Man pages for xqzou/MMRDetect
Mutational Signature-based Classifier for Detecting Mismatch Repair Deficiency in Tumors
| Calculae_Cossim_catalogue_RepIndel | Compute cosine similarity between one sample indel profile... |
| cos_similarity | Compute cosine similarity between two vectors |
| findsmallestrep | This finds the smallest repeating subunit of the deletion |
| GenCatalogue | Generate 96 channel catalogue for substitutions |
| Generate_CossimVector_SingleSample_RepIndel | Compute cosine similarity between one sample and MMR gene... |
| gen_indelmuttype_MMRD | Generate 45 channel indel catalogue |
| get_all_factors | get all factors of an integer |
| indel_classifier | Generate indel catalogue for substitutions |
| mhcaller | micro-homology between the deleted sequence and 3' sequence... |
| mh_indel_v2 | find mh indels |
| MMRDclassifier | Default MMRDclassifier. |
| MMRDetect.classify | MMRDetect classifier |
| MMRDetect.compute.Repindelcatalogue.similarity | Compute cosine similarity between given indel profile and MMR... |
| MMRDetect.compute.Repindel.similarity | Compute cosine similarity between given indel profile and MMR... |
| MMRDetect.compute.subcatalogue.exposure | Compute substitution signature exposure for a given catalogue |
| MMRDetect.compute.subcatalogue.similarity | Compute cosine similarity between given sub profiles and MMR... |
| MMRDetect.compute.variables | Compute variables for MMRDetect |
| MMRDetect.train | Train MMRDetect |
| MMRKO_indelsig | Indel signature of MMR gene knockouts |
| MMRKO_subsig | Substitution signature of MMR gene knockouts |
| SigCossim | Compute cosine similarity between a set of catalogue and a... |
| subtype_indel_mmrd | classify indels |
