Files in BRGenomics

Tools for the Efficient Analysis of High-Resolution Genomics Data

NEWS.md README.md R/BRGenomics-package.R R/bootstrap_counts.R R/deseq_functions.R R/dataset_functions.R R/utils.R R/ndimensional_binning.R R/spikein_functions.R R/data_import.R R/signal_counting.R R/roi_functions.R R/data.R R/normalization.R vignettes/SequenceExtraction.Rmd vignettes/Overview.Rmd vignettes/DESeq2WithGlobalPerturbations.Rmd vignettes/SignalCounting.Rmd vignettes/ImportingProcessingData.Rmd vignettes/ProfilePlotsAndBootstrapping.Rmd vignettes/SpikeInNormalization.Rmd vignettes/ImportingModifyingAnnotations.Rmd vignettes/GettingStarted.Rmd vignettes/AnalyzingMultipleDatasets.Rmd man/PROseq-data.Rd man/BRGenomics-package.Rd man/getDESeqDataSet.Rd man/subsampleBySpikeIn.Rd man/makeGRangesBRG.Rd man/intersectByGene.Rd man/import_bam.Rd man/getCountsByRegions.Rd man/subsampleGRanges.Rd man/bootstrap-signal-by-position.Rd man/txs_dm6_chr4.Rd man/tidyChromosomes.Rd man/genebodies.Rd man/mergeReplicates.Rd man/getCountsByPositions.Rd man/binNDimensions.Rd man/import-functions.Rd man/getPausingIndices.Rd man/applyNFsGRanges.Rd man/mergeGRangesData.Rd man/getSpikeInNFs.Rd man/getMaxPositionsBySignal.Rd man/getSpikeInCounts.Rd man/getStrandedCoverage.Rd man/subsetRegionsBySignal.Rd man/getDESeqResults.Rd tests/testthat.R tests/testthat/test_merging_subsampling_GRanges.R tests/testthat/test_bootstrapping.R tests/testthat/test_getCounts_getPausingIndices.R tests/testthat/test_genebodies_transformByGene_fxns.R tests/testthat/test_getStrandedCoverage_makeGRangesBPres.R tests/testthat/test_subsetRegionsBySignal.R tests/testthat/test_deseq_functions.R tests/testthat/test_getMaxPositions.R tests/testthat/test_spikein_and_normalization.R tests/testthat/test_data_import.R tests/testthat/test_ndim_binning.R inst/doc/SequenceExtraction.Rmd inst/doc/Overview.Rmd inst/doc/SignalCounting.R inst/doc/SpikeInNormalization.R inst/doc/DESeq2WithGlobalPerturbations.Rmd inst/doc/DESeq2WithGlobalPerturbations.R inst/doc/SignalCounting.Rmd inst/doc/GettingStarted.R inst/doc/ImportingProcessingData.Rmd inst/doc/AnalyzingMultipleDatasets.R inst/doc/ImportingProcessingData.R inst/doc/SequenceExtraction.R inst/doc/ProfilePlotsAndBootstrapping.Rmd inst/doc/SpikeInNormalization.Rmd inst/doc/ImportingModifyingAnnotations.Rmd inst/doc/ImportingModifyingAnnotations.R inst/doc/GettingStarted.Rmd inst/doc/ProfilePlotsAndBootstrapping.R inst/doc/AnalyzingMultipleDatasets.Rmd inst/script/PROseq_data.R