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 ----------------------- 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)