Files in BrentLab/brentlabRnaSeqTools

Management/QC for brentlab RNAseq data

LICENSE.md R/AllClasses.R R/AllGenerics.R R/Database.R R/ExperimentSetFunctions.R R/FilterLowRepParameters.R R/IgvFunctions.R R/NextflowProcessing.R R/ProcessingPipelineFunctions.R R/RegularizedLogExpression.R R/RemoveParameterEffects.R R/SetPerturbedLociToZero.R R/Utils.R R/callingCardsFunctions.R R/data_documentation.R R/global_variables.R R/methods.R R/parse_cnvpytor.R R/reexports.R R/snpeff_summary_to_long.R R/test.R README.md index.md inst/R_executable/deseq_de.R man/VariantExplorer.Rd man/addQcColsToMeta.Rd man/addRleSummaryStats.Rd man/archiveDatabase.Rd man/autoAuditQcTable.Rd man/brentlabRnaSeqExperiment.Rd man/brentlabRnaSeqSet.Rd man/brentlabRnaSeqSetTransform.Rd man/calculateGeneWiseMedians.Rd man/calculateRLE.Rd man/coerceToDds.Rd man/connectToDatabase.Rd man/createEPTally.Rd man/createEnvPertSet_perturbed.Rd man/createEnvPertSet_titrationWT.Rd man/createEnvPert_epWT.Rd man/createExperimentSet.Rd man/createIgvBatchscript.Rd man/createInductionSetTally.Rd man/createNfCorePipelineSampleSheet.Rd man/createNinetyMinuteInduction_2016grant.Rd man/createNinetyMinuteInduction_2016grantWithDoubles.Rd man/createNinetyMinuteInduction_all.Rd man/createNinetyMinuteInduction_non2016grant.Rd man/createNovoalignPipelineSamplesheet.Rd man/create_partitions.Rd man/database_colnames.Rd man/database_info.Rd man/decomposeStatus2Bit.Rd man/estimateSizeFactorsByProtocol.Rd man/extractColData.Rd man/extractDesignMatrix.Rd man/filterWtByExperimentalLibdate_90min.Rd man/fltrLowReplicateParams.Rd man/geneGRanges.Rd man/getCapsuleImageSet.Rd man/getGeneNames.Rd man/getMetadata.Rd man/getRawCounts.Rd man/getRunNumberLeadingZero.Rd man/getTable.Rd man/getUserAuthToken.Rd man/grant_df.Rd man/htseq_libraryComplexity.Rd man/htseq_locusLog2cpm.Rd man/htseq_notAlignedTotalPercent.Rd man/htseq_proteinCodingTotal.Rd man/igv_script.Rd man/isNumeric.Rd man/is_integer64.Rd man/kn99_novo_htseq_status.Rd man/kn99_novo_htseq_thresholds.Rd man/listTables.Rd man/localView.Rd man/locusCoverage.Rd man/moveNfCoFastqFiles.Rd man/novoalignPipelineQC.Rd man/parseComparatives.Rd man/parseNovoalignLog.Rd man/passing_genes_all.Rd man/patchTable.Rd man/plotRLEhistograms.Rd man/postCapsuleJpeg.Rd man/postCapsuleJpeg_batch.Rd man/postCounts.Rd man/postCountsToDatabase.Rd man/postFastqSheet.Rd man/postImageAnnotationsToDatabase.Rd man/postQcSheet.Rd man/postTable.Rd man/qaFilter.Rd man/rank_response_plot.Rd man/readHTSeqFile.Rd man/readInData.Rd man/reexports.Rd man/removeLibdateByReplicate.Rd man/removeParameterEffects.Rd man/replicateByProtocolTally.Rd man/replicateByProtocolTally_90min.Rd man/rleByReplicateGroup.Rd man/rlePlot.Rd man/rlePlotCompareEffectRemoved.Rd man/rlePlot_helper.Rd man/rleSummary.Rd man/rleTransform.Rd man/run_numbers_with_leading_zero.Rd man/setPerturbedLociToZero.Rd man/snpeff_to_long.Rd man/sort_rank_mean_expr.Rd man/splitProtocolGroups.Rd man/strandedScanBamParam.Rd man/testBamPath.Rd man/test_train_partition.Rd renv/activate.R tests/testthat.R tests/testthat/test-AllClasses.R tests/testthat/test-AllGenerics.R tests/testthat/test-IgvFunctions.R tests/testthat/test-ModelMatrixFunctions.R tests/testthat/test-NextflowProcessing.R tests/testthat/test-QualityAssessmentFilter.R tests/testthat/test-RegularizedLogExpression.R tests/testthat/test-RemoveParameterEffects.R tests/testthat/test-SizeFactorFunctions.R tests/testthat/test-database_utils.R tests/testthat/test-methods.R tests/testthat/test-rank_response.R vignettes/ProcessRun.Rmd vignettes/QC_Library_Quality.Rmd vignettes/QC_Sample_Agreement_Objects.Rmd vignettes/Rank_Response_Plot.Rmd vignettes/Tally.Rmd vignettes/access_data_in_archive.Rmd vignettes/brentlabRnaSeqTools.Rmd vignettes/create_R_package.Rmd vignettes/envPerturbation.Rmd vignettes/exploring_dna_variants.Rmd vignettes/image_table_interactions.Rmd vignettes/ninetyMinuteInduction_analysis.Rmd vignettes/posit_projects.Rmd