CancerSEA
The goal of CancerSEA is to …
Installation
You can install the released version of CancerSEA from github with:
devtools::install_github("CancerSEA")Example
This is a basic example which shows you how to solve a common problem:
library(CancerSEA)
## basic example code
available_pathways
#> [1] "angiogenesis" "apoptosis" "cell_cycle" "differentiation"
#> [5] "dna_damage" "dna_repair" "emt" "hypoxia"
#> [9] "inflammation" "invasion" "metastasis" "proliferation"
#> [13] "quiescence" "stemness"
head(cell_cycle)
#> ensembl_gene_id symbol
#> 1 ENSG00000011426 ANLN
#> 2 ENSG00000143401 ANP32E
#> 3 ENSG00000156802 ATAD2
#> 4 ENSG00000087586 AURKA
#> 5 ENSG00000136492 BRIP1
#> 6 ENSG00000118412 CASP8AP2## state score
scores <- state_score(expr, gene_set = list(cell_cycle$symbol, angiogenesis$symbol))