.appendSignatures	dot-appendSignatures
.build_mut_matrices	dot-build_mut_matrices
.create_mut_matrix	dot-create_mut_matrix
add_iobr_mirror	add_iobr_mirror
add_riskscore	add_riskscore
anno_eset	anno_eset
assimilate_data	assimilate_data
batch_cor	batch_cor
batch_kruskal	batch_kruskal
batch_pcc	batch_pcc
batch_sig_surv_plot	batch_sig_surv_plot
batch_surv	batch_surv
batch_wilcoxon	batch_wilcoxon
best_cutoff	best_cutoff
best_cutoff2	best_cutoff2
BinomialAUC	BinomialAUC
BinomialModel	BinomialModel
CalculatePref	CalculatePref
CalculateTimeROC	CalculateTimeROC
calculate_break_month	calculate_break_month
calculate_sig_score	calculate_sig_score
calculate_sig_score_integration	calculate_sig_score_integration
calculate_sig_score_pca	calculate_sig_score_pca
calculate_sig_score_ssgsea	calculate_sig_score_ssgsea
calculate_sig_score_zscore	calculate_sig_score_zscore
cell_bar_plot	cell_bar_plot
check_cancer_types	check_cancer_types
check_eset	check_eset
CIBERSORT	CIBERSORT
clear_iobr_cache	clear_iobr_cache
combine_pd_eset	combine_pd_eset
Construct_con	Construct_con
ConvertRownameToLoci	ConvertRownameToLoci
CoreAlg	CoreAlg
count2tpm	count2tpm
creat_folder	creat_folder
DClsei	DClsei
DCrr	DCrr
deconvolute_quantiseq.default	deconvolute_quantiseq.default
deconvolute_timer.default	deconvolute_timer.default
deconvo_cibersort	deconvo_cibersort
deconvo_epic	deconvo_epic
deconvo_estimate	deconvo_estimate
deconvo_ips	deconvo_ips
deconvo_mcpcounter	deconvo_mcpcounter
deconvo_quantiseq	deconvo_quantiseq
deconvo_ref	deconvo_ref
deconvo_timer	deconvo_timer
deconvo_tme	deconvo_tme
deconvo_xcell	deconvo_xcell
design_mytheme	design_mytheme
doPerm	doPerm
download_iobr_data	download_iobr_data
DrawQQPlot	DrawQQPlot
Enet	Enet
enrichment_barplot	enrichment_barplot
EPIC	EPIC
eset_distribution	eset_distribution
estimateScore	estimateScore
exact_pvalue	exact_pvalue
extract_sc_data	extract_sc_data
feature_manipulation	feature_manipulation
feature_select	feature_select
filterCommonGenes	filterCommonGenes
find_markers_in_bulk	find_markers_in_bulk
find_mutations	find_mutations
find_outlier_samples	find_outlier_samples
find_variable_genes	find_variable_genes
fixMixture	fixMixture
format_msigdb	format_msigdb
format_signatures	format_signatures
generateRef	generateRef
generateRef_DEseq2	generateRef_DEseq2
generateRef_limma	generateRef_limma
generateRef_rnaseq	generateRef_rnaseq
generateRef_seurat	generateRef_seurat
GetFractions.Abbas	GetFractions.Abbas
getHRandCIfromCoxph	getHRandCIfromCoxph
GetOutlierGenes	GetOutlierGenes
get_cols	get_cols
get_cor	get_cor
get_cor_matrix	get_cor_matrix
get_default_mirrors	get_default_mirrors
get_sig_sc	get_sig_sc
gsva_use_new_api	gsva_use_new_api
high_var_fea	high_var_fea
imvigor210_pdata	imvigor210_pdata
iobr_cor_plot	iobr_cor_plot
iobr_deconvo_pipeline	iobr_deconvo_pipeline
iobr_deg	iobr_deg
iobr_pca	iobr_pca
ipsmap	ipsmap
IPS_calculation	IPS_calculation
lasso_select	lasso_select
limma.dif	limma.dif
list_github_datasets	list_github_datasets
list_iobr_mirrors	list_iobr_mirrors
load_data	load_data
log2eset	log2eset
LR_cal	LR_cal
makeQN	makeQN
make_mut_matrix	make_mut_matrix
mapbw	mapbw
mapcolors	mapcolors
mapGenes	mapGenes
MCPcounter.estimate	MCPcounter.estimate
merge_duplicate	merge_duplicate
merge_duplicates	merge_duplicates
merge_eset	merge_eset
microenvironmentScores	microenvironmentScores
mouse2human_eset	mouse2human_eset
null_models	null_models
outputGCT	outputGCT
output_sig	output_sig
palettes	palettes
parallel_doperm	parallel_doperm
ParseInputExpression	ParseInputExpression
patterns_to_na	patterns_to_na
pdata_stad	pdata_stad
percent_bar_plot	percent_bar_plot
pie_chart	pie_chart
PlotAUC	PlotAUC
plotPurity	plotPurity
PlotTimeROC	PlotTimeROC
ProcessingData	ProcessingData
PrognosticAUC	PrognosticAUC
PrognosticModel	PrognosticModel
PrognosticResult	PrognosticResult
quanTIseq	quanTIseq
quantiseq_helper	quantiseq_helper
random_strata_cells	random_strata_cells
rawEnrichmentAnalysis	rawEnrichmentAnalysis
rbind_iobr	rbind_iobr
RegressionResult	RegressionResult
RemoveBatchEffect	RemoveBatchEffect
remove_batcheffect	remove_batcheffect
remove_duplicate_genes	remove_duplicate_genes
remove_names	remove_names
reset_iobr_mirrors	reset_iobr_mirrors
roc_time	roc_time
scaleCounts	scaleCounts
scale_matrix	scale_matrix
select_method	select_method
signature_collection	signature_collection
signature_score_calculation_methods	signature_score_calculation_methods
sigScore	sigScore
sig_box	sig_box
sig_box_batch	sig_box_batch
sig_forest	sig_forest
sig_group	sig_group
sig_gsea	sig_gsea
sig_heatmap	sig_heatmap
sig_pheatmap	sig_pheatmap
sig_roc	sig_roc
sig_surv_plot	sig_surv_plot
spillOver	spillOver
SplitTrainTest	SplitTrainTest
stad_group	stad_group
subgroup_data	subgroup_data
subgroup_survival	subgroup_survival
surv_group	surv_group
tcga_rna_preps	tcga_rna_preps
tcga_stad_pdata	tcga_stad_pdata
test_for_infiltration	test_for_infiltration
timer_available_cancers	timer_available_cancers
timer_info	timer_info
tme_cluster	tme_cluster
tme_deconvolution_methods	tme_deconvolution_methods
Top_probe	Top_probe
transformScores	transformScores
transform_data	transform_data
xCellAnalysis	xCellAnalysis
xCellSignifcanceBetaDist	xCellSignifcanceBetaDist
xCellSignifcanceRandomMatrix	xCellSignifcanceRandomMatrix
