API for IOBR/IOBR
Immune Oncology Biological Research

Global functions
.onAttach	Source code
.onLoad	Source code
BinomialAUC	Man page Source code
BinomialModel	Man page Source code
CIBERSORT	Man page Source code
CalculatePref	Man page Source code
CalculateTimeROC	Man page
Construct_con	Man page Source code
ConvertRownameToLoci	Man page Source code
CoreAlg	Man page Source code
DClsei	Source code
DCrr	Source code
DrawQQPlot	Man page Source code
EPIC	Man page Source code
Enet	Man page Source code
GetFractions.Abbas	Man page Source code
GetOutlierGenes	Man page
IPS_calculation	Man page Source code
LR_cal	Man page Source code
MCPcounter.estimate	Source code
ParseInputExpression	Man page Source code
PlotAUC	Man page Source code
PlotTimeROC	Man page
ProcessingData	Man page Source code
PrognosticAUC	Man page
PrognosticModel	Man page Source code
PrognosticResult	Man page Source code
RegressionResult	Man page Source code
RemoveBatchEffect	Man page Source code
SplitTrainTest	Man page Source code
TimerINFO	Man page Source code
Top_probe	Man page Source code
anno_eset	Man page Source code
appendSignatures	Source code
assimilate_data	Man page Source code
batch_cor	Man page Source code
batch_kruskal	Man page Source code
batch_pcc	Man page Source code
batch_sig_surv_plot	Man page Source code
batch_surv	Man page Source code
batch_wilcoxon	Man page Source code
best_cutoff	Man page Source code
best_cutoff2	Man page Source code
break_month	Man page Source code
calculate_sig_score	Man page Source code
calculate_sig_score_integration	Man page Source code
calculate_sig_score_pca	Man page Source code
calculate_sig_score_ssgsea	Man page Source code
calculate_sig_score_zscore	Man page Source code
cell_bar_plot	Man page Source code
check_cancer_types	Man page Source code
check_eset	Man page Source code
combine_pd_eset	Man page Source code
count2tpm	Man page Source code
creat_folder	Man page Source code
deconvo_cibersort	Man page Source code
deconvo_epic	Man page Source code
deconvo_estimate	Man page Source code
deconvo_ips	Man page Source code
deconvo_mcpcounter	Man page Source code
deconvo_quantiseq	Man page Source code
deconvo_ref	Man page Source code
deconvo_timer	Man page Source code
deconvo_tme	Man page Source code
deconvo_xcell	Man page Source code
deconvolute_quantiseq.default	Man page Source code
deconvolute_timer.default	Man page Source code
design_mytheme	Man page Source code
doPerm	Man page Source code
enrichment_barplot	Man page Source code
eset_distribution	Man page Source code
estimateScore	Man page Source code
exact_pvalue	Man page Source code
extract_sc_data	Man page Source code
feature_manipulation	Man page Source code
feature_select	Man page Source code
filterCommonGenes	Man page Source code
find_markers_in_bulk	Man page Source code
find_mutations	Man page Source code
find_outlier_samples	Man page Source code
find_variable_genes	Man page Source code
fixMixture	Source code
format_msigdb	Man page Source code
format_signatures	Man page Source code
generateRef	Man page Source code
generateRef_DEseq2	Man page Source code
generateRef_limma	Man page Source code
generateRef_rnaseq	Man page Source code
generateRef_seurat	Man page Source code
getHRandCIfromCoxph	Man page Source code
get_cols	Man page Source code
get_cor	Man page Source code
get_cor_matrix	Man page Source code
get_sig_sc	Man page Source code
high_var_fea	Man page Source code
iobr_cor_plot	Man page Source code
iobr_deconvo_pieline	Man page Source code
iobr_deg	Man page Source code
iobr_pca	Man page Source code
ipsmap	Man page
lasso_select	Man page Source code
limma.dif	Man page Source code
log2eset	Man page Source code
makeQN	Source code
make_mut_matrix	Man page Source code
mapGenes	Source code
mapbw	Man page
mapcolors	Man page
merge_duplicate	Man page Source code
merge_duplicates	Man page Source code
merge_eset	Man page Source code
microenvironmentScores	Man page Source code
mouse2human_eset	Man page Source code
outputGCT	Man page Source code
output_sig	Man page Source code
palettes	Man page Source code
percent_bar_plot	Man page Source code
pie_chart	Man page Source code
plotPurity	Man page Source code
quanTIseq	Source code
quantiseq_helper	Man page
rawEnrichmentAnalysis	Man page Source code
rbind_iobr	Man page Source code
remove_batcheffect	Man page Source code
remove_duplicate_genes	Man page Source code
remove_names	Man page Source code
roc_time	Man page Source code
scaleCounts	Man page Source code
scale_matrix	Man page Source code
select_method	Man page Source code
sigScore	Man page Source code
sig_box	Man page Source code
sig_box_batch	Man page Source code
sig_forest	Man page Source code
sig_gsea	Man page Source code
sig_heatmap	Man page Source code
sig_pheatmap	Man page Source code
sig_roc	Man page Source code
sig_surv_plot	Man page Source code
signature_score_calculation_methods	Man page
spillOver	Man page Source code
subgroup_survival	Man page Source code
surv_group	Man page Source code
tcga_rna_preps	Man page Source code
test_for_infiltration	Source code
timer_available_cancers	Man page
tme_cluster	Man page Source code
tme_deconvolution_methods	Man page
transformScores	Man page Source code
transform_data	Man page Source code
xCellAnalysis	Man page Source code
xCellSignifcanceBetaDist	Man page Source code
xCellSignifcanceRandomMatrix	Man page Source code