NEWS.md

In edpratt1/KINATESTID: A Pipeline for Kinase-Specific Artificial Peptide Design

KINATESTID (development version)

KINATESTID 2.1.1

Minor improvements and bug fixes

• Re-build bug fix so provided data files (e.g. ptm_key, screener_raw) don't have to be manually imported.

KINATESTID 2.1.0

New features

• All analysis and scoring functions only use the -4 to +4 flanking positions instead of -7 to +7.

• There are now file checks for data inputs for main functions to ensure all files are formatted properly prior to analysis.

KINATESTID 2.0.2

New features

• multi_screener() now outputs a list containing relevant analysis settings (e.g. method, pval_corr, etc) which will be automatically used by all downstream functions that take screener as an input. It is no longer necessary to manually specify these in any function that requires screener. Example functions this applies to:

  • generate_substrates()
  • score_candidates()
  • multi_candidate_screener()

• multi_candidate_screener now accepts an boolean(T/F) value to screen against a kinase family instead of the full screener library.

Minor improvements and bug fixes

• multi_candidate_screener() and multi_screener() now include percent progress bars.

• multi_screener() now provides ROC curves labeled with the optimal cutpoint for every kinase in the screener library.

• multi_screener() now accepts a user-defined specificity constraint using variable constrain. The default remains 90% specificity.

• generate_substrates()now allows user to manually curate amino acid residues when a maximum number of permutations (currently 250,000) is exceeded.

• Manual installation of Bioconductor is no longer necessary.

KINATESTID 2.0.1

Minor improvements and bug fixes

• multi_screener() now accepts any user-generated screener and uniprot files rather than only the package-provided ones.

• substrate_fisher_test() now works with amino acid properties.

• Vignette no longer requires the motifStack package to render properly.

edpratt1/KINATESTID documentation built on Feb. 5, 2022, 1:21 p.m.