Files in jrboyd/peakrefine
Peak Refinement Metric Gathering and Evalutation by Motif Enrichment
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/class_peakrefine.R
R/functions_PWM_modify.R
R/functions_cache.R
R/functions_calc_fragLen.R
R/functions_crossCorrExtension.R
R/functions_crossCorrRle.R
R/functions_crossCorrShift.R
R/functions_motif.R
R/functions_utils.R
README.md
README.rmd
README_figs/README-corr_profile-1.png
README_figs/README-metric_corr-1.png
README_figs/README-metric_shift-1.png
check_fraglen.R
dev_calc_fragLen.R
dev_chipqc_full_chrom_corr.R
dev_chipsim.R
dev_chipsim_check_res.R
dev_chipsim_functions.R
dev_compare_corr_methods.R
dev_egr1_example.R
dev_motif.R
dev_parallel_fetch.R
dev_pipeline.R
dev_pipeline_IK.R
dev_pipeline_fun.R
dev_pipeline_sim.R
dev_resim.R
inst/extdata/MCF10A_CTCF.random5.bam
inst/extdata/MCF10A_CTCF.random5.bam.bai
inst/extdata/MCF10A_CTCF.random5.narrowPeak
inst/extdata/MCF10A_input.random5.bam
inst/extdata/MCF10A_input.random5.bam.bai
man/PWMEnrich.affinitySequenceSet.Rd
man/PWMEnrich.cloverScore.Rd
man/PeakRefiner-class.Rd
man/PeakRefiner.Rd
man/add_MotifEnrichmentResults.Rd
man/bfcif.Rd
man/calcCorrMetrics.Rd
man/calcMotifEnrichment.Rd
man/calcSCCMetrics.Rd
man/crossCorrByExtension.Rd
man/crossCorrByExtensionFull.Rd
man/crossCorrByRle.Rd
man/crossCorrByShift.Rd
man/dot-calc_cross_corr.Rd
man/dot-calc_stranded_coverage.Rd
man/dot-extend_reads.Rd
man/dot-fetch_bam_stranded.Rd
man/dot-remove_duplicates.Rd
man/dot-shift_anchor.Rd
man/dot-view_gr_by_window_sample.Rd
man/getReadLength.Rd
man/harmonize_seqlengths.Rd
man/initialize-PeakRefiner-method.Rd
man/pre_motif.Rd
man/scoreMetrics.Rd
man/score_motif.Rd
man/subset_MotifEnrichmentResults.Rd
peakrefine.Rproj
poster_figs.R
resub_low_qual_peaks.R
run_cov.R
test_my_writeFASTQ.R
tests/testthat.R
tests/testthat/test_class_PeakRefine.R
tests/testthat/test_corr_by_Rle_shiftApply.R
tests/testthat/test_corr_by_extension.R
tests/testthat/test_fetch_utils.R
tests/testthat/test_strand_anchor.R
