markrobinsonuzh/treesummarizedexperiment issues and pull requests

#85 - Coercion from phyloseq to TreeSummarizedExperiment

Issue - State: open - Opened by hpages over 1 year ago - 2 comments

#84 - About rarefaction

Issue - State: open - Opened by john123lol over 1 year ago

#83 - subsetByLeaf(tse) mixes up the rowTree tips and rownames of the new object

Issue - State: open - Opened by Begia over 1 year ago

#82 - Method to merge TreeSE objects?

Issue - State: open - Opened by antagomir over 2 years ago - 2 comments

#81 - Node information is not stored in rowLinks and subsetting problem

Issue - State: closed - Opened by dktanwar over 3 years ago - 1 comment

#80 - add subsetByLeaf; fix bugs in subsetByNode;

Pull Request - State: closed - Opened by fionarhuang over 3 years ago - 1 comment

#79 - add subsetByLeaf

Issue - State: closed - Opened by fionarhuang over 3 years ago

#78 - add asPhylo

Pull Request - State: closed - Opened by fionarhuang over 3 years ago - 1 comment

#77 - toTree function causing an error when the levels dont follow an ascending order of the group types

Issue - State: closed - Opened by NPSDC over 3 years ago - 8 comments

#76 - Fix warnings

Pull Request - State: closed - Opened by fionarhuang about 4 years ago

#75 - fix the issue 74

Pull Request - State: closed - Opened by fionarhuang about 4 years ago

#74 - setting rowTree throws error if some rows are dropped

Issue - State: closed - Opened by FelixErnst about 4 years ago - 2 comments

#73 - fix issue #72

Pull Request - State: closed - Opened by fionarhuang about 4 years ago

#72 - Can't install TSE successfully

Issue - State: closed - Opened by fionarhuang about 4 years ago - 1 comment

#71 - addLabel

Pull Request - State: closed - Opened by fionarhuang about 4 years ago - 1 comment

#70 - names of referenceSeq are set dynamically

Pull Request - State: closed - Opened by FelixErnst about 4 years ago - 1 comment

#69 - Rename signalNode to joinNode

Pull Request - State: closed - Opened by fionarhuang about 4 years ago

#68 - Subsetting an object with duplicated rownames

Issue - State: closed - Opened by FelixErnst about 4 years ago - 4 comments

#67 - fix a bug: allow colTree()/rowTree() to be set to NULL

Pull Request - State: closed - Opened by fionarhuang about 4 years ago

#66 - Create Codecov.yml

Pull Request - State: closed - Opened by fionarhuang about 4 years ago - 1 comment

#65 - upload Github action report to Codecov

Pull Request - State: closed - Opened by fionarhuang about 4 years ago

#64 - fix issue #62

Pull Request - State: closed - Opened by fionarhuang about 4 years ago

#63 - version bump

Pull Request - State: closed - Opened by fionarhuang about 4 years ago

#62 - bug: subsetting doesn't work anymore with saved objects

Issue - State: closed - Opened by FelixErnst about 4 years ago - 6 comments

#61 - Parallel

Pull Request - State: closed - Opened by fionarhuang about 4 years ago

#60 - Parallel

Pull Request - State: closed - Opened by fionarhuang about 4 years ago

#59 - feature: Adding a slot for information relating to rowData/FeatureIDs in addition to taxonomy

Issue - State: closed - Opened by microsud about 4 years ago - 10 comments

#58 - Parallel

Pull Request - State: closed - Opened by fionarhuang about 4 years ago

#57 - enable 'aggTSE' to provide parallel computation

Pull Request - State: closed - Opened by fionarhuang about 4 years ago

#56 - Bind

Pull Request - State: closed - Opened by fionarhuang about 4 years ago

#55 - Create r.yml

Pull Request - State: closed - Opened by fionarhuang about 4 years ago

#54 - Create r.yml

Pull Request - State: closed - Opened by fionarhuang about 4 years ago

#53 - allow rowTree & colTree as setters

Pull Request - State: closed - Opened by fionarhuang about 4 years ago

#52 - add rowTree & colTree as setters

Issue - State: closed - Opened by fionarhuang about 4 years ago

#51 - rbind, cbind #49

Pull Request - State: closed - Opened by fionarhuang about 4 years ago - 2 comments

#50 - version bump

Pull Request - State: closed - Opened by FelixErnst about 4 years ago

#49 - rbind, cbind

Issue - State: closed - Opened by fionarhuang about 4 years ago

#48 - test slack

Issue - State: closed - Opened by fionarhuang about 4 years ago - 1 comment

#47 - test slack

Issue - State: closed - Opened by fionarhuang about 4 years ago

#46 - Revert "fix node.label issue #44"

Pull Request - State: closed - Opened by fionarhuang about 4 years ago

#45 - fix node.label issue #44

Pull Request - State: closed - Opened by fionarhuang about 4 years ago

#44 - node.label issue

Issue - State: closed - Opened by antagomir over 4 years ago - 2 comments

#43 - added MicrobiomeExperiment class

Pull Request - State: closed - Opened by FelixErnst over 4 years ago - 12 comments

#42 - To do list

Issue - State: closed - Opened by fionarhuang over 4 years ago - 1 comment

#41 - added coercion methods to be able to coerce SummarizedExperiment to …

Pull Request - State: closed - Opened by FelixErnst over 4 years ago - 1 comment

#40 - Feature request: toTree with na.rm

Issue - State: closed - Opened by FelixErnst over 4 years ago - 5 comments
Labels: enhancement

#39 - Travis CI (error)

Issue - State: closed - Opened by fionarhuang over 4 years ago - 1 comment

#38 - Add test

Pull Request - State: closed - Opened by fionarhuang over 4 years ago

#37 - added additional tests

Pull Request - State: closed - Opened by FelixErnst over 4 years ago - 1 comment

#36 - #35

Pull Request - State: closed - Opened by fionarhuang over 4 years ago

#35 - bugfix in changeTree and fixed travis-CI config

Pull Request - State: closed - Opened by FelixErnst over 4 years ago - 2 comments

#34 - Tree inside TreeSummarizedExperiment is not subset

Issue - State: closed - Opened by FelixErnst over 4 years ago - 4 comments

#33 - add subsetByNode

Pull Request - State: closed - Opened by fionarhuang over 4 years ago

#33 - add subsetByNode

Pull Request - State: closed - Opened by fionarhuang over 4 years ago

#32 - Fix issue31

Pull Request - State: closed - Opened by fionarhuang over 4 years ago

#31 - fixes subsetting by rownames

Pull Request - State: closed - Opened by FelixErnst over 4 years ago

#30 - Subsetting by rownames is not available

Issue - State: closed - Opened by FelixErnst over 4 years ago - 6 comments