Man pages for claraqin/neonMicrobe
Downloading, Pre-processing, and Assembling NEON Soil Microbe Marker Gene Sequence Data
| assign_final | Assign Final Value |
| checkArgsAgainstBatchParams | Check Function Arguments against Batch-Specific Parameters |
| collapseNoMismatch2 | Combine together sequences that are identical up to shifts... |
| combineReadTrackingTables16S | Combine 16S Read-Tracking Tables |
| combineReadTrackingTablesITS | Combine ITS Read-Tracking Tables |
| downloadRawSequenceData | Download NEON Marker Gene Sequencing Raw Data |
| downloadRawSoilData | Alias for downloadSoilData() |
| downloadSequenceMetadata | Download Sequence Metadata |
| downloadSoilData | Download NEON Soil Data Associated with Marker Gene... |
| getBatch | Get Current Processing Batch ID |
| getBatchParam | Get Processing Batch Parameter(s) |
| getN | Get Number of Reads |
| getPairedFastqFiles | Get Paired Fastq Files |
| getSampleName | Get Sample Name from Fastq Filename (DEPRECATED) |
| getTruncationLength | Get Truncation Length |
| listBatches | List Processing Batches |
| loadParams | Load Processing Parameters from File |
| makeDataDirectories | Make Data Directories |
| matchFastqToMetadata | Match Fastq Files to Metadata |
| NEONMICROBE_DIR_BASE | Dynamic Directory Name for Base Directory |
| NEONMICROBE_DIR_BATCHES | Dynamic Directory Name for Processing Batch Outputs |
| NEONMICROBE_DIR_MIDPROCESS | Dynamic Directory Name for Mid-Processing Fastq Files |
| NEONMICROBE_DIR_OUTPUTS | Dynamic Directory Name for Outputs |
| NEONMICROBE_DIR_SEQMETA | Dynamic Directory Name for Sequence Metadata |
| NEONMICROBE_DIR_SEQUENCE | Dynamic Directory Name for Raw Sequence Data |
| NEONMICROBE_DIR_SOIL | Dynamic Directory Name for Soil Data |
| NEONMICROBE_DIR_TAXREF | Dynamic Directory Name for Taxonomic Reference Data |
| NEONMICROBE_DIR_TRACKREADS | Dynamic Directory Name for Read-Tracking Tables |
| newBatch | Create New Processing Batch |
| organizeRawSequenceData | Organize Raw Sequence Data |
| parseParamsFromRownames | Parse Parameter Values from Rownames |
| plotEEProfile | Plot Expected Errors Profile |
| qcMetadata | QC Sequence Metadata |
| qualityFilter16S | Filter 16S Sequences (with metadata) |
| qualityFilterITS | Filter ITS Sequences (with metadata) |
| readSequenceMetadata | Read Sequence Metadata into Function |
| remove_unmatched_files | Remove Unmatched Fastq Files (DEPRECATED) |
| removeUnpairedFastqFiles | Remove Unpaired Fastq Files |
| runDada16S | Run Dada on Paired-End 16S Sequences (with metadata) |
| runDadaITS | Run Dada on R1 ITS Sequences (with metadata) |
| saveParams | Save Processing Parameters to File |
| seqmeta_greatplains_16s | 16S Sequence Metadata for NEON Great Plains Sites |
| seqmeta_greatplains_its | ITS Sequence Metadata for NEON Great Plains Sites |
| seqtab_greatplains_16s | 16S Sequence Abundance Table for NEON Great Plains Sites |
| setBaseDirectory | Set Base Directory for neonMicrobe Workspace |
| setBatch | Switch to Existing Processing Batch |
| setBatchParam | Set Processing Batch Parameter(s) |
| soil_greatplains | Soil Physical and Chemical Properties for NEON Great Plains... |
| trimPrimers16S | Trim Primers from 16S Sequences (with metadata) |
| trimPrimersITS | Trim Primers from ITS Sequences (with metadata) |
| validateIO | Validate Input/Output Arguments to DADA2 Wrappers |
