Man pages for serratus-bio/tantalus
R Data Exploration for Serratus
| Atys | SraRunInfo |
| extracSrting | extract strings from the heading |
| extractNumber | extract numbers from the heading |
| familyPctID | Plot a histogram of percentage identity for a given family |
| familyScore | Plot a histogram of scores for a given family |
| familyScorPctID | Plot a scatterplot/histogram of percentage identity vs family... |
| getBAM | Downloads an SRA accession from an experiment S3 directory 1)... |
| getHeatmap | getHeatmap |
| getLoadedSummaryFiles | getLoadedSummaryFiles |
| getReference | Downlaods a Serratus Reference Sequence and associated... |
| getSraRunInfo | Downloads an SRA runInfo file and parses into a RunInfo S4... |
| getSummary | Downloads an S3 directory of Serratus .summary files to local... |
| getSummaryFiles | getSummaryFiles Downloads a specified list of summary files... |
| parseAtys | Parse folder with Atys objects and retreive info about number... |
| parseFamilies | Extract a family information from a file line |
| parseHits | Extract an organism information from a file line |
| parseSummaryFiles | Parse specified summary files into compressed fst data frames... |
| pctidInScoreIntervals | Plot a histogram of pctid for the given family within family... |
| readDFs | readDFs |
| readDfSQL | readDfSQL |
| readHeader | Extract header information |
| readHits | Extract all family or organism information from the provided... |
| readSerratus | Parse list of files into S4 Serratus class |
| readSra | read SRA identifiers from provided files |
| readSraRunInfo | Parse a SraRunInfo csv file into a clean data.frame and... |
| scoreInPctidIntervals | Plot a histogram of family score for the given family within... |
| seqReference | seqReference |
| Serratus-class | An S4-Object definition for storing Serratus output data |
| SraRunInfo | SraRunInfo |
| tantalus | tantalus package |
