AUTHORS.rst
CONTRIBUTING.rst
HISTORY.md
LICENCE
MANIFEST.in
README.md
setup.py
tox.ini
SIRVsuite/SIRVsuite.py
SIRVsuite/__init__.py
SIRVsuite/__main__.py
SIRVsuite/_version.py
SIRVsuite.egg-info/PKG-INFO
SIRVsuite.egg-info/SOURCES.txt
SIRVsuite.egg-info/dependency_links.txt
SIRVsuite.egg-info/entry_points.txt
SIRVsuite.egg-info/not-zip-safe
SIRVsuite.egg-info/requires.txt
SIRVsuite.egg-info/top_level.txt
SIRVsuite/Pipeline/__init__.py
SIRVsuite/Pipeline/countReader.py
SIRVsuite/Pipeline/helper.py
SIRVsuite/Pipeline/Concentration/SIRV_concentration.py
SIRVsuite/Pipeline/Concentration/__init__.py
SIRVsuite/Pipeline/Correlation/ERCC_correlation.py
SIRVsuite/Pipeline/Correlation/__init__.py
SIRVsuite/Pipeline/Coverage/SIRVset_coverage.py
SIRVsuite/Pipeline/Coverage/__init__.py
SIRVsuite/Pipeline/Coverage/cairoDrawer.py
SIRVsuite/Resources/ERCC92_Concentration.tsv
SIRVsuite/Resources/SIRV_isoforms_multi-fasta-annotation_190418a.gtf
SIRVsuite/Resources/SIRV_isoforms_multi-fasta_190418a.fasta
SIRVsuite/Resources/SIRV_isoforms_multi-fasta_190418a.fasta.fai
SIRVsuite/Resources/igv_session.xml
docs/Makefile
docs/README_summary.md
docs/authors.rst
docs/conf.py
docs/contributing.rst
docs/history.rst
docs/index.rst
docs/installation.rst
docs/make.bat
docs/readme.rst
docs/usage.rst
docs/formulas/CoD.svg
docs/formulas/FPKM_exp.svg
docs/formulas/FPKM_rel.svg
docs/formulas/scale_factor.svg
docs/output_preview/ERCC_correlation_preview.png
docs/output_preview/SIRV_boxplot_preview.png
docs/output_preview/SIRV_heatmap_preview_SIRV12.png
docs/output_preview/coverage_preview.png
tests/__init__.py
tests/test_parse.py
tests/test_pipeline.py
tests/test_data/alignment/SIRVset3/test_alignment_1.bam
tests/test_data/alignment/SIRVset3/test_alignment_1.bam.bai
tests/test_data/alignment/SIRVset3/test_alignment_2.bam
tests/test_data/alignment/SIRVset3/test_alignment_2.bam.bai
tests/test_data/alignment/SIRVset4/test_alignment_4.bam
tests/test_data/alignment/SIRVset4/test_alignment_4.bam.bai
tests/test_data/alignment/SIRVset4/test_alignment_5.bam
tests/test_data/alignment/SIRVset4/test_alignment_5.bam.bai
tests/test_data/mix2/SIRVset3/test_transcript_count_1
tests/test_data/mix2/SIRVset3/test_transcript_count_2
tests/test_data/mix2/SIRVset4/test_transcript_count_4
tests/test_data/mix2/SIRVset4/test_transcript_count_5
tests/test_data/sample_sheet_fail/sample_sheet_concentration.tsv
tests/test_data/sample_sheet_fail/sample_sheet_coverage.tsv
tests/test_data/sample_sheet_fail/sample_sheet_empty.tsv
tests/test_data/sample_sheet_fail/sample_sheet_noval.tsv
tests/test_data/sample_sheet_fail/sample_sheet_separators.tsv
tests/test_data/sample_sheet_fail/sample_sheet_skipval.tsv
tests/test_data/sample_sheet_pass/sample_sheet_test_SIRVset3.tsv
tests/test_data/sample_sheet_pass/sample_sheet_test_SIRVset4.tsv