| annotate_data | Add peptide/protein annotation to data file. |
| check_order | Maintains specified order of panlibrary data after a call to... |
| compute_hits | For multilibrary enrichment, identify libraries, and identify... |
| compute_polycl | For multilibrary hits data, identify libraries, and call... |
| compute_promax | For multilibrary hits data, identify libraries, and call... |
| compute_prosum | For multilibrary data, identify libraries, and call... |
| define_plan | Initialize and return drake_plan object. New for github drake... |
| emphasize_hit_data | emphasize_hit_data |
| emphasize_hit_data_list | emphasize_hit_data_list |
| gather_samples | read in multiple input files and extract specified columns |
| getparam | Function to retreive value of parameter from param name. |
| independence_filter | Compute independent hits usingg network graphing. |
| library_polycl | For one peptide library, identify proteins from annotation... |
| library_promax | For one peptide library, identify proteins from annotation... |
| library_prosum | For one peptide library, identify proteins from annotation... |
| merge_annotations | Merge epitopefindr fields from library annotation files |
| pbar | Wrapper for txtProgressBar with some defualt settings. |
| phipmake | phipmake: PhIP-seq Data Analysis Pipeline. |
| prepare_avarda_names | swap out u_pep_id names for older pep_id names to improve... |
| prepare_blast_pairs | Convert BLAST+ alignment table to two outputs. First, a full... |
| protein_polycl | Take data frame input and calculate the polyclonal score in... |
| protein_promax | Take data frame input and calculate the maximum value in each... |
| protein_prosum | Take data frame input and calculate the sum of values in each... |
| read_annot | Read annotation file based on md path and library name. |
| read_annot_list | Read annotation files based on library names and metadata... |
| read_pairs | Read BLAST pairs file based on md path and library name. |
| read_pairs_list | Read blast alignment pair files based on library names and... |
| run_epitopefindr | Assemble hit files and call epitopefindr |
| split_data | Separate multilibrary peptide data into a phipmake list. |
| subset_data | Pull out specific sublibrary data from a larger data frame... |
| trimDictionary | trim alignment dictionary to not include self alignments or... |
| u_pep_id_to_libnames | Take ids of the form HumanLarma_000_<sequence> and returns... |
| write_data | A wrapper for data.table::fwrite to write file to drive. |
| write_drake_params | write_drake_params |
