CITATION.cff
CODE_OF_CONDUCT.md
Changelog.txt
INSTALL.txt
LICENCE.txt
MANIFEST.in
README.md
pyproject.toml
setup.py
coalispr/__init__.py
coalispr/__main__.py
coalispr/coalispr.py
coalispr.egg-info/PKG-INFO
coalispr.egg-info/SOURCES.txt
coalispr.egg-info/dependency_links.txt
coalispr.egg-info/entry_points.txt
coalispr.egg-info/not-zip-safe
coalispr.egg-info/requires.txt
coalispr.egg-info/top_level.txt
coalispr/LICENCES/EUPL v1_2 NL.txt
coalispr/LICENCES/EUPL-1.2 EN.txt
coalispr/LICENCES/Licenses_used.txt
coalispr/LICENCES/Logo_EUPL.svg
coalispr/bedgraph_analyze/__init__.py
coalispr/bedgraph_analyze/bam_keys_collators.py
coalispr/bedgraph_analyze/bam_sample_counters.py
coalispr/bedgraph_analyze/bedgraph_plots.py
coalispr/bedgraph_analyze/collect_bedgraphs.py
coalispr/bedgraph_analyze/compare.py
coalispr/bedgraph_analyze/experiment.py
coalispr/bedgraph_analyze/genom.py
coalispr/bedgraph_analyze/info_plots.py
coalispr/bedgraph_analyze/process_bamdata.py
coalispr/bedgraph_analyze/process_bedgraphs.py
coalispr/bedgraph_analyze/references.py
coalispr/bedgraph_analyze/store.py
coalispr/bedgraph_analyze/tracks.py
coalispr/bedgraph_analyze/unselected.py
coalispr/count_analyze/__init__.py
coalispr/count_analyze/annot.py
coalispr/count_analyze/countfile_plots.py
coalispr/count_analyze/filter_data.py
coalispr/count_analyze/groupcompare_plots.py
coalispr/count_analyze/load_countfile.py
coalispr/count_analyze/panel_plotters.py
coalispr/count_analyze/regioncount_plots.py
coalispr/resources/__init__.py
coalispr/resources/cmd_parser.py
coalispr/resources/constant.py
coalispr/resources/dialog.py
coalispr/resources/experiment_table.tsv
coalispr/resources/plot_utilities.py
coalispr/resources/utilities.py
coalispr/resources/constant_in/1_heading.txt
coalispr/resources/constant_in/2_shared.txt
coalispr/resources/constant_in/2_shared_shelve.txt
coalispr/resources/constant_in/3_EXP.txt
coalispr/resources/constant_in/3_h99t.txt
coalispr/resources/constant_in/__init__.py
coalispr/resources/constant_in/make_constant.py
coalispr/resources/constant_out/__init__.py
coalispr/resources/constant_out/_constant_RESET.py
coalispr/resources/profilehooks/CHANGES.rst
coalispr/resources/profilehooks/LICENSE
coalispr/resources/profilehooks/README.rst
coalispr/resources/profilehooks/__init__.py
coalispr/resources/profilehooks/enable.patch
coalispr/resources/profilehooks/profilehooks.py
coalispr/resources/profilehooks/profilehooks_enable.py
coalispr/resources/share/__init__.py
coalispr/resources/share/clean_fasta.py
coalispr/resources/share/cols_from_csv_to_tab.py
coalispr/resources/share/convert_gff3.py
coalispr/resources/share/convert_plusmin_bedgraph_to_plusplus.py
coalispr/resources/share/genbank2gtf.py
coalispr/resources/share/get_smallRNAs_and_targets.py
coalispr/resources/share/gtf_frm_tsv.py
coalispr/resources/share/ncfasta2gtf.py
coalispr/resources/share/no_empty_fa.py
coalispr/resources/share/reduce_gtf.py
coalispr/resources/share/revseq.py
coalispr/resources/share/sub_gtf.py
coalispr/resources/share/bash_scripts/bm2bg.sh
coalispr/resources/share/bash_scripts/wget_resources.sh
coalispr/resources/share/conversion_tables/H99_conv.tab
coalispr/resources/share/conversion_tables/JEC21_conv.tab
coalispr/tk_gui/__init__.py
coalispr/tk_gui/__main__.py
coalispr/tk_gui/gui_constants.py
coalispr/tk_gui/gui_utilities.py
coalispr/tk_gui/tk_coalispr.py
coalispr/tk_gui/assets/coalispr_logo_300.png
coalispr/tk_gui/assets/fonts/JetBrainsMonoNL-Regular.ttf
coalispr/tk_gui/assets/fonts/OFL.txt
coalispr/tk_gui/customtkinter/LICENSE_CustomTkinter
coalispr/tk_gui/customtkinter/__init__.py
coalispr/tk_gui/customtkinter/font_manager.py
coalispr/tk_gui/gui_widgets/__init__.py
coalispr/tk_gui/gui_widgets/base_app.py
coalispr/tk_gui/gui_widgets/menu_main.py
coalispr/tk_gui/gui_widgets/opt.py
coalispr/tk_gui/gui_widgets/opt2.py
coalispr/tk_gui/gui_widgets/parquet_view.py
docs/Makefile
docs/make.bat
docs/_source/README.rst
docs/_source/background.rst
docs/_source/changelog.rst
docs/_source/conf.py
docs/_source/errors.rst
docs/_source/glossary.rst
docs/_source/howtoguides.rst
docs/_source/index.rst
docs/_source/paper.rst
docs/_source/properties.rst
docs/_source/reference.rst
docs/_source/tutorials.rst
docs/_source/furo/_admonitions.scss
docs/_source/furo/_colors.scss
docs/_source/supplemental/18s-tab.rst
docs/_source/supplemental/jec21-ncRNA.gtf
docs/_source/supplemental/otherRNA/rnasep.rst
docs/_source/supplemental/otherRNA/srp.rst
docs/_source/supplemental/otherRNA/u1snrna.rst
docs/_source/supplemental/snoRNAs/ascnag12486.rst
docs/_source/supplemental/snoRNAs/boxcd.rst
docs/_source/supplemental/snoRNAs/cnag00458.rst
docs/_source/supplemental/snoRNAs/cnag03967_z107.rst
docs/_source/supplemental/snoRNAs/cnag12093.rst
docs/_source/supplemental/snoRNAs/cne03050.rst
docs/_source/supplemental/snoRNAs/cne03520.rst
docs/_source/supplemental/snoRNAs/cng02860.rst
docs/_source/supplemental/snoRNAs/cng03660.rst
docs/_source/supplemental/snoRNAs/cnh01600-2boxcd.rst
docs/_source/supplemental/snoRNAs/cnk02420pseu.rst
docs/_source/supplemental/snoRNAs/cnm01680.rst
docs/_source/supplemental/snoRNAs/cnn00700.rst
docs/_source/supplemental/snoRNAs/haca_list.rst
docs/_source/supplemental/snoRNAs/scarna6.rst
docs/_source/supplemental/snoRNAs/snor30.rst
docs/_source/supplemental/snoRNAs/snord110.rst
docs/_source/supplemental/snoRNAs/snord15-targets.rst
docs/_source/supplemental/snoRNAs/snord16.rst
docs/_source/supplemental/snoRNAs/snord17-targets.rst
docs/_source/supplemental/snoRNAs/snord46-snr63.rst
docs/_source/supplemental/snoRNAs/snord49a.rst
docs/_source/supplemental/snoRNAs/snord79.rst
docs/_source/supplemental/snoRNAs/snou31b.rst
docs/_source/supplemental/snoRNAs/snr13.rst
docs/_source/supplemental/snoRNAs/snr38.rst
docs/_source/supplemental/snoRNAs/snr39b.rst
docs/_source/supplemental/snoRNAs/snr40like.rst
docs/_source/supplemental/snoRNAs/snr47-snord36c.rst
docs/_source/supplemental/snoRNAs/snr48-snord60.rst
docs/_source/supplemental/snoRNAs/snr51-snr79.rst
docs/_source/supplemental/snoRNAs/snr51s.rst
docs/_source/supplemental/snoRNAs/snr52-z13.rst
docs/_source/supplemental/snoRNAs/snr60.rst
docs/_source/supplemental/snoRNAs/snr61.rst
docs/_source/supplemental/snoRNAs/snr64-snord74.rst
docs/_source/supplemental/snoRNAs/snr66.rst
docs/_source/supplemental/snoRNAs/snr67d.rst
docs/_source/supplemental/snoRNAs/snr69.rst
docs/_source/supplemental/snoRNAs/snr71.rst
docs/_source/supplemental/snoRNAs/snr72.rst
docs/_source/supplemental/snoRNAs/snr76.rst
docs/_source/supplemental/snoRNAs/snrcnag12093-species.rst
docs/_source/supplemental/snoRNAs/snrcnag12093-targets.rst
docs/_source/supplemental/snoRNAs/snrcnag12441.rst
docs/_source/supplemental/snoRNAs/snrcne03050-targets.rst
docs/_source/supplemental/snoRNAs/snrcnf04440-targets.rst
docs/_source/supplemental/snoRNAs/snrcnf04440.rst
docs/_source/supplemental/snoRNAs/snrcng00300-targets.rst
docs/_source/supplemental/snoRNAs/snrcng00300.rst
docs/_source/supplemental/snoRNAs/snrcnk02420pseu-targets.rst
docs/_source/supplemental/snoRNAs/tri-with-snr41-snr70.rst
docs/_source/supplemental/snoRNAs/u14.rst
docs/_source/supplemental/snoRNAs/u18.rst
docs/_source/supplemental/snoRNAs/u24.rst
docs/_source/supplemental/snoRNAs/u3.rst
docs/_source/supplemental/snoRNAs/u3_snr45.rst
docs/_source/supplemental/snoRNAs/utp12.rst
docs/_source/supplemental/snoRNAs/utp17.rst
docs/_source/tutorials/h99.rst
docs/_source/tutorials/mouse.rst
docs/_source/tutorials/oligos_crac.rst
docs/_source/tutorials/yeast.rst
docs/_source/tutorials/H99/rde1-6xN_rde2-7xN.rst
docs/_source/tutorials/H99/rde1-mulmappers.rst
docs/_source/tutorials/H99/shared_contents_h.rst
docs/_source/tutorials/H99/shared/0_0-SRAaccess.sh
docs/_source/tutorials/H99/shared/0_1-SRAaccess.sh
docs/_source/tutorials/H99/shared/0_2-gzip-fastq.sh
docs/_source/tutorials/H99/shared/1_0-flexbar-trim.sh
docs/_source/tutorials/H99/shared/2_0-collapse.sh
docs/_source/tutorials/H99/shared/3_0-createSTARindex.sh
docs/_source/tutorials/H99/shared/3_1-run-star-collapsed-14mer-strict.sh
docs/_source/tutorials/H99/shared/3_1_1-run-make-SJDB.sh
docs/_source/tutorials/H99/shared/3_2-run-make-bedgraphs.sh
docs/_source/tutorials/H99/shared/3_2_0-run-sortBAM-star-Bedgraph.sh
docs/_source/tutorials/H99/shared/4_1-run-star-uncollapsed-14mer-strict.sh
docs/_source/tutorials/H99/shared/4_2-run-make-bedgraphs-uncollapsed.sh
docs/_source/tutorials/H99/shared/5_1-QC-reports.sh
docs/_source/tutorials/H99/shared/5_1_0-run-RSeQC-bam_stat-FASTQC.sh
docs/_source/tutorials/H99/shared/check/2_SraRunTable.txt
docs/_source/tutorials/H99/shared/check/3_h99.txt
docs/_source/tutorials/H99/shared/check/SRR_Acc_List.txt
docs/_source/tutorials/H99/shared/check/SraRunTable.txt
docs/_source/tutorials/H99/shared/check/h99-chr-lengths.txt
docs/_source/tutorials/H99/shared/check/h99-siRNAsegments.gtf
docs/_source/tutorials/H99/shared/check/mito.gtf
docs/_source/tutorials/H99/shared/check/ncRNA-pseu.gtf
docs/_source/tutorials/H99/shared/source/NAT_G418_HYG.fa
docs/_source/tutorials/H99/shared/source/NAT_G418_HYG.gbk
docs/_source/tutorials/H99/shared/source/SpliceJunctionDataBase-sorted-uniq.txt
docs/_source/tutorials/H99/shared/source/crypNeof_VAR_GRUBII_H99-mature-tRNAs.fa
docs/_source/tutorials/H99/shared/source/crypNeof_VAR_GRUBII_H99-tRNAs.fa
docs/_source/tutorials/H99/shared/source/gene_id.txt
docs/_source/tutorials/H99/shared/source/h99-dumesic2013-genes.fasta
docs/_source/tutorials/H99/shared/source/h99-experiment_table.tsv
docs/_source/tutorials/H99/shared/source/h99-ncRNAxtra.gtf
docs/_source/tutorials/H99/shared/source/h99-siRNAsegments.tsv
docs/_source/tutorials/H99/shared/source/h99-xtra.gtf
docs/_source/tutorials/Mouse/shared_contents.rst
docs/_source/tutorials/Mouse/unmap_table.rst
docs/_source/tutorials/Mouse/shared/0_0-SRAaccess.sh
docs/_source/tutorials/Mouse/shared/0_1-SRAaccess.sh
docs/_source/tutorials/Mouse/shared/0_2-gzip-fastq.sh
docs/_source/tutorials/Mouse/shared/1_1-star-indices.sh
docs/_source/tutorials/Mouse/shared/2_1-collapse-pre-trimmed-seqs.sh
docs/_source/tutorials/Mouse/shared/2_2-clean-uncollapsed-pre-trimmed-seqs.sh
docs/_source/tutorials/Mouse/shared/3_1-run-star-collapsed-14mer.sh
docs/_source/tutorials/Mouse/shared/3_2-run-make-bedgraphs.sh
docs/_source/tutorials/Mouse/shared/3_2_0-run-sortBAM-star-Bedgraph.sh
docs/_source/tutorials/Mouse/shared/4_1-run-star-uncollapsed-14mer.sh
docs/_source/tutorials/Mouse/shared/4_1_2-remove-genome-from-shared-memory.sh
docs/_source/tutorials/Mouse/shared/4_2-run-make-bedgraphs-uncollapsed.sh
docs/_source/tutorials/Mouse/shared/5_1-QC-reports.sh
docs/_source/tutorials/Mouse/shared/5_1_0-run-RSeQC-bam_stat-FASTQC.sh
docs/_source/tutorials/Mouse/shared/6_0-genomelength.sh
docs/_source/tutorials/Mouse/shared/6_1-common-ncRNAs.sh
docs/_source/tutorials/Mouse/shared/6_2-collect-miRNAs-and-targets.sh
docs/_source/tutorials/Mouse/shared/GSE108799_ExpTable.tab
docs/_source/tutorials/Mouse/shared/Rn45s.gtf
docs/_source/tutorials/Mouse/shared/SRR_Acc_List.txt
docs/_source/tutorials/Mouse/shared/SraRunTable.txt
docs/_source/tutorials/Mouse/shared/XtraColumns.txt
docs/_source/tutorials/Mouse/shared/check-3_mouse.txt
docs/_source/tutorials/Mouse/shared/check-3_mouse45s.txt
docs/_source/tutorials/Mouse/shared/mmu-45S-NR_046233.gb
docs/_source/tutorials/Mouse/shared/mmu-45S_ENA-X82564.fa
docs/_source/tutorials/Mouse/shared/source-references.txt
docs/_source/tutorials/Mouse/shared/fastqc_settings/fastqc_adapters.txt
docs/_source/tutorials/Mouse/shared/fastqc_settings/fastqc_contaminants.txt
docs/_source/tutorials/Mouse/shared/fastqc_settings/fastqc_limits.txt
docs/_source/tutorials/Mouse/shared/fastqc_settings/fastqc_limits_collapsed.txt
docs/_source/tutorials/Yeast/shared_contents_y.rst
docs/_source/tutorials/Yeast/checks/3_yeast.txt
docs/_source/tutorials/Yeast/checks/Readme.txt
docs/_source/tutorials/Yeast/checks/check_Kre33-SRR_Acc_List.txt
docs/_source/tutorials/Yeast/checks/check_Kre33Puf6_Exp.tsv
docs/_source/tutorials/Yeast/checks/check_Nab3-SRR_Acc_List.txt
docs/_source/tutorials/Yeast/checks/check_Puf6-SRR_Acc_List.txt
docs/_source/tutorials/Yeast/checks/meta_BYRNASEQ-SraRunTable.txt
docs/_source/tutorials/Yeast/checks/meta_Kre33-SraRunTable.txt
docs/_source/tutorials/Yeast/checks/meta_Nab3-SraRunTable.txt
docs/_source/tutorials/Yeast/checks/meta_Puf6-SraRunTable.txt
docs/_source/tutorials/Yeast/shared/0_0-SRAaccess.sh
docs/_source/tutorials/Yeast/shared/0_1-SRAaccess.sh
docs/_source/tutorials/Yeast/shared/0_1_2-SRAaccess-ref.sh
docs/_source/tutorials/Yeast/shared/0_2-gzip-fastq.sh
docs/_source/tutorials/Yeast/shared/1_1-star-indices.sh
docs/_source/tutorials/Yeast/shared/2_0-flexbar-trim.sh
docs/_source/tutorials/Yeast/shared/2_1-collapse-pre-trimmed-seqs.sh
docs/_source/tutorials/Yeast/shared/3_1-run-starPE-collapsed-14mer.sh
docs/_source/tutorials/Yeast/shared/3_2-run-make-bedgraphs.sh
docs/_source/tutorials/Yeast/shared/3_2_0-run-sortBAM-star-Bedgraph.sh
docs/_source/tutorials/Yeast/shared/4_1-run-starPE-uncollapsed-14mer.sh
docs/_source/tutorials/Yeast/shared/4_1_2-remove-genome-from-shared-memory.sh
docs/_source/tutorials/Yeast/shared/4_2-run-make-bedgraphs-uncollapsed.sh
docs/_source/tutorials/Yeast/shared/Saccharomyces_cerevisiae.R64-1-1.75_1.2.gtf
docs/_source/tutorials/Yeast/shared/Saccharomyces_cerevisiae.R64-1-1.75_chromosome_lengths.txt
docs/_source/tutorials/Yeast/shared/XtraColumns.txt
docs/_source/tutorials/Yeast/shared/barcodes-BC1-shortestlast.txt
docs/_source/tutorials/Yeast/shared/barcodes-BC5-shortestlast.txt
docs/_static/NOTE_images_are_at_source.txt
docs/_static/coalispr_logo_light_ed.svg
docs/_static/favicon.ico
docs/_static/program_settings_only_ed.svg
docs/_static/css/coalispr_alabaster.css
docs/_static/css/coalispr_furo.css
docs/_static/downloads/cols_from_csv_to_tab.py
docs/_static/downloads/convert_gff3.py
docs/_static/downloads/convert_plusmin_bedgraph_to_plusplus.py
docs/_static/downloads/genbank2gtf.py
docs/_static/downloads/get_smallRNAs_and_targets.py
docs/_static/downloads/gtf_frm_tsv.py
docs/_static/downloads/h99-ncRNAxtra.gtf
docs/_static/downloads/jec21-ncRNA.gtf
docs/_static/downloads/no_empty_fa.py
docs/_static/downloads/sub_gtf.py
docs/_templates/layout.html
docs/_templates/page.html
docs/_templates/snorna.rst
docs/_templates/autoapi/index.rst
docs/_templates/autoapi/macros.rst
docs/_templates/autoapi/python/attribute.rst
docs/_templates/autoapi/python/class.rst
docs/_templates/autoapi/python/data.rst
docs/_templates/autoapi/python/exception.rst
docs/_templates/autoapi/python/function.rst
docs/_templates/autoapi/python/method.rst
docs/_templates/autoapi/python/module.rst
docs/_templates/autoapi/python/module.rstOLD
docs/_templates/autoapi/python/package.rst
docs/_templates/autoapi/python/property.rst