Man pages for aeolianine/CRCsubtyping
Subtyping Colorectal Expression Data
| CMScolors | Hard-code the CMS subtype colors, so that they can be reused... |
| combat_to_ref | Normalize a given dataset to a reference dataset, using... |
| compare_RF_to_SSP | Print quick comparison stats on the consensus between the RF... |
| compare_to_training_labels | Compare the subtypeCMS.RF assigned nearest subtypes to the RF... |
| entrez2symbol | Convert Entrez ID to gene symbols. Note: uses the... |
| get_GSE33113_synapse | Downloads the frozen-RMA-normalized of the GSE33113... |
| get_synapse_table | This functions shows how to download data from Synapse. The... |
| get_TCGA_synapse | Download the merged (Illumina -HiSeq and -GA ) TCGA... |
| inmf_signatures_entrez | iNMF (Schlicker) subtypes signatures. |
| inmf_signatures_sym | iNMF (Schlicker) subtypes signatures. |
| intersect_signature | Intersect a signature with the data's available genes |
| load_CMS_genes | Load random-forest genes from CMS classifier, stored in... |
| load_sadanandam_signature | Loading Sadanandam's subtype signatures. |
| load_schlicker_signature | Loading the Schlicker (iNMF) subtype signatures from the... |
| plot_mCombat_effect | Visualize the effect that M-combat has on normalization. Uses... |
| plotSadanandamSubtypeCentroids | Plotting the scores from the signature table... |
| plotSubtypesCMS.RF | Visualization of the results of subtypeCMS.RF(). Creates... |
| plotSubtypesCMS.SSP | Visualization of the results of subtypeCMS.SSP(). Creates... |
| sadanandam_786_genes | The 786 genes identified in the PAM analysis by Sadandandam... |
| subtypeCMS.RF | Applying the random forest classifier of the CMS consortium... |
| subtypeCMS.SSP | Applying the single-sample classifier of the CMS consortium... |
| symbol2entrez | Convert Entrez ID to gene symbols. Note 1: Uses the... |
