methylprep

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Bumps [setuptools](https://github.com/pypa/setuptools) from 63.1.0 to 65.5.1. Changelog Sourced from setuptools's changelog. v65.5.1 Misc ^^^^ #3638: Drop a test dependency on the mock package, always use :external+python:py:mod:unittest.mock -- by :user:hroncok #3659:...

dependabot[bot]

RUVm (postprocessing method to reduce batch effects)

1

>As with other types of microarray platforms, technical artifacts are a concern, including background fluorescence, dye-bias from the use of two color channels, bias caused by type I/II probe design,...

marcmaxson

- need to update pipeline to handle multi-batch processing and saving controls for each batch - loads manifest for each batch, which is slower, but allows run_pipeline to process separate...

marcmaxson

- For files of the `_signals.txt.gz` variety, it won't apply p-value detection to probes if the p-value column is there for each sample. - IF meth and unmeth column names...

marcmaxson

download support TAR of BED files too

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test with https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135770

marcmaxson

Hi, I've updated Methylprep to support custom manifests. All the APIs should work the same as they did before. Now the code will parse a manifest csv if the path...

notmaurox

I am trying to run methylprep process from the command line without poobah filtering. Documentation says: ``` --poobah By default, any beta-values or m-values output will contain all probes. If...

rowanhowellGE

Manifest

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Marc, I'm trying in vain to import my own manifest (version b5) with methylprep. Can you give me more explanation about this. BR Stef L

stefdecondor31

Control of output file location/names

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I would like to be able to specify where/with what prefixes output files should go - right now my workflow involves copying an entire BeadChip sequencing directory from separate sequencing...

paulaberry

I ran into this error in trying to create sample_sheets: ``` File "sample_sheets.py", line 198, in create_sample_sheet raise ValueError(file_name_error_msg.format(idat)) ValueError: This .idat file does not have the right pattern to...

f-marchi