├── .coverage ├── .gitignore ├── .travis.yml ├── AUTHORS ├── CHANGELOG ├── LICENSE ├── MANIFEST.in ├── README.md ├── README_SHORT ├── data ├── README.md ├── rep4.tar.gz └── rep9.tar.gz ├── docs ├── .buildinfo ├── .doctrees │ ├── changes.doctree │ ├── contact.doctree │ ├── environment.pickle │ ├── example.doctree │ ├── index.doctree │ ├── installation.doctree │ ├── intro.doctree │ ├── license.doctree │ └── manual.doctree ├── .nojekyll ├── _sources │ ├── changes.rst.txt │ ├── contact.rst.txt │ ├── example.rst.txt │ ├── index.rst.txt │ ├── installation.rst.txt │ ├── intro.rst.txt │ ├── license.rst.txt │ └── manual.rst.txt ├── _static │ ├── basic.css │ ├── classic.css │ ├── doctools.js │ ├── documentation_options.js │ ├── file.png │ ├── jquery-3.4.1.js │ ├── jquery.js │ ├── language_data.js │ ├── minus.png │ ├── plus.png │ ├── pygments.css │ ├── searchtools.js │ ├── sidebar.js │ ├── underscore-1.3.1.js │ └── underscore.js ├── changes.html ├── contact.html ├── example.html ├── genindex.html ├── index.html ├── installation.html ├── intro.html ├── license.html ├── manual.html ├── objects.inv ├── search.html └── searchindex.js ├── docsrc ├── Makefile ├── changes.rst ├── conf.py ├── contact.rst ├── example.rst ├── index.rst ├── installation.rst ├── intro.rst ├── license.rst └── manual.rst ├── ids ├── 1000L2_barcodes.txt ├── 1000L3_barcodes.txt ├── 1000L5_barcodes.txt ├── 1000L6_barcodes.txt ├── 1000L7_barcodes.txt ├── 1000L8_barcodes.txt └── 1000L9_barcodes.txt ├── requirements.txt ├── scripts ├── adjust_matrix_coordinates.py ├── convertEnsemblToNames.py ├── filter_gene_type_matrix.py ├── merge_fastq.py ├── multi_qa.py ├── st_pipeline_run.py └── st_qa.py ├── setup.cfg ├── setup.py ├── stpipeline ├── __init__.py ├── common │ ├── __init__.py │ ├── adaptors.py │ ├── cdistance.pyx │ ├── clustering.py │ ├── dataset.py │ ├── fastq_utils.py │ ├── filterInputReads.pyx │ ├── gff_reader.py │ ├── sam_utils.py │ ├── saturation.py │ ├── stats.py │ ├── unique_events_parser.pyx │ └── utils.py ├── core │ ├── __init__.py │ ├── annotation.py │ ├── mapping.py │ └── pipeline.py └── version.py ├── testrun.py ├── tests ├── __init__.py ├── adaptors_test.py ├── clustering_test.py ├── config │ ├── Homo_sapiens.GRCh38.dna.chromosome.19.fa.gz │ ├── annotations │ │ └── Homo_sapiens.GRCh38.79_chr19.gtf │ ├── contaminant_genomes │ │ └── R45S5_R5S1 │ │ │ └── Rn45s_Rn5s.fasta │ └── idfiles │ │ └── 150204_arrayjet_1000L2_probes.txt └── input │ └── arrayjet_1002 │ ├── testdata_R1.fastq │ └── testdata_R2.fastq ├── workflow.pdf └── workflow_extended.pdf /.coverage: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpatialTranscriptomicsResearch/st_pipeline/HEAD/.coverage -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 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