i.score

How to use i.score to rank/score the cells:

This data is from this publication (GEO number: GSE156246 and pubmed id: TBD (accepted in Cancer Discovery))

All the codes here are for reproducibility and a how to guide to run i.score function in iCellR.

Download the samples from here: https://genome.med.nyu.edu/results/external/iCellR/i.score/

Download gene signatures from here: https://genome.med.nyu.edu/results/external/iCellR/i.score/gene_signatures.tar.gz

# load sample gene signature in iCellR

library(iCellR)
G0 <- readLines(system.file('extdata', 'G0.txt', package = 'iCellR'))
G1S <- readLines(system.file('extdata', 'G1S.txt', package = 'iCellR'))
G2M <- readLines(system.file('extdata', 'G2M.txt', package = 'iCellR'))
M <- readLines(system.file('extdata', 'M.txt', package = 'iCellR'))
MG1 <- readLines(system.file('extdata', 'MG1.txt', package = 'iCellR'))
S <- readLines(system.file('extdata', 'S.txt', package = 'iCellR'))

# load all the gene signatures 

Melnick_10_GILMORE_CORE_NFKB_PATHWAY.txt <- readLines("10_GILMORE_CORE_NFKB_PATHWAY.txt")
Melnick_11_HALLMARK_MYC_TARGETS_V1.txt <- readLines("11_HALLMARK_MYC_TARGETS_V1.txt")
Melnick_12_GO_BETA_CATENIN_BINDING.txt <- readLines("12_GO_BETA_CATENIN_BINDING.txt")
Melnick_13_PID_BETA_CATENIN_NUC_PATHWAY.txt <- readLines("13_PID_BETA_CATENIN_NUC_PATHWAY.txt")
Melnick_14_PID_WNT_SIGNALING_PATHWAY.txt <- readLines("14_PID_WNT_SIGNALING_PATHWAY.txt")
Melnick_15_PID_WNT_CANONICAL_PATHWAY.txt <- readLines("15_PID_WNT_CANONICAL_PATHWAY.txt")
Melnick_16_Pribluda_SENESCENCE_INFLAMMATORY_GENES.txt <- readLines("16_Pribluda_SENESCENCE_INFLAMMATORY_GENES.txt")
Melnick_17_FRIDMAN_SENESCENCE_DN.txt <- readLines("17_FRIDMAN_SENESCENCE_DN.txt")
Melnick_18_FRIDMAN_SENESCENCE_UP.txt <- readLines("18_FRIDMAN_SENESCENCE_UP.txt")
Melnick_19_DeJONGE_LSC_TOP50_genes.txt <- readLines("19_DeJONGE_LSC_TOP50_genes.txt")
Melnick_1_AML1566_AraC_UP.txt <- readLines("1_AML1566_AraC_UP.txt")
Melnick_20_GAL_LEUKEMIC_STEM_CELL_UP.txt <- readLines("20_GAL_LEUKEMIC_STEM_CELL_UP.txt")
Melnick_21_GAL_LEUKEMIC_STEM_CELL_DN.txt <- readLines("21_GAL_LEUKEMIC_STEM_CELL_DN.txt")
Melnick_22_EPPERT_CE_HSC_LSC.txt <- readLines("22_EPPERT_CE_HSC_LSC.txt")
Melnick_23_JAATINEN_HEMATOPOIETIC_STEM_CELL_UP.txt <- readLines("23_JAATINEN_HEMATOPOIETIC_STEM_CELL_UP.txt")
Melnick_24_JAATINEN_HEMATOPOIETIC_STEM_CELL_DN.txt <- readLines("24_JAATINEN_HEMATOPOIETIC_STEM_CELL_DN.txt")
Melnick_25_INFLAMMATORY_RESPONSE.txt <- readLines("25_INFLAMMATORY_RESPONSE.txt")
Melnick_26_RAMALHO_STEMNESS_DN.txt <- readLines("26_RAMALHO_STEMNESS_DN.txt")
Melnick_27_RAMALHO_STEMNESS_UP.txt <- readLines("27_RAMALHO_STEMNESS_UP.txt")
Melnick_28_REACTOME_REGULATION_OF_MITOTIC_CELL_CYCLE.txt <- readLines("28_REACTOME_REGULATION_OF_MITOTIC_CELL_CYCLE.txt")
Melnick_2_AML1566_AraC_DN.txt <- readLines("2_AML1566_AraC_DN.txt")
Melnick_3_DUY_CISG_UP.txt <- readLines("3_DUY_CISG_UP.txt")
Melnick_4_DUY_CISG_DN.txt <- readLines("4_DUY_CISG_DN.txt")
Melnick_5_DIAPAUSE_UP_BOROVIAK.txt <- readLines("5_DIAPAUSE_UP_BOROVIAK.txt")
Melnick_6_BOROVIAK_DIAPAUSE_DN.txt <- readLines("6_BOROVIAK_DIAPAUSE_DN.txt")
Melnick_7_SASP_COPPE.txt <- readLines("7_SASP_COPPE.txt")
Melnick_8_SALDIVAR_ATR_SUPPRESSED_TARGETS.txt <- readLines("8_SALDIVAR_ATR_SUPPRESSED_TARGETS.txt")
Melnick_9_BIOCARTA_NFKB_PATHWAY.txt <- readLines("9_BIOCARTA_NFKB_PATHWAY.txt")
diapause_neg.txt <- readLines("diapause_neg.txt")
diapause_pos_and_neg.txt <- readLines("diapause_pos_and_neg.txt")
diapause_pos.txt <- readLines("diapause_pos.txt")
DTP_sig_150_Down.txt <- readLines("DTP_sig_150_Down.txt")
DTP_sig_150_up.txt <- readLines("DTP_sig_150_up.txt")
Lum_uniq_down.txt <- readLines("Lum_uniq_down.txt")
Lum_uniq_up.txt <- readLines("Lum_uniq_up.txt")
Mes_uniq_down.txt <- readLines("Mes_uniq_down.txt")
Mes_uniq_up.txt <- readLines("Mes_uniq_up.txt")
panDTP_DN.txt <- readLines("new_panDTP_DN.txt")
panDTP_up.txt <- readLines("new_panDTP_up.txt")
mes_DTP_included_DEG_DN.txt <- readLines("new_mes_DTP_included_DEG_DN.txt")
mes_DTP_included_DEG_UP.txt <- readLines("new_mes_DTP_included_DEG_UP.txt")
lum_DTP_included_DEG_DN.txt <- readLines("new_lum_DTP_included_DEG_DN.txt")
lum_DTP_included_DEG_UP.txt <- readLines("new_lum_DTP_included_DEG_UP.txt")
lum_DTP_specific_UP_noCC.txt <- readLines("new_lum_DTP_specific_UP_noCC_.txt")
mes_DTP_specific_UP_noCC.txt <- readLines("new_mes_DTP_specific_UP_noCC_.txt")