Files in dieterich-lab/JACUSA2helper
Post-processing for JACUSA2 output
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.github/workflows/pkgdown.yaml-BACKUP
.github/workflows/pr-commands.yaml
.github/workflows/test-coverage.yaml
.gitignore
DESCRIPTION
JACUSA2helper.Rproj
LICENSE
NAMESPACE
R/JACUSA2helper-package.R
R/RcppExports.R
R/arrest-rate.R
R/base-count.R
R/base-ratio.R
R/base_sub.R
R/common.R
R/data.R
R/helper-filter.R
R/helper-robust.R
R/helper-sub.R
R/helper.R
R/io-guess.R
R/io.R
R/nmf.R
R/non-ref-ratio.R
R/score.R
R/sub-ratio.R
R/write-bedGraph.R
README.md
_pkgdown.yml
codecov.yml
data-raw/Cutoff005_MazF_vs_cond2_FTO_RC18_rtarrest_plain_result.out
data-raw/Cutoff01_MazF_vs_cond2_FTO_RC22_rtarrest_plain_result.out
data-raw/Cutoff01_MazF_vs_cond2_FTO_RC22_rtarrest_with_seq.out
data-raw/Cutoff01_MazF_vs_cond2_FTO_RC22_rtarrest_with_seq_and_ann.out
data-raw/DATASET.R
data-raw/JACUSA2helper-dart-seq.html
data-raw/JACUSA2helper-mazf.Rmd
data-raw/JACUSA2helper-meta-condtions.Rmd
data-raw/Score2_APOBEC1YTH_APOBEC1YTHmut_RC18_call2_result.out
data-raw/call-2-HIVRT.out
data-raw/call-2-SIIIRTMg.out
data-raw/call-2-SIIIRTMn.out
data-raw/call-2-rdd.out
data-raw/call-2-rrd.out
data-raw/miCLIP_union_flat_exclude_Y_chromosome.bed
data-raw/nmf_results_paper.rds
data-raw/rnam.bed
data-raw/rt-arrest-HIVRT.out
data-raw/rt-arrest-SIIIRTMg.out
data-raw/rt-arrest-SIIIRTMn.out
data/DARTseq.rda
data/HIVRT_call2.rda
data/HIVRT_rt_arrest.rda
data/MazF_FTO.rda
data/SIIIRTMg_call2.rda
data/SIIIRTMg_rt_arrest.rda
data/SIIIRTMn_call2.rda
data/SIIIRTMn_rt_arrest.rda
data/Zhou2018_call2.rda
data/Zhou2018_rt_arrest.rda
data/m6a_miclip.rda
data/m6a_nmf_reduced.rda
data/m6a_nmf_results.rda
data/rdd.rda
data/rnam.rda
data/rrd.rda
man/All.Rd
man/Allnum.Rd
man/Any.Rd
man/DARTseq.Rd
man/HIVRT_call2.Rd
man/HIVRT_rt_arrest.Rd
man/JACUSA2helper.Rd
man/MazF_FTO.Rd
man/SIIIRTMg_call2.Rd
man/SIIIRTMg_rt_arrest.Rd
man/SIIIRTMn_call2.Rd
man/SIIIRTMn_rt_arrest.Rd
man/Zhou2018_call2.Rd
man/Zhou2018_rt_arrest.Rd
man/add_arrest_rate.Rd
man/arrest_rate.Rd
man/base_call.Rd
man/base_count.Rd
man/base_ratio.Rd
man/base_sub.Rd
man/clean_tag.Rd
man/coverage.Rd
man/create_data.Rd
man/expand_tag.Rd
man/extend.Rd
man/fast_unpack_info.Rd
man/filter_artefact.Rd
man/gather_repl.Rd
man/get_info_keys.Rd
man/get_motif.Rd
man/id.Rd
man/is_DRACH.Rd
man/lapply_cond.Rd
man/lapply_repl.Rd
man/learn_nmf.Rd
man/m6a_miclip.Rd
man/m6a_nmf_reduced.Rd
man/m6a_nmf_results.Rd
man/mapply_repl.Rd
man/mask_sub.Rd
man/max_observed_bc.Rd
man/merge_sub.Rd
man/non_ref_ratio.Rd
man/observed_bc.Rd
man/predict_mods.Rd
man/rdd.Rd
man/read_result.Rd
man/read_results.Rd
man/reduce_coef.Rd
man/rnam.Rd
man/robust.Rd
man/rrd.Rd
man/sub_counts.Rd
man/sub_ratio.Rd
man/unpack_info.Rd
man/variant_bc.Rd
man/write_bedGraph.Rd
src/.gitignore
src/RcppExports.cpp
src/utils.cpp
tests/testthat.R
tests/testthat/call-1.out
tests/testthat/call-2-missing-header.out
tests/testthat/call-2.out
tests/testthat/lrt-arrest.out
tests/testthat/pileup.out
tests/testthat/rt-arrest.out
tests/testthat/test-base-count.R
tests/testthat/test-base-ratio.R
tests/testthat/test-base-sub.R
tests/testthat/test-coverage.R
tests/testthat/test-filter-by-filter-info.R
tests/testthat/test-guess-cond-count.R
tests/testthat/test-guess-file-type.R
tests/testthat/test-helper-sub.R
tests/testthat/test-io-guess.R
tests/testthat/test-io.R
tests/testthat/test-mask.R
tests/testthat/test-merge-sub.R
tests/testthat/test-non-ref-ratio.R
tests/testthat/test-read-result.R
tests/testthat/test-sub-ratio.R
tests/testthat/test-unpack-info.R
tests/testthat/testthat-problems.rds
tests/testthat/unknown-type.out
vignettes/.gitignore
vignettes/JACUSA2helper-dart-seq.Rmd
vignettes/JACUSA2helper-dart-seq.bib
vignettes/JACUSA2helper-intro.Rmd
vignettes/JACUSA2helper-mazf.Rmd
vignettes/JACUSA2helper-mazf.bib
vignettes/JACUSA2helper-meta-conditions.Rmd
vignettes/JACUSA2helper-meta-conditions.bib
vignettes/JACUSA2helper.bib
vignettes/web_only/JACUSA2helper-nanopore.Rmd
vignettes/web_only/JACUSA2helper-nanopore.bib
