LICENSE
MANIFEST.in
README.md
README_SHORT
requirements.txt
setup.cfg
setup.py
scripts/adjust_matrix_coordinates.py
scripts/convertEnsemblToNames.py
scripts/filter_gene_type_matrix.py
scripts/merge_fastq.py
scripts/multi_qa.py
scripts/st_pipeline_run.py
scripts/st_qa.py
stpipeline/__init__.py
stpipeline/version.py
stpipeline.egg-info/PKG-INFO
stpipeline.egg-info/SOURCES.txt
stpipeline.egg-info/dependency_links.txt
stpipeline.egg-info/not-zip-safe
stpipeline.egg-info/requires.txt
stpipeline.egg-info/top_level.txt
stpipeline/common/__init__.py
stpipeline/common/adaptors.py
stpipeline/common/cdistance.pyx
stpipeline/common/clustering.py
stpipeline/common/dataset.py
stpipeline/common/fastq_utils.py
stpipeline/common/filterInputReads.pyx
stpipeline/common/gff_reader.py
stpipeline/common/sam_utils.py
stpipeline/common/saturation.py
stpipeline/common/stats.py
stpipeline/common/unique_events_parser.pyx
stpipeline/common/utils.py
stpipeline/core/__init__.py
stpipeline/core/annotation.py
stpipeline/core/mapping.py
stpipeline/core/pipeline.py
tests/__init__.py
tests/adaptors_test.py
tests/clustering_test.py
tests/__pycache__/__init__.cpython-37.pyc
tests/__pycache__/adaptors_test.cpython-37.pyc
tests/__pycache__/clustering_test.cpython-37.pyc
tests/__pycache__/pipeline_run_test.cpython-37.pyc
tests/config/Homo_sapiens.GRCh38.dna.chromosome.19.fa.gz
tests/config/annotations/Homo_sapiens.GRCh38.79_chr19.gtf
tests/config/contaminant_genomes/R45S5_R5S1/Rn45s_Rn5s.fasta
tests/config/idfiles/150204_arrayjet_1000L2_probes.txt
tests/input/arrayjet_1002/testdata_R1.fastq
tests/input/arrayjet_1002/testdata_R2.fastq