Files in neurogenomics/PeakyFinders
Mining, Calling, and Importing Epigenomic Peaks in R
.Rbuildignore
.github/.gitignore
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/feature_request.md
.github/workflows/rworkflows.yml
.gitignore
.merged.bam
.merged.bedGraph
DESCRIPTION
NAMESPACE
NEWS.md
R/add_mcol.R
R/annot_macs.R
R/bam_to.R
R/bed_to.R
R/bigwig_to_bedgraph.R
R/call_peaks.R
R/call_peaks_macsr.R
R/call_peaks_seacr.R
R/categorise_links.R
R/check_groups.R
R/clean_granges.R
R/condense_granges.R
R/construct_searches.R
R/create_trackhub.R
R/create_trackhub_description.R
R/create_trackhub_genomes.R
R/create_trackhub_hub.R
R/create_trackhub_trackdb.R
R/data.R
R/download_bedgraph.R
R/drop_empty_cols.R
R/dropna_granges.R
R/dt_to_granges.R
R/example_bam.R
R/example_bg_bw.R
R/filter_by_args.R
R/filter_chrom.R
R/filter_genome.R
R/find_executable_seacr.R
R/find_links.R
R/fix_seqinfo.R
R/get_encode_peaks_metadata.R
R/get_genome.R
R/get_geo_links.R
R/get_geo_supplementary_files.R
R/get_links_annotationhub.R
R/get_links_encode.R
R/get_links_roadmap.R
R/import_bedgraph_chroms.R
R/import_bigwig_filtered.R
R/import_peaks.R
R/import_peaks_annotationhub.R
R/import_peaks_bedgraph.R
R/import_peaks_bigbed.R
R/import_peaks_bigwig.R
R/import_peaks_broadpeak.R
R/import_peaks_encode.R
R/import_peaks_files.R
R/import_peaks_genericpeak.R
R/import_peaks_geo.R
R/import_peaks_macs.R
R/import_peaks_multi.R
R/import_peaks_narrowpeak.R
R/import_peaks_roadmap.R
R/import_peaks_seacr.R
R/is_bedgraph.R
R/is_bigwig.R
R/is_granges.R
R/is_local.R
R/is_macs.R
R/is_url.R
R/liftover_grlist.R
R/list_to_char.R
R/make_conda_env.R
R/merge_bam.R
R/message_parallel.r
R/messager.R
R/parse_build.R
R/peaks_metadata_encode.R
R/pooled_peaks.R
R/pooled_peaks_macsr.R
R/pooled_peaks_seacr.R
R/process_ids.R
R/report_time.R
R/rtracklayer_bigwig_error.R
R/seacr_tmp_files.R
R/search_annotationhub.R
R/search_encode.R
R/search_roadmap.R
R/split_chromosomes_run.R
R/stopper.R
R/subset_peaks.R
R/top_dir.R
R/translate_genome.R
R/unlist_dt.R
R/unnest_wider_dt.R
README.Rmd
README.md
data/peaks_metadata_annotationhub.rda
data/peaks_metadata_roadmap.rda
inst/CITATION
inst/conda/PeakyFinders.yml
inst/hex/brain2.png
inst/hex/gene1.png
inst/hex/hex.png
inst/hex/hexSticker.Rmd
man/bam_to.Rd
man/bed_to.Rd
man/call_peaks.Rd
man/call_peaks_macsr.Rd
man/call_peaks_seacr.Rd
man/clean_granges.Rd
man/condense_granges.Rd
man/construct_searches.Rd
man/create_trackhub.Rd
man/dt_to_granges.Rd
man/example_bam.Rd
man/example_bg_bw.Rd
man/filter_chrom.Rd
man/find_executable_seacr.Rd
man/find_links.Rd
man/fix_seqinfo.Rd
man/get_encode_peaks_metadata.Rd
man/get_genome.Rd
man/get_geo_links.Rd
man/get_geo_supplementary_files.Rd
man/import_bedgraph_chroms.Rd
man/import_bigwig_filtered.Rd
man/import_peaks.Rd
man/import_peaks_annotationhub.Rd
man/import_peaks_encode.Rd
man/import_peaks_files.Rd
man/import_peaks_geo.Rd
man/import_peaks_multi.Rd
man/import_peaks_roadmap.Rd
man/is_granges.Rd
man/is_local.Rd
man/is_url.Rd
man/liftover_grlist.Rd
man/make_conda_env.Rd
man/merge_bam.Rd
man/message_parallel.Rd
man/messager.Rd
man/peaks_metadata_annotationhub.Rd
man/peaks_metadata_encode.Rd
man/peaks_metadata_roadmap.Rd
man/pooled_peaks.Rd
man/pooled_peaks_macsr.Rd
man/pooled_peaks_seacr.Rd
man/report_time.Rd
man/search_annotationhub.Rd
man/search_encode.Rd
man/search_roadmap.Rd
man/stopper.Rd
man/translate_genome.Rd
man/unlist_dt.Rd
man/unnest_wider_dt.Rd
tests/testthat.R
tests/testthat/test-call_peaks.R
tests/testthat/test-find_links.R
tests/testthat/test-import_bedgraph_chroms.R
tests/testthat/test-import_peaks.R
tests/testthat/test-liftover_grlist.R
tests/testthat/test-pooled_peaks.R
tests/testthat/test-stopper.R
vignettes/docker.Rmd
vignettes/peakyfinders.Rmd
