API for SQMtools
Analyze Results Generated by the 'SqueezeMeta' Pipeline
| Global functions | |
|---|---|
| .onAttach | Source code |
| CheckMProkaryote | Man page |
| Hadza | Man page |
| MGKOs | Man page |
| MGOGs | Man page |
| Npercent | Source code Source code |
| RecA | Man page |
| SQM_to_microeco | Man page Source code |
| SQM_to_phyloseq | Man page Source code |
| SQMtoSQMlite | Source code |
| USiCGs | Man page |
| `[.generic.data.table` | Source code |
| aggregate_bin | Source code |
| aggregate_fun | Source code |
| aggregate_taxa | Source code |
| as.data.frame.generic.data.table | Source code |
| as.data.table.generic.data.table | Source code |
| as.matrix.generic.data.table | Source code |
| check.samples | Source code |
| combineSQM | Man page Source code |
| combineSQM_ | Source code |
| combineSQMlite | Man page Source code |
| combineSQMlite_ | Source code |
| create_bin | Man page Source code |
| dimnames.generic.data.table | Source code |
| exportBins | Man page Source code |
| exportContigs | Man page Source code |
| exportKrona | Man page Source code |
| exportORFs | Man page Source code |
| exportPathway | Man page Source code |
| exportSeqs | Source code |
| exportTable | Man page Source code |
| file.exists.zip | Source code |
| find_redundant_contigs | Man page Source code |
| generic.table | Source code |
| get.bin.abunds | Source code |
| get.bin.stats | Source code |
| get_counts | Source code |
| get_median_single_copy_cov | Source code |
| has_copy_numbers | Source code |
| list.files.zip | Source code |
| loadSQM | Man page Source code |
| loadSQM_ | Source code |
| loadSQMlite | Man page Source code |
| merge_numeric_matrices | Source code |
| mostAbundant | Man page Source code |
| mostVariable | Man page Source code |
| most_abundant_row | Source code |
| named.unique | Source code |
| open_conn_zip | Source code |
| plotBars | Man page Source code |
| plotBins | Man page Source code |
| plotFunctions | Man page Source code |
| plotHeatmap | Man page Source code |
| plotTaxonomy | Man page Source code |
| prepare_export_tables | Source code |
| print.generic.data.table | Source code |
| print.summary.SQM | Source code |
| print.summary.SQMbunch | Source code |
| print.summary.SQMlite | Source code |
| rbind.generic.data.table | Source code |
| read.generic.table.zip | Source code |
| read.namedvector | Source code |
| read.namedvector.zip | Source code |
| remove_contigs_from_bin | Man page Source code |
| rowMaxs | Man page Source code |
| rowMedians | Source code |
| rowMins | Man page Source code |
| seqvec2fasta | Man page Source code |
| subsetBins | Man page Source code |
| subsetBins_ | Source code |
| subsetContigs | Man page Source code |
| subsetContigs_ | Source code |
| subsetDispatch | Source code |
| subsetFun | Man page Source code |
| subsetFun_ | Source code |
| subsetORFs | Man page Source code |
| subsetORFs_ | Source code |
| subsetRand | Man page Source code |
| subsetSamples | Man page Source code |
| subsetTax | Man page Source code |
| subsetTax_ | Source code |
| summary.SQM | Man page Source code |
| summary.SQMbunch | Man page Source code |
| summary.SQMlite | Man page Source code |
