/PASS-ON-codes

Primary LanguageR

PASS-ON-codes

  1. System requirements:
  • R version 4.0.3 & Rstudio Version 1.3.1093 has to be installed.
  1. R Dependencies and version:
  • here 1.0.1
  • openxlsx 4.2.3
  • org.Hs.eg.db 3.12.0
  • annotate 1.68.0
  • BiocParallel 1.24.1
  • DESeq2 1.30.1
  • fgsea 1.16.0
  • GSVA 1.38.2
  • glmnet 4.1-1
  • pROC 1.17.0.1
  • ROCR 1.0-11
  • survival 3.2-7
  • survminer 0.4.9
  • ggplot2 3.3.3
  • ggplot2 3.3.3
  • ggrepel 0.9.1
  • plotmo 3.6.0
  • ggpubr 0.4.0
  • RColorBrewer 1.1-2
  1. Installation Guide:

Packages install from R CRAN (https://cran.r-project.org/):

  • install.packages(c("here", "openxlsx", "glmnet", "pROC","ROCR","survival" "survminer", "ggplot2", "plotmo", "ggpubr", "RColorBrewer"))

Packages install from Bioconductor (https://www.bioconductor.org/):

  • if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
  • BiocManager::install(c("org.Hs.eg.db","annotate","BiocParallel","DESeq2", "fgsea" "GSVA"))

  1. Other Public Signatures:

    IMPRES: https://github.com/noamaus/IMPRES-codes

    CIBERSORT: https://cibersort.stanford.edu/index.php

  2. Licenses:

GNU General Public License (GPL)