LICENSE
MANIFEST.in
README.md
README_SHORT
requirements.txt
setup.cfg
setup.py
doc/Makefile
doc/changes.rst
doc/conf.py
doc/contact.rst
doc/example.rst
doc/index.rst
doc/installation.rst
doc/intro.rst
doc/license.rst
doc/manual.rst
scripts/adjust_matrix_coordinates.py
scripts/convertEnsemblToNames.py
scripts/filter_gene_type_matrix.py
scripts/merge_fastq.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/gff_reader.py
stpipeline/common/sam_utils.py
stpipeline/common/saturation.py
stpipeline/common/stats.py
stpipeline/common/utils.py
stpipeline/core/__init__.py
stpipeline/core/annotation.py
stpipeline/core/mapping.py
stpipeline/core/pipeline.py
tests/__init__.py
tests/__init__.pyc
tests/adaptors_test.py
tests/adaptors_test.pyc
tests/clustering_test.py
tests/clustering_test.pyc
tests/pipeline_run_test.py
tests/pipeline_run_test.pyc
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