lgatto/pbase issues and pull requests

#51 - Pbase check errors on BioC

Issue - State: closed - Opened by sgibb over 5 years ago - 3 comments
Labels: bug

#50 - Fix check

Pull Request - State: closed - Opened by jorainer over 6 years ago

#50 - Fix check

Pull Request - State: closed - Opened by jorainer over 6 years ago

#49 - ensembldb-related check errors

Issue - State: closed - Opened by jorainer over 6 years ago - 5 comments

#48 - mapToGenome fail to map protein domain

Issue - State: open - Opened by apastore about 7 years ago - 2 comments

#47 - Add PRanges and move part of functionality to ensembldb?

Issue - State: open - Opened by jorainer over 7 years ago - 7 comments

#46 - Mapping to genome fails without apparent reason

Issue - State: open - Opened by jorainer over 7 years ago - 1 comment

#45 - Add/replace pranges in Proteins object

Issue - State: open - Opened by jorainer over 7 years ago

#44 - Support proteogenomics formats

Issue - State: open - Opened by lgatto almost 8 years ago

#43 - Check strand checks in .mapToGenome2

Issue - State: open - Opened by jorainer almost 8 years ago

#42 - Pbase build failure on bioc devel/release

Issue - State: closed - Opened by sgibb almost 8 years ago - 13 comments
Labels: FTBFS

#41 - Pbase API

Issue - State: open - Opened by lgatto about 8 years ago - 3 comments
Labels: enhancement, Roadmap to 1.0.0

#40 - pranges selection

Issue - State: open - Opened by lgatto about 8 years ago - 3 comments

#39 - Documentating EnsDb methods

Issue - State: closed - Opened by lgatto about 8 years ago - 2 comments

#38 - RFC: changing Proteins class

Issue - State: open - Opened by lgatto about 8 years ago - 11 comments
Labels: enhancement, Roadmap to 1.0.0

#37 - Merge the ensembldb branch to master

Pull Request - State: closed - Opened by jorainer about 8 years ago

#36 - Documentation for Proteins,EnsDb and mapToGenome,EnsDb methods

Issue - State: closed - Opened by jorainer about 8 years ago - 1 comment
Labels: Roadmap to 1.0.0

#35 - No Uniprot ID support yet for ensembl methods

Issue - State: closed - Opened by jorainer about 8 years ago - 10 comments
Labels: Roadmap to 1.0.0

#34 - What names to be used for the GRangesList returned by mapToGenome?

Issue - State: open - Opened by jorainer about 8 years ago - 4 comments

#33 - New 1.0.0 Project and how to keep track of changes, ideas etc

Issue - State: closed - Opened by jorainer about 8 years ago - 1 comment

#32 - Pbase roadmap to version 1.0.0: changes in Proteins

Issue - State: closed - Opened by jorainer about 8 years ago - 1 comment
Labels: Roadmap to 1.0.0

#31 - Pbase roadmap to version 1.0.0: ensembldb integration

Issue - State: closed - Opened by jorainer about 8 years ago - 6 comments
Labels: Roadmap to 1.0.0

#30 - benchmark for .mapToGenome2

Issue - State: open - Opened by jorainer about 8 years ago

#29 - mapToGenome fails to map - strand features correctly

Issue - State: closed - Opened by jorainer about 8 years ago - 3 comments
Labels: bug

#28 - Is unique seqnames required for Proteins?

Issue - State: open - Opened by jorainer over 8 years ago - 7 comments

#27 - pcols/pmetadata method fails to return empty elements

Issue - State: closed - Opened by jorainer over 8 years ago - 2 comments
Labels: bug

#26 - Proteins object good to represent protein annotation?

Issue - State: closed - Opened by jorainer over 8 years ago - 1 comment

#25 - pcols accessor and replacement method

Issue - State: closed - Opened by lgatto almost 9 years ago - 12 comments
Labels: enhancement

#24 - New accessor for peptide ranges via AAStringSet

Issue - State: closed - Opened by baderd about 9 years ago - 12 comments
Labels: feature request

#23 - Packages for BioC 3.2 (devel) build/check errors

Issue - State: closed - Opened by lgatto over 9 years ago - 1 comment

#22 - Document plotting helper functions

Issue - State: closed - Opened by lgatto almost 10 years ago

#21 - Use plotting helper functions in vignettes

Issue - State: closed - Opened by lgatto almost 10 years ago

#20 - Parallelise pmapToGenome

Issue - State: open - Opened by lgatto almost 10 years ago - 3 comments
Labels: enhancement

#19 - Protein coverage

Issue - State: closed - Opened by lgatto almost 10 years ago - 4 comments

#18 - Failing test in test_heavylabels-functions

Issue - State: closed - Opened by lgatto almost 10 years ago - 1 comment

#17 - Functions instead of generics

Issue - State: closed - Opened by lgatto almost 10 years ago - 1 comment

#16 - Document non-unique peptide hits

Issue - State: open - Opened by lgatto almost 10 years ago - 2 comments

#15 - Align peptide and protein sequences

Issue - State: open - Opened by lgatto almost 10 years ago

#14 - Exon junction

Issue - State: closed - Opened by lgatto almost 10 years ago - 2 comments

#13 - mapToGenome,Proteins,GRangesList

Issue - State: closed - Opened by lgatto almost 10 years ago - 1 comment

#12 - Use names

Issue - State: closed - Opened by lgatto almost 10 years ago - 1 comment

#11 - sandbox on github but not svn

Issue - State: open - Opened by lgatto almost 10 years ago - 4 comments

#10 - remove GNU Makefile extensions

Pull Request - State: closed - Opened by sgibb almost 10 years ago

#9 - Building vignette `Pbase-data.Rmd` fails

Issue - State: closed - Opened by sgibb about 10 years ago - 2 comments
Labels: FTBFS

#8 - Building vignette `mapping.Rmd` fails.

Issue - State: closed - Opened by sgibb about 10 years ago
Labels: FTBFS

#7 - .fastaCommentParser fails when GN has a space

Issue - State: closed - Opened by lgatto over 10 years ago - 5 comments
Labels: bug

#6 - Calculate heavy labeled peptides

Pull Request - State: closed - Opened by sgibb over 10 years ago - 2 comments

#5 - .peptidePosition doesn't work for multiple peptides per protein

Issue - State: closed - Opened by sgibb over 10 years ago - 10 comments
Labels: bug

#4 - Pbase FTBFS

Issue - State: closed - Opened by sgibb over 10 years ago - 3 comments
Labels: FTBFS

#3 - add .calculateIsoelectricPoint

Pull Request - State: closed - Opened by sgibb over 10 years ago - 3 comments
Labels: wontfix

#2 - Plot Proteins

Issue - State: open - Opened by lgatto over 10 years ago

#1 - Empty pranges

Issue - State: closed - Opened by lgatto over 10 years ago - 2 comments

GitHub / lgatto/pbase issues and pull requests