iferres/pagoo issues and pull requests

#65 - Change Shell and Cloud levels

Issue - State: open - Opened by alegione 9 months ago - 1 comment

#64 - Is it possible to run panaroo_2_pagoo without removing "refound_"?

Issue - State: open - Opened by emilywollmuth 12 months ago - 2 comments

#63 - Failing to process gene_presence_absence.csv file

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

#62 - how to add metadata in gene_presence_absence.csv file?

Issue - State: closed - Opened by neelam19051 over 1 year ago - 1 comment

#61 - Reading gffs: Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE, : row names contain missing values

Issue - State: closed - Opened by iferres over 1 year ago - 3 comments

#60 - gene IDs from Panaroo (1.3.2) presence/absence matrix file do not match IDs in GFF files

Issue - State: closed - Opened by qisun2 over 1 year ago - 6 comments

#59 - roary_2_pagoo Error: subscript contains invalid names

Issue - State: closed - Opened by jhcuarta almost 2 years ago - 35 comments

#58 - Is there a function pagoo_2_roary ?

Issue - State: open - Opened by diaspj about 2 years ago - 4 comments

#57 - panaroo to pagoo, support for bakta annos

Issue - State: closed - Opened by herber4 about 2 years ago - 29 comments

#56 - Failed with error: ‘package ‘S4Vectors’ required by ‘pagoo’ could not be found’

Issue - State: closed - Opened by MauriAndresMU1313 over 2 years ago - 14 comments

#55 - Cluster annotations do not match cluster names

Issue - State: closed - Opened by eam12 over 2 years ago - 5 comments

#54 - Remove metadata option

Issue - State: open - Opened by g1o almost 3 years ago - 3 comments
Labels: bug, enhancement

#53 - panaroo_2_pagoo error

Issue - State: closed - Opened by hayleyjaywilson almost 3 years ago - 6 comments

#52 - Add Willenbrock et al. 2007 coregenome fit function

Issue - State: open - Opened by iferres about 3 years ago

#51 - Bug when `$add_metadata()` with missing key at the end

Issue - State: closed - Opened by iferres about 3 years ago

#50 - Develop

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

#49 - Improve internal ggplot2 functions handling

Issue - State: open - Opened by iferres over 3 years ago
Labels: enhancement

#48 - load_pangenomeRDS() fails with old third party objects

Issue - State: closed - Opened by iferres over 3 years ago - 1 comment
Labels: bug

#47 - Implement $drop(hard = TRUE)

Issue - State: open - Opened by iferres over 3 years ago - 1 comment
Labels: enhancement

#46 - Re-assign genes to other clusters

Issue - State: open - Opened by iferres almost 4 years ago
Labels: enhancement, low-priority

#45 - Add `phylo` object as metadata

Issue - State: open - Opened by iferres almost 4 years ago - 5 comments
Labels: enhancement

#44 - $add_metadata() should override columns with same name

Issue - State: closed - Opened by iferres almost 4 years ago - 2 comments
Labels: bug, enhancement

#43 - Code coverage - shiny on tests

Issue - State: open - Opened by iferres almost 4 years ago
Labels: enhancement

#42 - added more recipes: ML phylogeny and nuc div vs distance

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

#41 - Develop

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

#40 - Develop

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

#39 - Develop

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

#38 - Develop

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

#37 - develop

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

#36 - Fixed most notes and warnings.

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

#35 - fixed core_seqs_4_phylo() and more tests (methods and plots)

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

#34 - add codecov badge

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

#33 - Add tests and covr workflow

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

#32 - bugfix

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

#31 - bugfix

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

#30 - Develop

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

#29 - Develop

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

#28 - Develop

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

#27 - Fixes vignettes. Add index.md different from README.md for pkgdown

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

#26 - New pkgdown site on docs/

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

#25 - Develop

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

#24 - bug fix. removed dep readr

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

#23 - Develop

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

#22 - Shiny

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

#21 - Develop

Pull Request - State: closed - Opened by iferres about 5 years ago