Man pages for BrentLab/brentlabRnaSeqTools
Management/QC for brentlab RNAseq data
| addQcColsToMeta | add qc metrics to metadata |
| addRleSummaryStats | calculate RLE by replicate groups |
| archiveDatabase | pull entire database (not counts) and save to output_dir for... |
| autoAuditQcTable | Audit a qc table with metrics added |
| brentlabRnaSeqExperiment | brentlabRnaSeqExperiment constructor. |
| brentlabRnaSeqSet | brentlabRnaSeqSet object and constructor |
| brentlabRnaSeqSetTransform | brentlabRnaSeqSetTransform object and constructor. This... |
| calculateGeneWiseMedians | calculate medians across rows of dataframe |
| calculateRLE | calculate RLE of a numeric dataframe |
| coerceToDds | coerce brentlabRnaSeqSet to DESeqDataSet |
| connectToDatabase | Connect to a remote postgresql database |
| createEnvPert_epWT | filter combined_df for environmental perturbation sample set |
| createEnvPertSet_perturbed | create Environmental Perturbation Perturbed set |
| createEnvPertSet_titrationWT | create Environmental Perturbation Titration (TDY451 only) set |
| createEPTally | Create the EP tally in long form |
| createExperimentSet | Create a pre-defined experiment 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 |
| createNinetyMinuteInduction_2016grant | 90minuteInduction set Definition |
| createNinetyMinuteInduction_2016grantWithDoubles | ninetyMin set where both doubles are in the grant_df |
| createNinetyMinuteInduction_all | Samples with genotypes not in the grant_df |
| createNinetyMinuteInduction_non2016grant | Samples with genotypes not in the grant_df |
| createNovoalignPipelineSamplesheet | create a sample sheet for the novoalign pipeline |
| create_partitions | Given a vector length adn the size of each parition, create a... |
| database_colnames | set global variables, mostly as a hack to make the tidyverse... |
| database_info | URLS to active databases |
| decomposeStatus2Bit | decompose sums of powers of two to a list of the summed... |
| estimateSizeFactorsByProtocol | Calculate Size Factors within protocol groups |
| extractColData | extract colData as tibble |
| extractDesignMatrix | extract the model.matrix using the design and colData |
| filterWtByExperimentalLibdate_90min | WT filtering helper for 90minInduction sets |
| fltrLowReplicateParams | filter low replicate parameters from metadata |
| geneGRanges | Given a GenomicFeatures annotation_db and a gene_id, extract... |
| getCapsuleImageSet | Retrieve, as a zip file, the set of images which correspond... |
| getGeneNames | Get gene names |
| 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 |
| getTable | Convenience function to pull a single table |
| getUserAuthToken | get (via a http POST request) your user authentication token... |
| grant_df | the 2016 grant summary represented as a dataframe |
| htseq_libraryComplexity | Calculate percentage of library accounted for by top... |
| htseq_locusLog2cpm | Get the log2cpm of a given locus in the htseq output |
| htseq_notAlignedTotalPercent | Extract notAlignedTotalPercent from novoalign log |
| htseq_proteinCodingTotal | Calculate KN99 protein coding total |
| igv_script | create IGV viewer batch script (single range, as many tracks... |
| is_integer64 | Test if value is datatype integer64 |
| isNumeric | test if argument is numeric |
| kn99_novo_htseq_status | QC status codes for the novo+htseq pipeline |
| kn99_novo_htseq_thresholds | thresholds set for the novo+htseq pipeline |
| listTables | list tables in databse |
| localView | To view a data.frame / data.table in LibreOffice Calc |
| locusCoverage | Calculate coverage over a given feature |
| moveNfCoFastqFiles | move fastq files from lts to scratch for nf-co/rnaseq... |
| novoalignPipelineQC | QC a crypto run output by the novoalign+htseq pipeline |
| parseComparatives | parse text comparative sentence |
| parseNovoalignLog | Parse a novoalign log |
| passing_genes_all | genes considered NOT to have 'high dispersion' |
| patchTable | PATCH entries in database table |
| plotRLEhistograms | composite plot of all rle_stats in one plot |
| postCapsuleJpeg | Send a single JPEG KN99 capsule image to the capsule image... |
| postCapsuleJpeg_batch | Send a set of JPEGs for a given bioSampleNumber to the... |
| postCounts | post counts to database |
| postCountsToDatabase | Send Counts to Database (legacy pipeline) |
| postFastqSheet | post new fastq sheet to database |
| postImageAnnotationsToDatabase | Send Capsule Image Annotation Data to Database |
| postQcSheet | post new qc sheet to database |
| postTable | Post a table to the database |
| qaFilter | Quality filter a brentlabRnaSeqSet object |
| rank_response_plot | Given expresion and binding signal, plot the rank response a... |
| readHTSeqFile | Parse HTSeq output to tibble |
| readInData | read in columnar data |
| reexports | Objects exported from other packages |
| removeLibdateByReplicate | Remove the libraryDate effects from KN99 dds objs |
| removeParameterEffects | remove some effects from the counts |
| replicateByProtocolTally | experimental replicates by libraryProtocol tally |
| replicateByProtocolTally_90min | 90min replicate by protocol tally |
| 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 |
| rleTransform | transform normalized counts into regularized log expression |
| run_numbers_with_leading_zero | A named list containing a run number without a leading zero,... |
| setPerturbedLociToZero | Zero out perturbed expression |
| snpeff_to_long | snpEff Summary to Long |
| sort_rank_mean_expr | Create a rank-response data frame |
| splitProtocolGroups | Split a brentlabRnaSeqSet into two by protocol |
| strandedScanBamParam | A helper function to create a ScanBamParam object |
| testBamPath | test bam path |
| test_train_partition | create test train set |
| VariantExplorer | VariantExplorer |
