NEWS

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dagLogo 1.35.1

• Update uniprot rest api.

dagLogo 1.29.1

• add citation.

dagLogo 1.27.9

• update the hyperlink of p.adjust.methods in documentation.

dagLogo 1.27.8

• add adjust p-value for testDAU function.

dagLogo 1.27.7

• optimize the label position of markers for logo.

dagLogo 1.27.6

• add markers for logo.

dagLogo 1.27.5

• allow multiple species for prepareProteome.

dagLogo 1.27.3

• fix the typo in dagLogo documentation.

dagLogo 1.27.2

• add availableSchemes function.
• fix the x-axis.

dagLogo 1.27.1

• adjust the Depends, Imports and Suggests packages

dagLogo 1.23.5

• add dontrun for prepareProteomeByFTP in case there is net connection issue.

dagLogo 1.23.4

• return errors when type of getSequence is not correct.

dagLogo 1.23.3

• Update documentation.

dagLogo 1.23.1

• Add function prepareProteomeByFTP
• fix the bug in addScheme

dagLogo 1.21.4

• Fix the bug if there are multiple position in one peptides for fetchSequence.

dagLogo 1.21.3

• Update to grImport2

dagLogo 1.21.2

• merge the change by Haibo.

dagLogo 1.21.1

• documentation generated by RoxygenNote.
• add function cleanPeptides.

dagLogo 1.17.2

• Fix the bug for formatSequence.R when seq is not character.

dagLogo 1.17.1

• add .globals environment.

dagLogo 1.9.3

• To catch the error when biomaRt server does not response correctly in documentations.

dagLogo 1.9.2

• change fetchSequence to accept sequences.

dagLogo 1.9.1

• update the test to testthat

dagLogo 1.7.2

NEW FEATURES

• add html documentation
• customize the x axis as the amino acid physical position
• update the documentation

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

dagLogo 1.7.1

NEW FEATURES

• No changes classified as 'new features' (package under active development)

BUG FIXES

• better layout of the sequence logo.

dagLogo 1.5.1

NEW FEATURES

• No changes classified as 'new features' (package under active development)

BUG FIXES

• try to catch the error when mart server does not work.

dagLogo 1.3.6

NEW FEATURES

• add test files for fetchSequence function

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)

dagLogo 1.3.4

NEW FEATURES

• No changes classified as 'bug fixes' (package under active development)

BUG FIXES

• fetchSequences(): when using proteome object created from AAStringSet, the columns 2 and 3 in the sequences data frame do not contain the expected values.
• 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.
• fix the typo in dagLogo()

dagLogo 1.3.3

NEW FEATURES

• add background Noise into test
• column label relative to the anchor when draw logos

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)