CLI betas, Methpype full tutorial #7
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marcmaxson
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Jul 23, 2019
marcmaxson
commented
- consolidate_values_for_sheet added to CLI (--betas, --m_values)
- consolidate_values_for_sheet option on CLI (--no_sample_sheet)
- readthedocs embedded on pypi now
- full tutorial markdown
note: structure of this 27k manifest was missing Strand (F/R) and Infinium_Design_Type (I or II). added columns; left blank.
* added function to create sample sheet, optional argument in run_pipeline * improved create_sample_sheet - don't rename builtin variables like `dict` - doesn't require GSM_ID to work - better logger info * added flag to allow process to work without a samplesheet. * make_sample_sheet flag
* tutorial and figures * added links in references * Update index.rst * Update index.rst * tutorial revisions * had to redo footnotes, github doesn't support default markdown footnotes * more revisions, focusing ease of use
marcmaxson
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Jul 25, 2019
* CLI betas, Methpype full tutorial (#7) * exporting beta values for methQC to use * exporting beta values for methQC to use * consolidate_scores function * consolidate function now part of pipeline --betas * consolidate part of pipeline * added 27k manifest note: structure of this 27k manifest was missing Strand (F/R) and Infinium_Design_Type (I or II). added columns; left blank. * added 27K ArrayType * bug fixes: ArrayTYpe to ArrayType and m_factor to m_value * CLI tweaks * Update README.md * Feature/create sample sheet (#4) * added function to create sample sheet, optional argument in run_pipeline * improved create_sample_sheet - don't rename builtin variables like `dict` - doesn't require GSM_ID to work - better logger info * added flag to allow process to work without a samplesheet. * make_sample_sheet flag * create_sample_sheet bug fixes * pipeline processing bugs fixed * added readthedocs embed and classifiers * Update setup.py * Full tutorial (#6) * tutorial and figures * added links in references * Update index.rst * Update index.rst * tutorial revisions * had to redo footnotes, github doesn't support default markdown footnotes * more revisions, focusing ease of use * updated links * 27k test was wrong * Update test_array.py * Update test_array.py * Update test_array.py * Update config.yml * Feature/beta (#8) * exporting beta values for methQC to use * exporting beta values for methQC to use * consolidate_scores function * consolidate function now part of pipeline --betas * consolidate part of pipeline * added 27k manifest note: structure of this 27k manifest was missing Strand (F/R) and Infinium_Design_Type (I or II). added columns; left blank. * added 27K ArrayType * bug fixes: ArrayTYpe to ArrayType and m_factor to m_value * CLI tweaks * Update README.md * Feature/create sample sheet (#4) * added function to create sample sheet, optional argument in run_pipeline * improved create_sample_sheet - don't rename builtin variables like `dict` - doesn't require GSM_ID to work - better logger info * added flag to allow process to work without a samplesheet. * make_sample_sheet flag * create_sample_sheet bug fixes * pipeline processing bugs fixed * added readthedocs embed and classifiers * Update setup.py * Full tutorial (#6) * tutorial and figures * added links in references * Update index.rst * Update index.rst * tutorial revisions * had to redo footnotes, github doesn't support default markdown footnotes * more revisions, focusing ease of use * updated links * 27k test was wrong * Update test_array.py * Update test_array.py * Update test_array.py * Update config.yml * permissions error on pipenv install --dev * fixed links and probe naming info * Update methpype_tutorial.md * trying different link format * trying relative path * relative path for all PNGs * more clean up * Update index.rst * Update index.rst * Update index.rst * Update conf.py * Delete Start_to_Finish_450KExample.ipynb * outdated * Update index.rst * Update cli.md * Update methpype_tutorial.md * Update methpype_tutorial.md
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