Man pages for CUGBF/deidentifiedDB
Utility to Manage Clemson University COVID-19 Surveillance Data
| assign_mode | Assign most common user-provided value in case of discrepancy... |
| build_us_zip | Build a tibble with US Zip Code Information |
| compile_biorepo | Compile Biorepository for inclusion in deidentifiedDB... |
| compile_diagnostics_data | Compile weekly diagnostics data from REDDI before appending... |
| compile_genbank | Compile Sequence and Metadata for GenBank Submission |
| compile_genbank_table | Compile GenBank Submission Information for Appending to... |
| compile_sc_data | Compile Sample Collection Data for deidentifiedDB SQLite... |
| compile_viralrecon | Compile Results from nf-core/viralrecon for inclusion in... |
| compute_ct | Calculate Mean and Median Ct values |
| create_fasta_genbank | Create DNAStringSet containing consensus sequences |
| detect_control | Label samples on whether they were used as controls |
| do_prelim_tidy_sc | Preliminary Tidy Up of the Demographics and Sample Collection... |
| get_ct | Get Ct values for Query Testkit IDs from Diagnostic Testing |
| get_daily_diagnostics | Get Daily Diagnostics Counts |
| get_global_entities | Build a Vector containing names of US and International... |
| get_metadata_genbank | Compile Metadata for GenBank Submission |
| get_mode | Find Mode |
| get_nextclade_distribution | Get Nextclade Distribution of Sequenced Samples |
| get_pangolin_distribution | Get Pangolin Lineage Distribution of Sequenced Samples |
| get_positivity | Compute Weekly Test Positivity Rate (TPR) |
| get_redundant_samples | Get Testkit IDs of redundant COVID-19 positive samples... |
| get_sc_wo_redundant | Get COVID-19 positive samples after excluding redundant... |
| get_us_entities | Build a Vector containing US State Codes |
| inspect_patient | Inspect deidentified demographics data for each patient |
| lookup_zip_code | Compile Reference Location Information |
| polish_diagnostics | Reorganize Diagnostics data |
| polish_sc | Polish Sample Collection Tibble |
| prepare_demographics_sc | Transform COVID19 Sample Collection and deidentified... |
| pull_demographics | Extract demographics data from table returned by... |
| pull_sc | Extract sample collection data from table returned by... |
| read_demographics_csv | Read CSV file containing COVID19 Sample Collection and... |
| read_diagnostics_csv | Read CSV file containing COVID19 Diagnostics Data from REDDI |
| tidy_up_birth_year | Format the column containing birth year to remove invalid... |
| tidy_up_ct | Format the columns containing Ct values to remove non-numeric... |
| tidy_up_location | Tidy Up Location Information |
| tidy_up_race | Tidy up the 'race' column |
| tidy_up_zip | Remove non-numeric characters from zip codes and extract 5... |
| week_dates_info | Tibble with Collection Week Info |
