Man pages for phac-nml/pavian
Visualize and analyze metagenomics classification results
| alignmentModule | Server part of alignment module |
| alignmentModuleUI | UI part of alignment module |
| beautify_colnames | Beautify colnames |
| comparisonModule | Server part of comparison module |
| comparisonModuleUI | UI part of the comparison module |
| dashboardUI | Function building dashboard UI, used in Shiny app |
| dataInputModule | Server part of pavian data input module. |
| dataInputModuleUI | UI part of pavian data input module |
| filter_cladeReads | Remove specified taxa or whole clades this function removes... |
| filter_taxa | Filter taxon |
| filter_taxon | Filter lines from a kraken report result based on the... |
| get_nreads | Get number of aligned reads from a bam file |
| get_pileup | Get the pileup-statistics from a bam file using Rsamtools |
| get_seqlengths | Get sequence lengths from a bam file |
| humanreadable | Make a number human readable |
| load_or_create | Load a file from a cache directory, or create and save it |
| merge_reports | Merge report files into a wide format, with column(s) for... |
| merge_reports2 | Merge report files into a wide format, with column(s) for... |
| normalize | Helper function to normalize data |
| pavianServer | Pavian server function |
| plot_pileup | Plot a pileup |
| read_report | Read Kraken-style and MetaPhlAn reports |
| read_report2 | Read kraken or centrifuge-style report |
| read_reports | Read metagenomics classification results ('reports'), with... |
| read_sample_data | Read sample definitions from a directory |
| read_server_directory1 | Search for classification results in a directory and its... |
| reportOverviewModule | Shiny modules to display an overview of metagenomics reports |
| reportOverviewModuleUI | UI part of report overview module |
| robust_zscore | Calculate robust z-score on matrix |
| runApp | Run Pavian web interface |
| sampleModule | Server part for sample module |
| sampleModuleUI | UI part for sample module |
| summarize_report | Summarize the result of a metagenomics report |
| summarize_reports | Summarize list of reports |
| zero_if_na | Helper function that sets NAs to zeros in a supplied... |
