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yezhengSTAT / ADTnorm

ADTnorm normalizes the cell surface protein measurement of CITE-seq data, facilitating across batches and across studies data integration.
https://yezhengstat.github.io/ADTnorm/articles/ADTnorm-tutorial.html
GNU General Public License v3.0
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Adding in peak detection overrides and other features #10

Closed Daniel-Caron closed 1 year ago

Daniel-Caron commented 1 year ago

This branch has new features for giving the user more control over landmark registration, including:

  1. Excluding zeroes, to prevent ADTnorm from altering zeroes (which in sequencing often result from dropout)
  2. Upper quantile clipping, to remove events with high outlier expression that may cause errors in warping
  3. Controls for altering min bandwidth for all markers (overwrites the previous keys specific to CD3, CD4, and CD8)
  4. Overrides for peak detection (to manually adjust the function in cases where peak detection fails)