.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
docs/source/_images/rnaseq-go-plots.png
docs/source/_images/rnaseq-notebooks.png
docs/source/_images/rnaseq-quantification-tpmcalculator-qc-workflow.png
docs/source/_images/rnaseq-star-aligner-workflow.png
docs/source/_images/sra-workflow.png
docs/source/_images/top-level-structure.png
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/rnaseqDGAPipeline.rst
docs/source/pipelines/sampleSheet.rst
docs/source/pipelines/starIndexes.rst
docs/source/pipelines/utils.rst
examples/chipexo-single.yaml
examples/chipseq-paired.yaml
examples/rnaseq-sra-paired.yaml
examples/transcriptome_annot.yaml
requirements/base.in
requirements/base.txt
requirements/test.in
requirements/test.txt
src/pm4ngs/__init__.py
src/pm4ngs/cookiecutter.py
src/pm4ngs/main.py
src/pm4ngs.egg-info/PKG-INFO
src/pm4ngs.egg-info/SOURCES.txt
src/pm4ngs.egg-info/dependency_links.txt
src/pm4ngs.egg-info/entry_points.txt
src/pm4ngs.egg-info/requires.txt
src/pm4ngs.egg-info/top_level.txt
src/pm4ngs/jupyterngsplugin/__init__.py
src/pm4ngs/jupyterngsplugin/databases/__init__.py
src/pm4ngs/jupyterngsplugin/databases/sra.py
src/pm4ngs/jupyterngsplugin/files/__init__.py
src/pm4ngs/jupyterngsplugin/files/fastq/__init__.py
src/pm4ngs/jupyterngsplugin/files/fastq/fastqc.py
src/pm4ngs/jupyterngsplugin/image/__init__.py
src/pm4ngs/jupyterngsplugin/image/pdftobase64.py
src/pm4ngs/jupyterngsplugin/image/pngtobase64.py
src/pm4ngs/jupyterngsplugin/markdown/__init__.py
src/pm4ngs/jupyterngsplugin/markdown/alignment.py
src/pm4ngs/jupyterngsplugin/markdown/chipexo.py
src/pm4ngs/jupyterngsplugin/markdown/chipseq.py
src/pm4ngs/jupyterngsplugin/markdown/fastqc.py
src/pm4ngs/jupyterngsplugin/markdown/phantompeakqualtools.py
src/pm4ngs/jupyterngsplugin/markdown/rseqc.py
src/pm4ngs/jupyterngsplugin/markdown/utils.py
src/pm4ngs/jupyterngsplugin/markdown/rnaseq/__init__.py
src/pm4ngs/jupyterngsplugin/markdown/rnaseq/dga.py
src/pm4ngs/jupyterngsplugin/markdown/rnaseq/go.py
src/pm4ngs/jupyterngsplugin/markdown/rnaseq/quantification.py
src/pm4ngs/jupyterngsplugin/utils/__init__.py
src/pm4ngs/jupyterngsplugin/utils/count_lines.py
src/pm4ngs/jupyterngsplugin/utils/errors.py
src/pm4ngs/jupyterngsplugin/utils/load_content_dict.py
src/pm4ngs/jupyterngsplugin/utils/notebook.py
src/pm4ngs/jupyterngsplugin/utils/run_command.py
src/pm4ngs/jupyterngsplugin/utils/samples.py
src/pm4ngs/jupyterngsplugin/utils/working_dir.py
src/pm4ngs/jupyterngsplugin/utils/yaml_utils.py
tests/test_pm4ngs.py