.gitignore
.readthedocs.yaml
CHANGELOG.md
LICENSE
MANIFEST.in
README.md
setup.py
tox.ini
.github/workflows/python-app.yml
.github/workflows/python-package.yml
.github/workflows/python-publish.yml
docs/Makefile
docs/make.bat
docs/requirements.txt
docs/source/conf.py
docs/source/index.rst
docs/source/_images/MEME-motif-workflow.png
docs/source/_images/chip-seq-alignment-workflow.png
docs/source/_images/chipexo-notebooks.png
docs/source/_images/chipseq-notebooks.png
docs/source/_images/logo.png
docs/source/_images/macs2-cutoff-analysis.png
docs/source/_images/peak-caller-mace-workflow.png
docs/source/_images/peak-caller-macs2-workflow.png
docs/source/_images/rnaseq-dga-plots.png
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docs/source/_images/rnaseq-notebooks.png
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docs/source/_images/gcp/vminstances1.png
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docs/source/_images/win/activatewsldocker.png
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docs/source/_static/theme_overrides.css
docs/source/_static/examples/rnaseq_table.csv
docs/source/_static/examples/sample_sheet_paired_end.csv
docs/source/_static/examples/sample_sheet_single_end.csv
docs/source/_static/examples/sample_sheet_sra.csv
docs/source/cwl/chip-seq-alignment.rst
docs/source/cwl/differential_binding-DiffBind.rst
docs/source/cwl/meme-motif.rst
docs/source/cwl/peak-caller-MACE.rst
docs/source/cwl/peak-caller-MACS2.rst
docs/source/cwl/rnaseq-GO-enrichment-workflow.rst
docs/source/cwl/rnaseq-dga-workflow.rst
docs/source/cwl/rnaseq-star-aligner-workflow.rst
docs/source/cwl/rnaseq-tpmcalculator-qc-workflow.rst
docs/source/cwl/sra_workflow.rst
docs/source/cwl/trimmomatic.rst
docs/source/pipelines/bwaIndexes.rst
docs/source/pipelines/chipexoPipeline.rst
docs/source/pipelines/chipseqPipeline.rst
docs/source/pipelines/createBEDFromGTF.rst
docs/source/pipelines/creatingNewPipeline.rst
docs/source/pipelines/genomes.rst
docs/source/pipelines/installation.rst
docs/source/pipelines/pm4ngsgcp.rst
docs/source/pipelines/rnaseqDGAPipeline.rst
docs/source/pipelines/sampleSheet.rst
docs/source/pipelines/starIndexes.rst
docs/source/pipelines/ubuntu.rst
docs/source/pipelines/utils.rst
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examples/chipexo-single.yaml
examples/chipseq-paired.yaml
examples/rnaseq-sra-paired.yaml
examples/transcriptome_annot.yaml
requirements/base.in
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requirements/test.in
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src/pm4ngs/jupyterngsplugin/__init__.py
src/pm4ngs/jupyterngsplugin/databases/__init__.py
src/pm4ngs/jupyterngsplugin/databases/sra.py
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src/pm4ngs/jupyterngsplugin/files/fastq/__init__.py
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src/pm4ngs/jupyterngsplugin/markdown/rnaseq/dga.py
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src/pm4ngs/jupyterngsplugin/utils/count_lines.py
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src/pm4ngs/jupyterngsplugin/utils/yaml_utils.py
tests/test_pm4ngs.py