Release History


  • exposed more beta_density_plot parameters, so it can be used to make a QC plot (highlighting one
    or several samples within a larger batch, and graying out the others in the plot).


  • improved read_geo() function, for downloading GEO methylation data sets and parsing meta_data from projects.
  • change org name from lifeepigenetics to FoxoBioScience on Github.


  • qc_plot bug fixes -99


  • -99 bug in negative controls fixed


  • tweaking custom-tables in ReportPDF


  • ReportPDF.run_qc() supports on_lambda, and any functions that require .methylprep_manifest_files can be set to look for manifests in /tmp using on_lambda=True


  • sklearn now optional for MDS


  • adds kwargs to functions for silent processing returning figure objects, and a report_pdf class that can run QC and generate a PDF report.
  • added version
  • p-value probe detection
  • hdbscan clustering functions
  • more QC methods testing


  • more tests, smart about df orientation, and re-organized files
  • added read_geo() for processed datafiles, and unit tests for it. Works with txt,csv,xlsx,pkl files
  • read_geo() docs
  • debugged filters.list_problem_probes:
  • updated the docs to have correct spelling for refs/reasons.
  • added a function that lets you see more detail on the probes and reasons/pubs criteria
  • added more genome studio QC functions,
    • improved .load function (but not consolidated through methyl-suite yet)
    • function .assign() for manually categorizing samples
    • unit testing on the function
    • get_sex() prediction
  • consolidated data loading for functions and uses fastest option