Files in LTLA/csaw

ChIP-Seq Analysis with Windows

DESCRIPTION

NAMESPACE

R/asDGEList.R R/calculateCPM.R R/checkBimodality.R R/cluster-direction.R R/clusterFDR.R R/clusterWindows.R R/clusterWindowsList.R R/combineTests.R R/correlateReads.R R/csawUsersGuide.R R/defunct.R R/detailRanges.R R/empiricalFDR.R R/extractReads.R R/filterWindows.R R/findMaxima.R R/findOverlapsList.R R/getBestTest.R R/getPESizes.R R/getWidths.R R/internal_extract.R R/internal_inputs.R R/internal_outputs.R R/internal_resize.R R/maximizeCcf.R R/mergeResults.R R/mergeResultsList.R R/mergeWindows.R R/mergeWindowsList.R R/minimalTests.R R/mixedTests.R R/namespace.R R/normFactors.R R/normOffsets.R R/overlapResults.R R/overlapResultsList.R R/overlapStats.R R/profileSites.R R/readParam.R R/regionCounts.R R/scaledAverage.R R/strandedCounts.R R/upweightSummit.R R/windowCounts.R

inst/CITATION

inst/NEWS.Rd

inst/exdata/autogen.R

inst/exdata/exrange.rds

inst/exdata/pet.bam

inst/exdata/pet.bam.bai

inst/exdata/pet.sam

inst/exdata/rep1.bam

inst/exdata/rep1.bam.bai

inst/exdata/rep2.bam

inst/exdata/rep2.bam.bai

man/SEmethods.Rd man/calculateCPM.Rd man/checkBimodality.Rd man/cluster-direction.Rd man/clusterFDR.Rd man/clusterWindows.Rd man/clusterWindowsList.Rd man/combineTests.Rd man/correlateReads.Rd man/csawUsersGuide.Rd man/defunct.Rd man/detailRanges.Rd man/empiricalFDR.Rd man/extractReads.Rd man/filterWindows.Rd man/findMaxima.Rd man/getBestTest.Rd man/getPESizes.Rd man/getWidths.Rd man/maximizeCcf.Rd man/mergeResults.Rd man/mergeResultsList.Rd man/mergeWindows.Rd man/mergeWindowsList.Rd man/minimalTests.Rd man/mixedTests.Rd man/normFactors.Rd man/normOffsets.Rd man/overlapStats.Rd man/profileSites.Rd man/readParam.Rd man/regionCounts.Rd man/scaledAverage.Rd man/strandedCounts.Rd man/upweightSummit.Rd man/windowCounts.Rd man/wwhm.Rd

src/Makevars

src/annotator.cpp

src/bam_utils.cpp

src/bam_utils.h

src/best_in_cluster.cpp

src/check_bimodality.cpp

src/correlate_reads.cpp

src/csaw.h

src/find_maxima.cpp

src/get_profile.cpp

src/get_rle_counts.cpp

src/init.cpp

src/intersector.cpp

src/intersector.h

src/merge_windows.cpp

src/pair_reads.cpp

src/single_reads.cpp

src/utils.cpp

src/utils.h

tests/testthat.R tests/testthat/setup.R tests/testthat/test-best.R tests/testthat/test-bimodal.R tests/testthat/test-ccf.R tests/testthat/test-cluster.R tests/testthat/test-combine.R tests/testthat/test-cons.R tests/testthat/test-detail.R tests/testthat/test-empirical.R tests/testthat/test-exprs.R tests/testthat/test-extract.R tests/testthat/test-filter.R tests/testthat/test-int_extract.R tests/testthat/test-int_input.R tests/testthat/test-int_output.R tests/testthat/test-int_resize.R tests/testthat/test-maxima.R tests/testthat/test-merge.R tests/testthat/test-minimal.R tests/testthat/test-mixed.R tests/testthat/test-norm.R tests/testthat/test-overlap.R tests/testthat/test-param.R tests/testthat/test-pet.R tests/testthat/test-profile.R tests/testthat/test-region.R tests/testthat/test-window.R tests/testthat/test-wrappers.R vignettes/csaw.Rmd

LTLA/csaw documentation built on Dec. 11, 2023, 5:11 a.m.