https://github.com/ccrgeneticsbranch/rnaseqlandscape
R code for paper "Immuno-Transcriptomic Profiling of Extracranial Pediatric Solid Malignancies"
Science Score: 10.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
○codemeta.json file
-
○.zenodo.json file
-
○DOI references
-
✓Academic publication links
Links to: sciencedirect.com -
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (8.1%) to scientific vocabulary
Last synced: 10 months ago
·
JSON representation
Repository
R code for paper "Immuno-Transcriptomic Profiling of Extracranial Pediatric Solid Malignancies"
Basic Info
- Host: GitHub
- Owner: CCRGeneticsBranch
- Language: R
- Default Branch: main
- Size: 371 MB
Statistics
- Stars: 0
- Watchers: 5
- Forks: 1
- Open Issues: 0
- Releases: 0
Created about 5 years ago
· Last pushed almost 4 years ago
https://github.com/CCRGeneticsBranch/RNAseqLandscape/blob/main/
# RNAseqLandscape R code for paper "Immuno-transcriptomic profiling of extracranial pediatric solid malignancies" https://www.sciencedirect.com/science/article/pii/S2211124721015333 Brohl, A. S., Sindiri, S., Wei, J. S., Milewski, D., Chou, H. C., Song, Y. K., ... & Khan, J. (2021). Immuno-transcriptomic profiling of extracranial pediatric solid malignancies. Cell reports, 37(8), 110047. ## Installation The easiest way to get this script is to clone the repository. SSH: ``` git clone git@github.com:CCRGeneticsBranch/RNAseqLandscape.git ``` HTTPS: ``` https://github.com/CCRGeneticsBranch/RNAseqLandscape.git ``` We need an extra data file (too large for GitHub). Please copy this to input/GeneRDS/: ``` cp /data/khanlab3/hsienchao/Landscape/RPKM_Data_Filt_Consolidated.GeneNames.all.TCGA.Khanlab.pc.log22019-03-19.rds RNAseqLandscape/input/GeneRDS/ ``` ## Requirements We need the following R packages. Please make sure they are installed properly: ``` plyr dplyr data.table ggplot2 tidyr gridExtra ggrepel RColorBrewer treemap lazyeval grid ggridges scales randomcoloR gplots pheatmap ape amap limma edgeR psych tibble Hmisc ``` ## Run the script Please change directory to the cloned folder: ``` cd RNAseqLandscape ``` Then run: ``` Rscript src/expressionAnalysis.R ``` You might see many warnings but they will not affect the results. This script has been tested in R 4.0. ## Output ``` output/Figures: all the figures output/FigureData: the data used to generate figures output/DiffExpResults: the output of differential expression analyses output/MiXCR: the output data for TCR analysis
Owner
- Name: CCR Genetics Branch
- Login: CCRGeneticsBranch
- Kind: organization
- Website: https://ccr.cancer.gov/Genetics-Branch
- Repositories: 13
- Profile: https://github.com/CCRGeneticsBranch
Genomics, and epigenetic pipelines developed by the OncoGenomics Section of the Genetics Branch, CCR.