| archiveDatabase | pull entire database (not counts) and save to output_dir for... |
| calculateGeneWiseMedians | calculate medians across rows of dataframe |
| calculateRLE | calculate RLE of a numeric dataframe |
| connectToDatabase | Connect to a remote postgresql database |
| createBamPath | create a bam path |
| createEnvPertSet | filter combined_df for environmental perturbation sample set |
| createIgvBatchscript | create IGV viewer batch script (single range, as many tracks... |
| createInductionSetTally | create 90 minute induction set tally |
| createNfCorePipelineSampleSheet | create nf-co sample sheet |
| createNinetyMinInductionModelMatrix | Create the libraryProtocol + libraryDate model matrix with... |
| createNinetyMinuteInductionSet | The current definition of the 90 minute induction dataset,... |
| createNinetyMinuteInductionWithDoubles | The current definition of the 90 minute induction dataset,... |
| createQCdatabase | create a sqlite database to hold the 'custom' qc data |
| database_colnames | set global variables, mostly as a hack to make the tidyverse... |
| database_info | URLS to active databases |
| deseqObjectWithProtocolSpecificSizeFactors | create deseq object with protocol specific size factors |
| determineLibraryStrandedness | from the metadata libraryProtocol column, determine the... |
| examineSingleGroupWithLibDateSizeFactors | temporary function to examine only PBS samples, eg |
| featureGRanges | Given a GenomicFeatures annotation_db and a gene_id, extract... |
| fltrLowReplicateParams | filter low replicate parameters from metadata |
| getBamIndexPath | helper function to add .bai to bam path |
| getMetadata | Get the combined metadata as a tibble from a remote database |
| getRawCounts | Get combined raw counts |
| getRunNumberLeadingZero | correct run number to add leading zero where approprirate |
| getUserAuthToken | get (via a http POST request) your user authentication token... |
| grant_df | the 2016 grant summary represented as a dataframe |
| graphYeastTimeCourse | Plot time vs normalized counts of a given gene over n... |
| is_integer64 | Test if value is datatype integer64 |
| isNumeric | test if argument is numeric |
| listTables | list tables in databse |
| loadAnnotationDatabase | Read in annotationbi tx_db |
| localView | To view a data.frame / data.table in LibreOffice Calc |
| moveNfCoFastqFiles | move fastq files from lts to scratch for nf-co/rnaseq... |
| parseComparatives | parse text comparative sentence |
| patchTable | PATCH entries in database table |
| plotCoverageOverLocus | plot coverage over locus |
| postCounts | post counts to database |
| postFastqSheet | post new fastq sheet to database |
| postQcSheet | post new qc sheet to database |
| postTable | Post a table to the database |
| proteinCodingCount | get total protein coding count from count dataframe |
| qualityAssessmentFilter | filter for manual passes (overrides auto fail) and automatic... |
| readInData | read in columnar data |
| removeOneRedoIqr | progressively remove max IQR sample and recalculate |
| removeParameterEffects | remove some effects from the counts |
| rleByReplicateGroup | calculate RLE by replicate groups |
| rlePlot | plot RLE for a given column filter |
| rlePlotCompareEffectRemoved | plots output of rleSummaryByReplicateGroup |
| rlePlot_helper | the actual plotting function for rlePlot |
| rleSummary | rleSummary calculates summary statistics of rleFullTable |
| run_numbers_with_leading_zero | A named list containing a run number without a leading zero,... |
| runSVA | run SVA |
| selectQaColumns | select fastqFileName, fastqFileNumber, and a pre-determined... |
| strandedScanBamParam | create coverage scanbamparam object |
| testBamPath | test bam path |
