Files in mdeber/BRGenomics
Tools for the Efficient Analysis of High-Resolution Genomics Data
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS.md
R/BRGenomics-package.R
R/bootstrap_counts.R
R/data.R
R/data_import.R
R/dataset_functions.R
R/deseq_functions.R
R/ndimensional_binning.R
R/normalization.R
R/roi_functions.R
R/signal_counting.R
R/spikein_functions.R
R/utils.R
README.Rmd
README.md
_pkgdown.yml
data/PROseq.rda
data/PROseq_paired.rda
data/txs_dm6_chr4.rda
inst/extdata/PROseq_dm6_chr4.bam
inst/extdata/PROseq_dm6_chr4_minus.bedGraph
inst/extdata/PROseq_dm6_chr4_minus.bw
inst/extdata/PROseq_dm6_chr4_plus.bedGraph
inst/extdata/PROseq_dm6_chr4_plus.bw
inst/extdata/dm6_chr4chrM.2bit
inst/script/PROseq_data.R
man/BRGenomics-package.Rd
man/PROseq-data.Rd
man/applyNFsGRanges.Rd
man/binNdimensions.Rd
man/bootstrap-signal-by-position.Rd
man/genebodies.Rd
man/getCountsByPositions.Rd
man/getCountsByRegions.Rd
man/getDESeqDataSet.Rd
man/getDESeqResults.Rd
man/getMaxPositionsBySignal.Rd
man/getPausingIndices.Rd
man/getSpikeInCounts.Rd
man/getSpikeInNFs.Rd
man/getStrandedCoverage.Rd
man/import-functions.Rd
man/import_bam.Rd
man/intersectByGene.Rd
man/makeGRangesBRG.Rd
man/mergeGRangesData.Rd
man/mergeReplicates.Rd
man/subsampleBySpikeIn.Rd
man/subsampleGRanges.Rd
man/subsetRegionsBySignal.Rd
man/tidyChromosomes.Rd
man/txs_dm6_chr4.Rd
tests/testthat.R
tests/testthat/test_bootstrapping.R
tests/testthat/test_data_import.R
tests/testthat/test_deseq_functions.R
tests/testthat/test_genebodies_transformByGene_fxns.R
tests/testthat/test_getCounts_getPausingIndices.R
tests/testthat/test_getMaxPositions.R
tests/testthat/test_getStrandedCoverage_makeGRangesBPres.R
tests/testthat/test_merging_subsampling_GRanges.R
tests/testthat/test_ndim_binning.R
tests/testthat/test_spikein_and_normalization.R
tests/testthat/test_subsetRegionsBySignal.R
vignettes/AnalyzingMultipleDatasets.Rmd
vignettes/DESeq2WithGlobalPerturbations.Rmd
vignettes/GettingStarted.Rmd
vignettes/ImportingModifyingAnnotations.Rmd
vignettes/ImportingProcessingData.Rmd
vignettes/Overview.Rmd
vignettes/ProfilePlotsAndBootstrapping.Rmd
vignettes/SequenceExtraction.Rmd
vignettes/SignalCounting.Rmd
vignettes/SpikeInNormalization.Rmd
