Man pages for a-thind/PathAnalyser
ER & HER2 Pathway Activity Analysis For Breast Cancer Transcriptomic Datasets
| calculate_accuracy | Accuracy calculation of classification method |
| check_signature_vs_dataset | Validity check in gene signatures and gene expression... |
| classes_pca | PCA plot visualising pathway-based classification of samples... |
| classify_gsva_abs | Classification Using Absolute GSVA Score Thresholds |
| classify_gsva_percent | Sample classification according to pathway activity using a... |
| ER_GEO_microarr | ER microarray data set obtained from GEO |
| ER_SET_sig | ER gene signature |
| ER_TCGA_RNAseq | ER RNA-seq gene expression data set from TCGA |
| gsva_scores_dist | GSVA score density distribution plot |
| HER2_GEO_microarr | HER2 microarray data set obtained from GEO |
| HER2_Smid_sig | HER2 gene signature |
| HER2_TCGA_RNAseq | HER2 RNA-seq gene expression data set from TCGA |
| log_cpm_transform | Log CPM transformation of RNA-seq raw count data by using log... |
| pam50 | Gene signature for ER and HER2 extracted from PAM50 |
| read_expression_data | Reading gene expression data from file |
| read_signature | Reads up-regulated and down-regulated gene signatures from... |
