LICENSE
MANIFEST.in
README.md
setup.py
celescope/__init__.py
celescope/celescope.py
celescope.egg-info/PKG-INFO
celescope.egg-info/SOURCES.txt
celescope.egg-info/dependency_links.txt
celescope.egg-info/entry_points.txt
celescope.egg-info/requires.txt
celescope.egg-info/top_level.txt
celescope/bulk_rna/__init__.py
celescope/bulk_rna/count.py
celescope/bulk_rna/multi_bulk_rna.py
celescope/bulk_vdj/__init__.py
celescope/bulk_vdj/consensus.py
celescope/bulk_vdj/count_vdj.py
celescope/bulk_vdj/mapping_vdj.py
celescope/bulk_vdj/multi_bulk_vdj.py
celescope/capture_virus/__init__.py
celescope/capture_virus/analysis_virus.py
celescope/capture_virus/count.py
celescope/capture_virus/count_virus.py
celescope/capture_virus/featureCounts.py
celescope/capture_virus/filter_virus.py
celescope/capture_virus/mkref.py
celescope/capture_virus/multi_capture_virus.py
celescope/capture_virus/star_virus.py
celescope/citeseq/__init__.py
celescope/citeseq/analysis_cite.py
celescope/citeseq/count_cite.py
celescope/citeseq/mapping_tag.py
celescope/citeseq/multi_citeseq.py
celescope/data/Clindex/tag_barcode.fasta
celescope/data/Clindex/tag_linker.fasta
celescope/data/HLA/hla_reference_rna.fasta
celescope/data/chemistry/bulk_rna/bclist384
celescope/data/chemistry/bulk_rna/bclist96
celescope/data/chemistry/bulk_vdj/bclist
celescope/data/chemistry/bulk_vdj/linker
celescope/data/chemistry/flv/bclist
celescope/data/chemistry/flv/linker
celescope/data/chemistry/flv_rna/bclist
celescope/data/chemistry/flv_rna/linker_4types
celescope/data/chemistry/scopeV2.0.0/bclist
celescope/data/chemistry/scopeV2.0.0/linker
celescope/data/chemistry/scopeV2.0.1/bclist
celescope/data/chemistry/scopeV2.0.1/linker_withC
celescope/data/chemistry/scopeV2.1.0/bclist
celescope/data/chemistry/scopeV2.1.0/linker
celescope/data/chemistry/scopeV2.1.1/bclist
celescope/data/chemistry/scopeV2.1.1/linker_withC
celescope/data/chemistry/scopeV2.2.1/bclist
celescope/data/chemistry/scopeV2.2.1/linker_4types
celescope/data/chemistry/scopeV3.0.1/bclist
celescope/data/chemistry/scopeV3.0.1/bclist1
celescope/data/chemistry/scopeV3.0.1/bclist2
celescope/data/chemistry/scopeV3.0.1/bclist3
celescope/data/chemistry/scopeV3.0.1/linker_4types
celescope/data/fusion/blood_1/BCR_ABL1_PML_RARA_all.fasta
celescope/data/fusion/blood_1/BCR_ABL1_PML_RARA_all_pos.txt
celescope/data/fusion/blood_1/mkref.sh
celescope/data/rRNA/human_ribo.fasta
celescope/data/snp/panel/blood_1.bed
celescope/data/snp/panel/lung_1.bed
celescope/data/sweetseq/sweetseq_barcode.fasta
celescope/data/sweetseq/sweetseq_linker.fasta
celescope/dynaseq/__init__.py
celescope/dynaseq/conversion.py
celescope/dynaseq/multi_dynaseq.py
celescope/dynaseq/replacement.py
celescope/dynaseq/substitution.py
celescope/flv_trust4/__init__.py
celescope/flv_trust4/annotation.py
celescope/flv_trust4/assemble.py
celescope/flv_trust4/mapping.py
celescope/flv_trust4/multi_flv_trust4.py
celescope/flv_trust4/summarize.py
celescope/fusion/__init__.py
celescope/fusion/analysis_fusion.py
celescope/fusion/count_fusion.py
celescope/fusion/filter_fusion.py
celescope/fusion/mkref.py
celescope/fusion/multi_fusion.py
celescope/fusion/star_fusion.py
celescope/hla/__init__.py
celescope/hla/mapping_hla.py
celescope/hla/multi_hla.py
celescope/rna/__init__.py
celescope/rna/analysis.py
celescope/rna/mkref.py
celescope/rna/multi_rna.py
celescope/rna/star.py
celescope/snp/__init__.py
celescope/snp/analysis_snp.py
celescope/snp/filter_snp.py
celescope/snp/mkref.py
celescope/snp/multi_snp.py
celescope/snp/variant_calling.py
celescope/sweetseq/__init__.py
celescope/sweetseq/analysis_tag.py
celescope/sweetseq/count_tag.py
celescope/sweetseq/mapping_tag.py
celescope/sweetseq/multi_sweetseq.py
celescope/tag/__init__.py
celescope/tag/analysis_tag.py
celescope/tag/count_tag.py
celescope/tag/mapping_tag.py
celescope/tag/multi_tag.py
celescope/tag/split_tag.py
celescope/templates/css/bootstrap.min.css
celescope/templates/css/buttons.dataTables.min.css
celescope/templates/css/dataTables.jqueryui.min.css
celescope/templates/css/jquery-ui-git.css
celescope/templates/css/jquery-ui.css
celescope/templates/css/jquery.dataTables.css
celescope/templates/css/fontello-323401c3/config.json
celescope/templates/css/fontello-323401c3/css/animation.css
celescope/templates/css/fontello-323401c3/css/fontello-codes.css
celescope/templates/css/fontello-323401c3/css/fontello-embedded.css
celescope/templates/css/fontello-323401c3/css/fontello-ie7-codes.css
celescope/templates/css/fontello-323401c3/css/fontello-ie7.css
celescope/templates/css/fontello-323401c3/css/fontello.css
celescope/templates/css/fontello-323401c3/font/fontello.eot
celescope/templates/css/fontello-323401c3/font/fontello.svg
celescope/templates/css/fontello-323401c3/font/fontello.ttf
celescope/templates/css/fontello-323401c3/font/fontello.woff
celescope/templates/css/fontello-323401c3/font/fontello.woff2
celescope/templates/html/bulk_rna/base.html
celescope/templates/html/bulk_rna/count.html
celescope/templates/html/bulk_vdj/base.html
celescope/templates/html/bulk_vdj/count_vdj.html
celescope/templates/html/capture_rna/base.html
celescope/templates/html/capture_rna/count_capture_rna_summary.html
celescope/templates/html/capture_virus/analysis_virus.html
celescope/templates/html/capture_virus/base.html
celescope/templates/html/citeseq/analysis_cite.html
celescope/templates/html/citeseq/base.html
celescope/templates/html/common/img1.html
celescope/templates/html/common/logo.html
celescope/templates/html/dynaseq/base.html
celescope/templates/html/dynaseq/conversion.html
celescope/templates/html/dynaseq/replacement.html
celescope/templates/html/dynaseq/substitution.html
celescope/templates/html/flv_trust4/annotation.html
celescope/templates/html/flv_trust4/base.html
celescope/templates/html/flv_trust4/summarize.html
celescope/templates/html/fusion/analysis_fusion.html
celescope/templates/html/fusion/base.html
celescope/templates/html/hla/base.html
celescope/templates/html/mut/base.html
celescope/templates/html/rna/analysis.html
celescope/templates/html/rna/base.html
celescope/templates/html/rna/count.html
celescope/templates/html/rna/star.html
celescope/templates/html/rna_virus/analysis_rna_virus_summary.html
celescope/templates/html/rna_virus/base.html
celescope/templates/html/snp/analysis_snp.html
celescope/templates/html/snp/base.html
celescope/templates/html/sweetseq/analysis_tag.html
celescope/templates/html/sweetseq/base.html
celescope/templates/html/tag/analysis_tag.html
celescope/templates/html/tag/base.html
celescope/templates/html/tcr_fl/analysis_tag_summary.html
celescope/templates/html/tcr_fl/base.html
celescope/templates/html/tcr_fl/count_tag_summary.html
celescope/templates/html/tcr_fl/mapping_tag_summary.html
celescope/templates/html/utils/analysis.html
celescope/templates/html/utils/col1_metrics.html
celescope/templates/html/utils/col2_metrics.html
celescope/templates/html/utils/end.html
celescope/templates/html/utils/head.html
celescope/templates/html/utils/help_info.html
celescope/templates/html/utils/preprocessing.html
celescope/templates/html/utils/start.html
celescope/templates/html/utils/step.html
celescope/templates/html/utils/table_dict.html
celescope/templates/html/utils/table_script/bulk_rna.html
celescope/templates/html/utils/table_script/bulk_vdj.html
celescope/templates/html/utils/table_script/dynaseq.html
celescope/templates/html/utils/table_script/rna.html
celescope/templates/html/utils/table_script/snp.html
celescope/templates/html/utils/table_script/vdj.html
celescope/templates/html/vdj/base.html
celescope/templates/html/vdj/count_vdj.html
celescope/templates/img/img1.png
celescope/templates/img/logo2.png
celescope/templates/js/bootstrap.min.js
celescope/templates/js/buttons.flash.min.js
celescope/templates/js/buttons.html5.min.js
celescope/templates/js/buttons.print.min.js
celescope/templates/js/dataTables.buttons.min.js
celescope/templates/js/dataTables.jqueryui.min.js
celescope/templates/js/jquery.dataTables.js
celescope/templates/js/jquery.dataTables.min.js
celescope/templates/js/jquery.min.3.3.1.js
celescope/templates/js/jquery.min.js
celescope/templates/js/jszip.min.js
celescope/templates/js/plotly-2.12.1.min.js
celescope/tools/__init__.py
celescope/tools/analysis_wrapper.py
celescope/tools/barcode.py
celescope/tools/cells.py
celescope/tools/consensus.py
celescope/tools/count.py
celescope/tools/cutadapt.py
celescope/tools/debug.py
celescope/tools/featureCounts.py
celescope/tools/make_ref.py
celescope/tools/matrix.py
celescope/tools/merge_table.py
celescope/tools/multi.py
celescope/tools/plotly_plot.py
celescope/tools/prep.py
celescope/tools/prep_map.py
celescope/tools/reference.py
celescope/tools/report.py
celescope/tools/sample.py
celescope/tools/star_mixin.py
celescope/tools/starsolo.py
celescope/tools/step.py
celescope/tools/target_metrics.py
celescope/tools/utils.py
celescope/tools/capture/__init__.py
celescope/tools/capture/analysis.py
celescope/tools/capture/count_bam.py
celescope/tools/capture/filter.py
celescope/tools/capture/threshold.py
celescope/tools/emptydrop_cr/__init__.py
celescope/tools/emptydrop_cr/cell_calling_3.py
celescope/tools/emptydrop_cr/get_plot_elements.py
celescope/tools/emptydrop_cr/sgt.py
celescope/tools/emptydrop_cr/stats.py
celescope/tools/tag/__init__.py
celescope/tools/tag/analysis_tag.py
celescope/tools/tag/count_tag.py
celescope/tools/tag/mapping_tag.py
celescope/tools/trust4/AddSequenceToCDR3File.pl
celescope/tools/trust4/GetFullLengthAssembly.pl
celescope/tools/trust4/Immune_marker.json
celescope/tools/trust4/barcoderep-filter.py
celescope/tools/trust4/trust-airr.pl
celescope/tools/trust4/trust-barcoderep-to-10X.pl
celescope/tools/trust4/trust-barcoderep.pl
celescope/tools/trust4/trust-cluster.py
celescope/tools/trust4/trust-simplerep.pl
celescope/tools/trust4/trust-stats.py
celescope/tools/trust4/database/GRCm38/BCR.fa
celescope/tools/trust4/database/GRCm38/IGH.fa
celescope/tools/trust4/database/GRCm38/IGK.fa
celescope/tools/trust4/database/GRCm38/IGL.fa
celescope/tools/trust4/database/GRCm38/IMGT+C.fa
celescope/tools/trust4/database/GRCm38/TCR.fa
celescope/tools/trust4/database/GRCm38/TRA.fa
celescope/tools/trust4/database/GRCm38/TRB.fa
celescope/tools/trust4/database/GRCm38/bcrtcr.fa
celescope/tools/trust4/database/Hsap/Hsap_IMGT+C.fa
celescope/tools/trust4/database/Hsap/Hsap_ref.fa
celescope/tools/trust4/database/Mmus/Mmus_IMGT+C.fa
celescope/tools/trust4/database/Mmus/Mmus_ref.fa
celescope/tools/trust4/database/Mmus/Mmus_ref.fa.fai
celescope/tools/trust4/database/hg19/IGH.fa
celescope/tools/trust4/database/hg19/IGK.fa
celescope/tools/trust4/database/hg19/IGL.fa
celescope/tools/trust4/database/hg19/IMGT+C.fa
celescope/tools/trust4/database/hg19/TRA.fa
celescope/tools/trust4/database/hg19/TRB.fa
celescope/tools/trust4/database/hg19/bcrtcr.fa
celescope/tools/trust4/database/hg38/IGH.fa
celescope/tools/trust4/database/hg38/IGK.fa
celescope/tools/trust4/database/hg38/IGL.fa
celescope/tools/trust4/database/hg38/IMGT+C.fa
celescope/tools/trust4/database/hg38/TRA.fa
celescope/tools/trust4/database/hg38/TRB.fa
celescope/tools/trust4/database/hg38/bcrtcr.fa
celescope/tools/trust4/database/other/IGH.fa
celescope/tools/trust4/database/other/IGK.fa
celescope/tools/trust4/database/other/IGL.fa
celescope/tools/trust4/database/other/IMGT+C.fa
celescope/tools/trust4/database/other/TRA.fa
celescope/tools/trust4/database/other/TRB.fa
celescope/tools/trust4/database/other/bcrtcr.fa
celescope/tools/trust4/database/other/raw.fa
celescope/utils/__init__.py
celescope/utils/mapping_vdj.py
celescope/utils/mkgtf.py
celescope/vdj/__init__.py
celescope/vdj/count_vdj.py
celescope/vdj/mapping_vdj.py
celescope/vdj/mkref.py
celescope/vdj/multi_vdj.py
scripts/__init__.py
scripts/add_tag.py
scripts/add_zero_count_genes.py
scripts/extract_read.py
scripts/generate_docs.py
scripts/release_local.py
tests/__init__.py
tests/conftest.py
tests/test_function.py
tests/test_multi.py
tests/unittests/__init__.py
tests/unittests/snp/__init__.py
tests/unittests/snp/test_snp.py
tests/unittests/snp/test_variant_calling.py