methylprep
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FoxoTech
Python-based preprocessing software for Illumina methylation arrays
Hello Many thanks for providing methylprep. May I ask if the analysis of files originating form Infinium MethylationEPIC v2.0 chips is already possible?
Because DataFrame.append is deprecated and replaced by concat 1) file methylprep/files/sample_sheets.py adjusted 2) file methylprep/processing/infer_channel_switch.py adjusted There might be others .append in the code that need replacement, but these two...
Hello, Thanks for making and maintaining the project. As far as I see, Bioinformatics are commonly in R language, and python devs should either learn R or don't do Bioinformatics...
Hi, I'm new to python and methylation. I ran the methylprep and it generates all the required output, but in .csv and not in .pkl. So when I do methylcheck...
Bumps [certifi](https://github.com/certifi/python-certifi) from 2022.6.15 to 2023.7.22. Commits 8fb96ed 2023.07.22 afe7722 Bump actions/setup-python from 4.6.1 to 4.7.0 (#230) 2038739 Bump dessant/lock-threads from 3.0.0 to 4.0.1 (#229) 44df761 Hash pin Actions and...
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Exception raised when running a pipeline: > Traceback (most recent call last): > File "", line 1, in > File "/home/paul/miniconda3/lib/python3.11/site-packages/methylprep/processing/pipeline.py", line 331, in run_pipeline > data_container = SampleDataContainer( >...
Bumps [scipy](https://github.com/scipy/scipy) from 1.8.0 to 1.10.0. Release notes Sourced from scipy's releases. SciPy 1.10.0 Release Notes SciPy 1.10.0 is the culmination of 6 months of hard work. It contains many...
Bumps [requests](https://github.com/psf/requests) from 2.27.1 to 2.31.0. Release notes Sourced from requests's releases. v2.31.0 2.31.0 (2023-05-22) Security Versions of Requests between v2.3.0 and v2.30.0 are vulnerable to potential forwarding of Proxy-Authorization...
This PR was automatically created by Snyk using the credentials of a real user.Snyk has created this PR to fix one or more vulnerable packages in the `pip` dependencies of...
Hi, I'm trying to use the package to obtaiin copy numbers from the idat files, however it gives me a message, that this is still unsupported. Is there maybe an...
