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/capture_rna/__init__.py
celescope/capture_rna/count_capture_rna.py
celescope/capture_rna/multi_capture_rna.py
celescope/capture_virus/__init__.py
celescope/capture_virus/analysis_capture_virus.py
celescope/capture_virus/count_capture_virus.py
celescope/capture_virus/mkref.py
celescope/capture_virus/multi_capture_virus.py
celescope/capture_virus/otsu.py
celescope/citeseq/Count_cite.py
celescope/citeseq/__init__.py
celescope/citeseq/analysis_cite.R
celescope/citeseq/analysis_cite.py
celescope/citeseq/count_cite.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/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/linker_4types
celescope/data/rRNA/human_ribo.fasta
celescope/data/snp/panel/lung_1.bed
celescope/dynaseq/Generate_T_C_matrix.R
celescope/dynaseq/__init__.py
celescope/dynaseq/conversion.py
celescope/dynaseq/multi_dynaseq.py
celescope/dynaseq/replace_tsne.py
celescope/dynaseq/replacement.py
celescope/dynaseq/substitution.py
celescope/fusion/__init__.py
celescope/fusion/count_fusion.py
celescope/fusion/mkref.py
celescope/fusion/multi_fusion.py
celescope/fusion/plot_fusion.R
celescope/fusion/star_fusion.py
celescope/hla/__init__.py
celescope/hla/mapping_hla.py
celescope/hla/multi_hla.py
celescope/mut/__init__.py
celescope/mut/count_mut.py
celescope/mut/mapping_mut.py
celescope/mut/multi_mut.py
celescope/mut/plot.R
celescope/rna/__init__.py
celescope/rna/analysis.py
celescope/rna/mkref.py
celescope/rna/multi_rna.py
celescope/rna/star.py
celescope/rna_virus/__init__.py
celescope/rna_virus/analysis_rna_virus.py
celescope/rna_virus/count_virus.py
celescope/rna_virus/multi_rna_virus.py
celescope/rna_virus/star_virus.py
celescope/scripts/gene_umi_summary.R
celescope/snp/__init__.py
celescope/snp/analysis_snp.py
celescope/snp/mkref.py
celescope/snp/multi_snp.py
celescope/snp/variant_calling.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/seurat_hashtag.R
celescope/tag/split_tag.py
celescope/tcr_fl/__init__.py
celescope/tcr_fl/assemble.py
celescope/tcr_fl/barcode_index.py
celescope/tcr_fl/multi_tcr_fl.py
celescope/tcr_fl/split_fq.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/capture_rna/base.html
celescope/templates/html/capture_rna/count_capture_rna_summary.html
celescope/templates/html/capture_virus/analysis_capture_virus_summary.html
celescope/templates/html/capture_virus/base.html
celescope/templates/html/capture_virus/star_virus_summary.html
celescope/templates/html/capture_virus/virus_summary.html
celescope/templates/html/citeseq/analysis_cite_summary.html
celescope/templates/html/citeseq/base.html
celescope/templates/html/citeseq/count_cite_summary.html
celescope/templates/html/common/barcode_summary.html
celescope/templates/html/common/consensus_summary.html
celescope/templates/html/common/cutadapt_summary.html
celescope/templates/html/common/img1.html
celescope/templates/html/common/logo.html
celescope/templates/html/common/sample_summary.html
celescope/templates/html/dynaseq/base.html
celescope/templates/html/dynaseq/replace_tsne_summary.html
celescope/templates/html/dynaseq/replacement_summary.html
celescope/templates/html/dynaseq/substitution_summary.html
celescope/templates/html/fusion/analysis_fusion_summary.html
celescope/templates/html/fusion/base.html
celescope/templates/html/fusion/star_fusion_summary.html
celescope/templates/html/hla/base.html
celescope/templates/html/mut/base.html
celescope/templates/html/rna/analysis_summary.html
celescope/templates/html/rna/base.html
celescope/templates/html/rna/featureCounts_summary.html
celescope/templates/html/rna/star_summary.html
celescope/templates/html/rna/umi_summary.html
celescope/templates/html/rna/umicount_distribution_summary.html
celescope/templates/html/rna_virus/analysis_rna_virus_summary.html
celescope/templates/html/rna_virus/base.html
celescope/templates/html/snp/analysis_snp_summary.html
celescope/templates/html/snp/base.html
celescope/templates/html/snp/target_metrics_summary.html
celescope/templates/html/snp/variant_calling_summary.html
celescope/templates/html/tag/analysis_tag_summary.html
celescope/templates/html/tag/base.html
celescope/templates/html/tag/count_tag_summary.html
celescope/templates/html/tag/mapping_tag_summary.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/trust_vdj/assemble_summary.html
celescope/templates/html/trust_vdj/res_sum_summary.html
celescope/templates/html/vdj/BCR_count_vdj_summary.html
celescope/templates/html/vdj/BCR_mapping_vdj_summary.html
celescope/templates/html/vdj/TCR_count_vdj_summary.html
celescope/templates/html/vdj/TCR_mapping_vdj_summary.html
celescope/templates/html/vdj/base.html
celescope/templates/html/vdj/clonetypes_table.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-1.58.4.min.js
celescope/templates/js/plotly-latest.min.js
celescope/tools/__init__.py
celescope/tools/analysis_mixin.py
celescope/tools/auto_assign.R
celescope/tools/barcode.py
celescope/tools/consensus.py
celescope/tools/count.py
celescope/tools/cutadapt.py
celescope/tools/debug.py
celescope/tools/featureCounts.py
celescope/tools/merge_table.py
celescope/tools/mkref.py
celescope/tools/multi.py
celescope/tools/report.py
celescope/tools/rescue.R
celescope/tools/run_analysis.R
celescope/tools/sample.py
celescope/tools/star_mixin.py
celescope/tools/step.py
celescope/tools/target_metrics.py
celescope/tools/utils.py
celescope/tools/cellranger3/__init__.py
celescope/tools/cellranger3/cell_calling_3.py
celescope/tools/cellranger3/get_plot_elements.py
celescope/tools/cellranger3/sgt.py
celescope/tools/cellranger3/stats.py
celescope/tools/cellranger3/wrapper.py
celescope/vdj/__init__.py
celescope/vdj/count_vdj.py
celescope/vdj/mapping_vdj.py
celescope/vdj/multi_vdj.py
scripts/__init__.py
scripts/add_tag.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