Files in neurogenomics/PeakyFinders

Mining, Calling, and Importing Epigenomic Peaks in R

.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md 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 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