├── .gitattributes ├── .github ├── ISSUE_TEMPLATE │ └── bug_report.md └── workflows │ ├── deploy-pypi.yml │ ├── docker.yml │ └── lint_code.yml ├── .gitignore ├── .pre-commit-config.yaml ├── Dockerfile ├── LICENSE ├── MANIFEST.in ├── README.md ├── celescope ├── __init__.py ├── bulk_rna │ ├── __init__.py │ ├── multi_bulk_rna.py │ ├── split.py │ └── starsolo.py ├── bulk_vdj │ ├── __init__.py │ ├── consensus.py │ ├── mapping_vdj.py │ └── multi_bulk_vdj.py ├── capture_virus │ ├── __init__.py │ ├── analysis_virus.py │ ├── count.py │ ├── count_virus.py │ ├── featureCounts.py │ ├── filter_virus.py │ ├── mkref.py │ ├── multi_capture_virus.py │ └── star_virus.py ├── celescope.py ├── chemistry_dict.py ├── citeseq │ ├── __init__.py │ ├── analysis_cite.py │ ├── count_cite.py │ ├── mapping_tag.py │ └── multi_citeseq.py ├── data │ ├── Clindex │ │ ├── tag_barcode.fasta │ │ └── tag_linker.fasta │ ├── HLA │ │ └── hla_reference_rna.fasta │ ├── __init__.py │ ├── chemistry │ │ ├── GEXSCOPE-V1 │ │ │ ├── bc.txt │ │ │ ├── linker1.txt │ │ │ └── linker2.txt │ │ ├── GEXSCOPE-V2 │ │ │ ├── bc1.txt │ │ │ ├── bc2.txt │ │ │ ├── bc3.txt │ │ │ ├── linker1.txt │ │ │ └── linker2.txt │ │ ├── GEXSCOPE-V3 │ │ │ ├── bc1.txt │ │ │ ├── bc2.txt │ │ │ ├── bc3.txt │ │ │ ├── linker1.txt │ │ │ └── linker2.txt │ │ ├── __init__.py │ │ ├── bulk_rna-V1 │ │ │ └── bc.txt │ │ ├── bulk_rna-V2 │ │ │ └── bc.txt │ │ ├── bulk_rna-V3 │ │ │ └── bc.txt │ │ ├── bulk_rna-bulk_vdj_match │ │ │ └── bc.txt │ │ ├── bulk_vdj │ │ │ ├── bc.txt │ │ │ └── linker.txt │ │ ├── flv-V2 │ │ │ ├── bc1.txt │ │ │ ├── bc2.txt │ │ │ ├── bc3.txt │ │ │ ├── linker1.txt │ │ │ ├── linker2.txt │ │ │ └── linker3.txt │ │ ├── flv │ │ │ ├── bc.txt │ │ │ ├── linker1.txt │ │ │ └── linker2.txt │ │ ├── flv_rna-V2 │ │ │ ├── bc1.txt │ │ │ ├── bc2.txt │ │ │ ├── bc3.txt │ │ │ ├── linker1.txt │ │ │ ├── linker2.txt │ │ │ └── linker3.txt │ │ ├── flv_rna │ │ │ ├── bc.txt │ │ │ ├── linker1.txt │ │ │ └── linker2.txt │ │ ├── space-ff │ │ │ └── bc.txt │ │ └── space-ffpe │ │ │ └── bc.txt │ ├── fusion │ │ └── blood_1 │ │ │ ├── BCR_ABL1_PML_RARA_all.fasta │ │ │ ├── BCR_ABL1_PML_RARA_all_pos.txt │ │ │ └── mkref.sh │ ├── rRNA │ │ └── human_ribo.fasta │ ├── snp │ │ └── panel │ │ │ ├── CHIP.bed │ │ │ ├── blood_1.bed │ │ │ └── lung_1.bed │ └── sweetseq │ │ ├── sweetseq_barcode.fasta │ │ └── sweetseq_linker.fasta ├── dynaseq │ ├── __init__.py │ ├── conversion.py │ ├── conversion_worker.py │ ├── multi_dynaseq.py │ ├── replacement.py │ └── substitution.py ├── ffpe │ ├── __init__.py │ ├── analysis.py │ ├── multi_ffpe.py │ └── starsolo.py ├── flv_trust4 │ ├── __init__.py │ ├── annotation.py │ ├── assemble.py │ ├── mapping.py │ ├── multi_flv_trust4.py │ └── summarize.py ├── fusion │ ├── __init__.py │ ├── analysis_fusion.py │ ├── count_fusion.py │ ├── filter_fusion.py │ ├── mkref.py │ ├── multi_fusion.py │ └── star_fusion.py ├── hla │ ├── __init__.py │ ├── mapping_hla.py │ └── multi_hla.py ├── pathseq │ ├── __init__.py │ ├── analysis_pathseq.py │ ├── count_pathseq.py │ ├── multi_pathseq.py │ ├── pathseq.py │ └── starsolo.py ├── probe │ ├── __init__.py │ ├── barcode.py │ └── multi_probe.py ├── rna │ ├── __init__.py │ ├── analysis.py │ ├── mkref.py │ └── multi_rna.py ├── snp │ ├── __init__.py │ ├── analysis_snp.py │ ├── filter_snp.py │ ├── mkref.py │ ├── multi_snp.py │ ├── star.py │ ├── starsolo.py │ └── variant_calling.py ├── space │ ├── __init__.py │ ├── analysis.py │ ├── multi_space.py │ ├── starsolo.py │ └── utils.py ├── sweetseq │ ├── __init__.py │ ├── analysis_tag.py │ ├── count_tag.py │ ├── mapping_tag.py │ └── multi_sweetseq.py ├── tag │ ├── __init__.py │ ├── analysis_tag.py │ ├── count_tag.py │ ├── mapping_tag.py │ ├── multi_tag.py │ └── split_tag.py ├── templates │ ├── css │ │ ├── bootstrap.min.css │ │ ├── buttons.dataTables.min.css │ │ ├── dataTables.jqueryui.min.css │ │ ├── fontello-323401c3 │ │ │ ├── config.json │ │ │ ├── css │ │ │ │ ├── animation.css │ │ │ │ ├── fontello-codes.css │ │ │ │ ├── fontello-embedded.css │ │ │ │ ├── fontello-ie7-codes.css │ │ │ │ ├── fontello-ie7.css │ │ │ │ └── fontello.css │ │ │ └── font │ │ │ │ ├── fontello.eot │ │ │ │ ├── fontello.svg │ │ │ │ ├── fontello.ttf │ │ │ │ ├── fontello.woff │ │ │ │ └── fontello.woff2 │ │ ├── jquery-ui-git.css │ │ ├── jquery-ui.css │ │ └── jquery.dataTables.css │ ├── html │ │ ├── bulk_rna │ │ │ ├── base.html │ │ │ └── cells.html │ │ ├── bulk_vdj │ │ │ ├── base.html │ │ │ └── count_vdj.html │ │ ├── capture_rna │ │ │ ├── base.html │ │ │ └── count_capture_rna_summary.html │ │ ├── capture_virus │ │ │ ├── analysis_virus.html │ │ │ └── base.html │ │ ├── citeseq │ │ │ ├── analysis_cite.html │ │ │ └── base.html │ │ ├── common │ │ │ ├── img1.html │ │ │ └── logo.html │ │ ├── dynaseq │ │ │ ├── base.html │ │ │ ├── conversion.html │ │ │ ├── replacement.html │ │ │ └── substitution.html │ │ ├── ffpe │ │ │ └── base.html │ │ ├── flv_trust4 │ │ │ ├── annotation.html │ │ │ ├── base.html │ │ │ └── summarize.html │ │ ├── fusion │ │ │ ├── analysis_fusion.html │ │ │ └── base.html │ │ ├── hla │ │ │ └── base.html │ │ ├── mut │ │ │ └── base.html │ │ ├── pathseq │ │ │ ├── analysis_pathseq.html │ │ │ └── base.html │ │ ├── probe │ │ │ └── base.html │ │ ├── rna │ │ │ ├── analysis.html │ │ │ ├── base.html │ │ │ ├── count.html │ │ │ └── star.html │ │ ├── rna_5p3p │ │ │ └── base.html │ │ ├── rna_virus │ │ │ ├── analysis_rna_virus_summary.html │ │ │ └── base.html │ │ ├── snp │ │ │ ├── analysis_snp.html │ │ │ └── base.html │ │ ├── space │ │ │ ├── analysis.html │ │ │ └── base.html │ │ ├── sweetseq │ │ │ ├── analysis_tag.html │ │ │ └── base.html │ │ ├── tag │ │ │ ├── analysis_tag.html │ │ │ └── base.html │ │ ├── tcr_fl │ │ │ ├── analysis_tag_summary.html │ │ │ ├── base.html │ │ │ ├── count_tag_summary.html │ │ │ └── mapping_tag_summary.html │ │ ├── utils │ │ │ ├── analysis.html │ │ │ ├── col1_metrics.html │ │ │ ├── col2_metrics.html │ │ │ ├── end.html │ │ │ ├── head.html │ │ │ ├── help_info.html │ │ │ ├── preprocessing.html │ │ │ ├── start.html │ │ │ ├── step.html │ │ │ ├── table.html │ │ │ ├── table_dict.html │ │ │ └── table_script │ │ │ │ ├── bulk_rna.html │ │ │ │ ├── bulk_vdj.html │ │ │ │ ├── dynaseq.html │ │ │ │ ├── pathseq.html │ │ │ │ ├── rna.html │ │ │ │ ├── snp.html │ │ │ │ └── vdj.html │ │ └── vdj │ │ │ ├── base.html │ │ │ └── count_vdj.html │ ├── img │ │ ├── img1.png │ │ └── logo2.png │ └── js │ │ ├── bootstrap.min.js │ │ ├── buttons.flash.min.js │ │ ├── buttons.html5.min.js │ │ ├── buttons.print.min.js │ │ ├── dataTables.buttons.min.js │ │ ├── dataTables.jqueryui.min.js │ │ ├── jquery.dataTables.js │ │ ├── jquery.dataTables.min.js │ │ ├── jquery.min.3.3.1.js │ │ ├── jquery.min.js │ │ ├── jszip.min.js │ │ └── plotly-2.12.1.min.js ├── tools │ ├── __init__.py │ ├── analysis_wrapper.py │ ├── barcode.py │ ├── capture │ │ ├── __init__.py │ │ ├── analysis.py │ │ ├── count_bam.py │ │ ├── filter.py │ │ └── threshold.py │ ├── cells.py │ ├── consensus.py │ ├── count.py │ ├── cutadapt.py │ ├── debug.py │ ├── emptydrop_cr │ │ ├── __init__.py │ │ ├── cell_calling_3.py │ │ ├── get_plot_elements.py │ │ ├── sgt.py │ │ └── stats.py │ ├── featureCounts.py │ ├── make_ref.py │ ├── matrix.py │ ├── merge_table.py │ ├── multi.py │ ├── parse_chemistry.py │ ├── plotly_plot.py │ ├── prep.py │ ├── reference.py │ ├── report.py │ ├── sample.py │ ├── split_fastq.py │ ├── star_mixin.py │ ├── starsolo.py │ ├── step.py │ ├── tag │ │ ├── __init__.py │ │ ├── analysis_tag.py │ │ ├── count_tag.py │ │ └── mapping_tag.py │ ├── target_metrics.py │ ├── trust4 │ │ ├── AddSequenceToCDR3File.pl │ │ ├── GetFullLengthAssembly.pl │ │ ├── Immune_marker.json │ │ ├── barcoderep-filter.py │ │ ├── database │ │ │ ├── human │ │ │ │ ├── IGH.fa │ │ │ │ ├── IGK.fa │ │ │ │ ├── IGL.fa │ │ │ │ ├── IMGT+C.fa │ │ │ │ ├── TRA.fa │ │ │ │ ├── TRB.fa │ │ │ │ └── bcrtcr.fa │ │ │ └── mouse │ │ │ │ ├── BCR.fa │ │ │ │ ├── IGH.fa │ │ │ │ ├── IGK.fa │ │ │ │ ├── IGL.fa │ │ │ │ ├── IMGT+C.fa │ │ │ │ ├── TCR.fa │ │ │ │ ├── TRA.fa │ │ │ │ ├── TRB.fa │ │ │ │ └── bcrtcr.fa │ │ ├── trust-airr.pl │ │ ├── trust-barcoderep-to-10X.pl │ │ ├── trust-barcoderep.pl │ │ ├── trust-cluster.py │ │ ├── trust-simplerep.pl │ │ └── trust-stats.py │ └── utils.py ├── utils │ ├── __init__.py │ ├── mapping_vdj.py │ └── mkgtf.py └── vdj │ ├── __init__.py │ ├── count_vdj.py │ ├── mapping_vdj.py │ ├── mkref.py │ └── multi_vdj.py ├── conda_pkgs.txt ├── conda_pkgs ├── pathseq-conda.txt └── snp-conda.txt ├── doc ├── CHANGELOG.md ├── CONTRIBUTING.md ├── assay │ ├── multi_bulk_rna.md │ ├── multi_bulk_vdj.md │ ├── multi_capture_virus.md │ ├── multi_citeseq.md │ ├── multi_dynaseq.md │ ├── multi_ffpe.md │ ├── multi_flv_trust4.md │ ├── multi_fusion.md │ ├── multi_pathseq.md │ ├── multi_rna.md │ ├── multi_snp.md │ ├── multi_space.md │ ├── multi_sweetseq.md │ ├── multi_tag.md │ └── multi_vdj.md ├── chemistry.md ├── images │ ├── 384_well_number.png │ ├── 96-well.png │ └── multiqc_report.png └── user_guide.md ├── methods ├── EBV-2.md ├── EBV.md ├── rna.txt ├── snp_v.1.5.1.md └── tag_algorithm.txt 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