Files in a-thind/PathAnalyser
ER & HER2 Pathway Activity Analysis For Breast Cancer Transcriptomic Datasets
.Rd2pdf9125/Rd2.tex
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
PathAnalyser.Rproj
R/calculate_accuracy.R
R/classes_pca.R
R/classification.R
R/data.R
R/input.R
R/qc_and_pre-processing.R
R/utils.R
README.md
data/ER_GEO_microarr.rda
data/ER_SET_sig.rda
data/ER_TCGA_RNAseq.rda
data/HER2_GEO_microarr.rda
data/HER2_Smid_sig.rda
data/HER2_TCGA_RNAseq.rda
data/pam50.rda
demo/00Index
demo/ER-activity-PathAnalyser.R
demo/HER2-activity-PathAnalyser.R
inst/extdata/ER_toydata_RNAseq.txt
inst/extdata/ESR1_DN.v1_DN.grp
inst/extdata/ESR1_UP.v1._UP.grp
inst/extdata/HER2_toydata_RNAseq.txt
inst/extdata/SMID_BREAST_CANCER_ERBB2_DN.grp
inst/extdata/SMID_BREAST_CANCER_ERBB2_UP.grp
inst/extdata/Sample_labels.txt
inst/extdata/Toy_dataset_HER2.txt
inst/extdata/toy_data.txt
inst/referenceManual/PathAnalyser.pdf
man/ER_GEO_microarr.Rd
man/ER_SET_sig.Rd
man/ER_TCGA_RNAseq.Rd
man/HER2_GEO_microarr.Rd
man/HER2_Smid_sig.Rd
man/HER2_TCGA_RNAseq.Rd
man/calculate_accuracy.Rd
man/check_signature_vs_dataset.Rd
man/classes_pca.Rd
man/classify_gsva_abs.Rd
man/classify_gsva_percent.Rd
man/gsva_scores_dist.Rd
man/log_cpm_transform.Rd
man/pam50.Rd
man/read_expression_data.Rd
man/read_signature.Rd
pathanalyser.png
tests/testthat.R
tests/testthat/ER_classes_df.default_actual.rda
tests/testthat/normalized_ER_TCGA_RNAseq.rda
tests/testthat/testClassify.R
vignettes/.gitignore
vignettes/ERBB2_UP.V1_UP.v7.5.1.gmt.png
vignettes/ESR1_DN.v1_DN.grp
vignettes/ESR1_UP.v1._UP.grp
vignettes/HER2_PAM50.png
vignettes/HER2_up.png
vignettes/PathAnalyser.Rmd
vignettes/Sample_labels.txt
vignettes/algorithm_diagram.png
vignettes/expr_dataset_example.png
vignettes/grp_file.png
vignettes/lumA_pam50.png
vignettes/lumB_pam50.png
vignettes/pca_plot.png
vignettes/toy_data.txt
vignettes/workflow_flowchart.png
