-cBioPortal (v3.5.3;https://www.cbioportal.org/)
-Picard tools (v2.20.7;https://broadinstitute.github.io/picard/)
-SEACR (v1.3;https://github.com/FredHutch/SEACR)
-CNVkit (v0.9.9;https://github.com/etal/cnvkit)
-GEPIA2 (v7.0;http://gepia2.cancer-pku.cn/)
-DisGenet Database (v7.0;https://www.disgenet.org/)

Installation Guide:

Instructions

All the above dependencies can be installed according to the instructions themselves 

License

This project is covered under the Apache 2.0 License.