Man pages for biodiversity-aq/OmicsMetaData
OmicsMetaData: an R-package for interoperable and re-usable biodiversity 'omics (meta)data
| check.valid.metadata.DwC | validate a DarwinCore class object |
| check.valid.MIxS.metadata | validate a MIxS.metadata class object |
| combine.data | merge MIxS.metadata objects |
| combine.data.frame | merge dataframes |
| commonTax.to.NCBI.TaxID | Convert a taxon name to an NCBI taxon ID |
| coordinate.to.decimal | convert a coordinate in degrees to decimal |
| dataQC.completeTaxaNamesFromRegistery | Complete a list of taxonomic names with information form an... |
| dataQC.dateCheck | find and standardize dates in a dataframe |
| dataQC.DwC | format dataframes into a DarwinCore object |
| dataQC.DwC_general | Quality Controll (QC) for DarwinCore data |
| dataQC.eventStructure | check a dataset for an event-structure |
| dataQC.findNames | find the samplenames in a dataset |
| dataQC.generate.footprintWKT | generate a footprintWKT from coordinates |
| dataQC.guess.env_package.from.data | make an educated guess to the MIxS environmental package of a... |
| dataQC.LatitudeLongitudeCheck | find and standardize geographic coordinates in a dataframe |
| dataQC.MIxS | format dataframes into a MIxS object |
| dataQC.taxaNames | perform a quality control onf taxonomic names |
| dataQC.TaxonListFromData | extract the finest resolution taxonomy from a dataset |
| dataQC.TermsCheck | make variable names in a dataset to comply to a standrad |
| download.sequences.INSDC | Download open sequence data to your computer. |
| DwC.event-class | an S4 class to document data formated in the DarwinCore event... |
| DwC.occurrence-class | an S4 class to document data formated in the DarwinCore... |
| eMoF.to.wideTable | convert a DarwinCore extended Measurement or Fact (eMoF) file... |
| ENA_allowed_terms | terms accepted by ENA-EMBL |
| ENA_checklistAccession | checklist accessions accepted by ENA-EMBL |
| ENA_geoloc | geographic locations names accepted by ENA-EMBL |
| ENA_instrument | instrument names accepted by ENA-EMBL |
| ENA_select | experiment names accepted by ENA-EMBL |
| ENA_strat | sequencing method names accepted by ENA-EMBL |
| FileNames.to.Table | collect the names of sequence files in a folder |
| find.dataset | find a column in a dataframe |
| get.BioProject.metadata.INSDC | Fetch BioProject metadata |
| get.boundingBox | get a rectagular bounding box from a set of coordinates |
| get.ENAName | convert a MIxS term into it's ENA variant |
| get.insertSize | Get the sequence length of the first sequence in a fastq or... |
| get.sample.attributes.INSDC | Downloads all sequence sample attributes |
| MIxS.metadata-class | an S4 class to document data formated in the MIxS standard |
| multi.warnings | collect warning messages troughout a running function |
| OmicsMetaData | OmicsMetaData: A package with tools to format and standardize... |
| OmicsMetaData.help | function to navigate through package |
| prep.metadata.ENA | Formatting metadata and environmental data to upload to... |
| renameSequenceFiles | renames sequence files in a directory |
| show-DwC.event-method | the show method for DwC.event |
| show-DwC.occurrence-method | the show method for DwC.occurrence |
| show-MIxS.metadata-method | the show method for MIxS.metadata |
| sync.metadata.sequenceFiles | Check if all samples in a dataframe have sequence data |
| TaxIDLib | non-exaustive library with some common INSDC taxon IDs |
| term.definition | Find the MIxS or DarwinCore standard term and definition of a... |
| TermsLib | central library with mapped terms of DwC, MIxS and... |
| TermsSyn | library with synonyms for standard terms |
| TermsSyn_DwC | library with synonyms for DwC terms |
| wideTable.to.eMoF | convert dataframe to a DarwinCore extended Measurement or... |
| wideTab.to.hierarchicalTab | convert a wide table to hierarchical table |
| write.MIxS | Data Output: write a MIxS.metadata class object to a CSV file |
