Man pages for kalganem/creedenzymatic
creedenzymatic
| annotate.gct | Add annotations to a GCT object |
| combine_tools | Combine data for quartile figure |
| creedenzymatic | Runs Creedenzymatic |
| dot-align_matrices | Align the rows and columns of two (or more) matrices |
| dot-append.dim | Append matrix dimensions to filename |
| dot-check_colnames | Check whether 'test_names' are columns in the 'data.frame' df |
| dot-check_dups | Check for duplicates in a vector |
| dot-extract.gct | Exract elements from a GCT matrix |
| dot-fix.datatypes | Adjust the data types for columns of a meta data frame |
| dot-is.wholenumber | Check if x is a whole number |
| dot-merge_with_precedence | Merge two 'data.frame's, but where there are common fields... |
| dot-na_pad_matrix | Pad a matrix with additional rows/columns of NA values |
| dot-parse.gctx | Parse a GCTX file into the workspace as a GCT object |
| dot-parse.gmt | Read a GMT file and return a list |
| dot-parse.gmx | Read a GMX file and return a list |
| dot-parse.grp | Read a GRP file and return a vector of its contents |
| dot-process_ids | Return a subset of requested GCTX row/colum ids out of the... |
| dot-read.gctx.ids | Read GCTX row or column ids |
| dot-read.gctx.meta | Parse row or column metadata from GCTX files |
| dot-subset_to_ids | Do a robust 'data.frame' subset to a set of ids |
| dot-update.gctx | Update the matrix of an existing GCTX file |
| dot-write.gct | Write a GCT object to disk in GCT format |
| dot-write.gctx | Write a GCT object to disk in GCTX format |
| dot-write.gctx.meta | Write a 'data.frame' of meta data to GCTX file |
| dot-write.gmt | Write a nested list to a GMT file |
| dot-write.grp | Write a vector to a GRP file |
| dot-write.tbl | Write a 'data.frame' to a tab-delimited text file |
| extract_top_kinases | Extract Top Kinases |
| GCT-class | An S4 class to represent a GCT object |
| kinome_mp_file | CDRL Complete mapping file (UKA+KRSA+KEA3+PTM-SEA) |
| kinome_mp_file_v1 | CDRL Complete mapping file (UKA+KRSA+KEA3+PTM-SEA) |
| kinome_mp_file_v2 | CDRL Complete mapping file (UKA+KRSA+KEA3+PTM-SEA) |
| kinome_mp_file_v3 | CDRL Complete mapping file (UKA+KRSA+KEA3+PTM-SEA) |
| kinome_mp_file_v4 | CDRL Complete mapping file (UKA+KRSA+KEA3+PTM-SEA) |
| melt.gct | Transform a GCT object in to a long form 'data.table' (aka... |
| merge.gct | Merge two GCT objects together |
| ptk_pamchip_86402_array_layout_ptmsea | CDRL Complete mapping of peptides - used for ptm-sea (PTK... |
| ptk_pamchip_86402_mapping | CDRL Complete mapping of peptides to HGNC symbols (PTK... |
| quartile_figure | Plot quartile Figure |
| rank.gct | Convert a GCT object's matrix to ranks |
| rank_kinases | Rank Kinases based on a score |
| read_kea | Reads a dataframe of Peptides IDs and their Scores and run... |
| read_krsa | Reads and Rank KRSA table |
| read_ptmsea | Reads a dataframe of Peptides IDs and their Scores and run... |
| read_uka | Reads and Rank UKA table |
| reexports | Objects exported from other packages |
| run_kea | Run KEA3 API based on a set of gene symbols |
| run_ptmsea | Run PTM-SEA API using a gct file as input |
| stk_pamchip_87102_array_layout_ptmsea | CDRL Complete mapping of peptides - used for ptm-sea (STK... |
| stk_pamchip_87102_mapping | CDRL Complete mapping of peptides to HGNC symbols (STK... |
| subset.gct | Subset a gct object using the provided row and column ids |
| transpose.gct | Transpose a GCT object |
| uka_db_full | UKA Complete DB mapping File (STK + PTK) |
