Files in LTLA/diffHic

Differential Analyis of Hi-C Data

DESCRIPTION

NAMESPACE

R/annotatePairs.R R/basefun.R R/boxPairs.R R/clusterPairs.R R/compartmentalize.R R/connectCounts.R R/consolidatePairs.R R/correctedContact.R R/cutGenome.R R/diClusters.R R/diffHicUsersGuide.R R/domainDirections.R R/enrichedPairs.R R/extractPatch.R R/filterPeaks.R R/filters.R R/getArea.R R/getPairData.R R/h5utils.R R/marginCounts.R R/mergeCMs.R R/mergePairs.R R/neighborCounts.R R/normalizeCNV.R R/pairParam.R R/plotPlaid.R R/preloader.R R/prepPseudoPairs.R R/preparePairs.R R/prunePairs.R R/readMTX2IntSet.R R/rotPlaid.R R/savePairs.R R/squareCounts.R R/totalCounts.R

inst/CITATION

inst/NEWS.Rd

inst/doc/diffHicUsersGuide.pdf

inst/exdata/cuts.rds

inst/exdata/generator.R

inst/exdata/hic_sort.bam

inst/python/iter_map.py

inst/python/presplit_map.py

inst/tests/run_all_tests.sh

inst/tests/simcounts.R inst/tests/simsam.R inst/tests/test-anno.R

inst/tests/test-anno.Rout.save

inst/tests/test-box.R

inst/tests/test-box.Rout.save

inst/tests/test-cluster.R

inst/tests/test-cluster.Rout.save

inst/tests/test-cmmerge.R

inst/tests/test-cmmerge.Rout.save

inst/tests/test-connect.R

inst/tests/test-connect.Rout.save

inst/tests/test-cut.Rout.save

inst/tests/test-diclust.R

inst/tests/test-diclust.Rout.save

inst/tests/test-dnase.R

inst/tests/test-dnase.Rout.save

inst/tests/test-domains.R

inst/tests/test-domains.Rout.save

inst/tests/test-empty.R

inst/tests/test-empty.Rout.save

inst/tests/test-filter.R

inst/tests/test-filter.Rout.save

inst/tests/test-hic-pair.R

inst/tests/test-hic-pair.Rout.save

inst/tests/test-interactions.R

inst/tests/test-interactions.Rout.save

inst/tests/test-itercor.R

inst/tests/test-itercor.Rout.save

inst/tests/test-margin.R

inst/tests/test-margin.Rout.save

inst/tests/test-neighbor.R

inst/tests/test-neighbor.Rout.save

inst/tests/test-pair-manip.R

inst/tests/test-pair-manip.Rout.save

inst/tests/test-patch.R

inst/tests/test-patch.Rout.save

inst/tests/test-prune.R

inst/tests/test-prune.Rout.save

man/DNaseHiC.Rd man/annotatePairs.Rd man/boxPairs.Rd man/clusterPairs.Rd man/compartmentalize.Rd man/connectCounts.Rd man/consolidatePairs.Rd man/correctedContact.Rd man/cutGenome.Rd man/diClusters.Rd man/diffHicUsersGuide.Rd man/domainDirections.Rd man/enrichedPairs.Rd man/extractPatch.Rd man/filterDiag.Rd man/filterPeaks.Rd man/filters.Rd man/getArea.Rd man/getPairData.Rd man/loadData.Rd man/marginCounts.Rd man/mergeCMs.Rd man/mergePairs.Rd man/neighborCounts.Rd man/normalizeCNV.Rd man/pairParam.Rd man/plotDI.Rd man/plotPlaid.Rd man/preparePairs.Rd man/prunePairs.Rd man/readMTX2IntSet.Rd man/savePairs.Rd man/squareCounts.Rd man/totalCounts.Rd

src/Makevars

src/binner.cpp

src/check_input.cpp

src/cluster_2d.cpp

src/count_background.cpp

src/count_connect.cpp

src/count_patch.cpp

src/diffhic.h

src/directionality.cpp

src/init.cpp

src/iterative_correction.cpp

src/neighbors.cpp

src/neighbors.h

src/pair_stats.cpp

src/quadrant_bg.cpp

src/read_count.h

src/report_hic_pairs.cpp

src/trended_filter.cpp

src/utils.cpp

src/utils.h

tests/test-basic.R

tests/test-basic.Rout.save

tests/testthat.R tests/testthat/test-cut.R tests/testthat/test-input.R

vignettes/diffHic.Rnw

LTLA/diffHic documentation built on April 1, 2024, 7:21 a.m.