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NEWS
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NEWS
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CHANGES IN VERSION 1.35.1
-----------------------
o Update uniprot rest api.
CHANGES IN VERSION 1.29.1
-----------------------
o add citation.
CHANGES IN VERSION 1.27.9
-----------------------
o update the hyperlink of p.adjust.methods in documentation.
CHANGES IN VERSION 1.27.8
-----------------------
o add adjust p-value for testDAU function.
CHANGES IN VERSION 1.27.7
-----------------------
o optimize the label position of markers for logo.
CHANGES IN VERSION 1.27.6
-----------------------
o add markers for logo.
CHANGES IN VERSION 1.27.5
-----------------------
o allow multiple species for prepareProteome.
CHANGES IN VERSION 1.27.3
-----------------------
o fix the typo in dagLogo documentation.
CHANGES IN VERSION 1.27.2
-----------------------
o add availableSchemes function.
o fix the x-axis.
CHANGES IN VERSION 1.27.1
-----------------------
o adjust the Depends, Imports and Suggests packages
CHANGES IN VERSION 1.23.5
-----------------------
o add dontrun for prepareProteomeByFTP in case there is net connection issue.
CHANGES IN VERSION 1.23.4
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o return errors when type of getSequence is not correct.
CHANGES IN VERSION 1.23.3
-----------------------
o Update documentation.
CHANGES IN VERSION 1.23.1
-----------------------
o Add function prepareProteomeByFTP
o fix the bug in addScheme
CHANGES IN VERSION 1.21.4
-----------------------
o Fix the bug if there are multiple position in one peptides for fetchSequence.
CHANGES IN VERSION 1.21.3
-----------------------
o Update to grImport2
CHANGES IN VERSION 1.21.2
-----------------------
o merge the change by Haibo.
CHANGES IN VERSION 1.21.1
-----------------------
o documentation generated by RoxygenNote.
o add function cleanPeptides.
CHANGES IN VERSION 1.17.2
-----------------------
o Fix the bug for formatSequence.R when seq is not character.
CHANGES IN VERSION 1.17.1
-----------------------
o add .globals environment.
CHANGES IN VERSION 1.9.3
-----------------------
o To catch the error when biomaRt server does not response correctly in
documentations.
CHANGES IN VERSION 1.9.2
-----------------------
o change fetchSequence to accept sequences.
CHANGES IN VERSION 1.9.1
-----------------------
o update the test to testthat
CHANGES IN VERSION 1.7.2
-----------------------
NEW FEATURES
o add html documentation
CHANGES IN VERSION 1.7.2
-----------------------
NEW FEATURES
o customize the x axis as the amino acid physical position
o update the documentation
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.7.1
-----------------------
NEW FEATURES
o No changes classified as 'new features' (package under active
development)
BUG FIXES
o better layout of the sequence logo.
CHANGES IN VERSION 1.5.1
-----------------------
NEW FEATURES
o No changes classified as 'new features' (package under active
development)
BUG FIXES
o try to catch the error when mart server does not work.
CHANGES IN VERSION 1.3.6
-----------------------
NEW FEATURES
o add test files for fetchSequence function
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
CHANGES IN VERSION 1.3.4
-----------------------
NEW FEATURES
o No changes classified as 'bug fixes' (package under active
development)
BUG FIXES
o fetchSequences(): when using proteome object created from AAStringSet,
the columns 2 and 3 in the sequences data frame do not contain the expected
values.
o testDAU(): the counts() function returned NA for letters that were missing
in a given matrix; that lead to NaNs in the background matrix and to errors
during dagLogo() plotting. changed counts() to return 0 for missing letters.
o fix the typo in dagLogo()
CHANGES IN VERSION 1.3.3
-----------------------
NEW FEATURES
o add background Noise into test
o column label relative to the anchor when draw logos
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)