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biocore / metagenomics_pooling_notebook

Jupyter notebooks to assist with sample processing
MIT License
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Spike in Analysis ported from R #97

Closed dhakim87 closed 1 year ago

dhakim87 commented 1 year ago

Can calculate coefficients for linear models to correct from relative to absolute abundance. Can rescale relative abundance read counts to absolute abundance read counts, relative abundance cell counts, or absolute abundance cell counts. TODO: absolute abundance cell counts per gram

antgonza commented 1 year ago

Merging as is to the dev branch. The plan is to keep working on it to improve functionality.

The planned changes are:

  1. divide cell counts by input grams [@justinshaffer]
  2. improve variable name of input grams [@justinshaffer]
  3. add the dilutions variable as a global variable and only leave available pool1 (the others should be commented) [@antgonza ]
  4. remove the R specific columns and requirements [@antgonza ]
justinshaffer commented 1 year ago

Just made the pull request to

  1. divide cell counts by input grams @.*** https://github.com/justinshaffer]
  2. improve variable name of input grams @.*** https://github.com/justinshaffer]

On Fri, Mar 24, 2023 at 9:49 AM Antonio Gonzalez @.***> wrote:

Merged #97 https://github.com/biocore/metagenomics_pooling_notebook/pull/97 into dev.

— Reply to this email directly, view it on GitHub https://github.com/biocore/metagenomics_pooling_notebook/pull/97#event-8840886119, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADSDCGA4XBB52GTEDMH563LW5XGDDANCNFSM6AAAAAAVJUWVLM . You are receiving this because you were mentioned.Message ID: <biocore/metagenomics_pooling_notebook/pull/97/issue_event/8840886119@ github.com>

-- Justin Shaffer, PhD Postdoctoral Researcher Rob Knight Group Department of Pediatrics, School of Medicine University of California, San Diego justinshafferbio.wordpress.com