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iferres
/
pagoo
A comprehensive and intuitive encapsulated OO class system for analyzing bacterial pangenomes in R.
https://iferres.github.io/pagoo/
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issue with "ord <- hclust(dist(t(p$pan_matrix[, names(hload) ])))$order"
#66
sushanta26
opened
1 month ago
0
Change Shell and Cloud levels
#65
alegione
opened
10 months ago
1
Is it possible to run panaroo_2_pagoo without removing "refound_"?
#64
emilywollmuth
opened
1 year ago
2
Failing to process gene_presence_absence.csv file
#63
LovaRandriantseheno
opened
1 year ago
0
how to add metadata in gene_presence_absence.csv file?
#62
neelam19051
closed
1 year ago
1
Reading gffs: Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE, : row names contain missing values
#61
iferres
closed
1 year ago
3
gene IDs from Panaroo (1.3.2) presence/absence matrix file do not match IDs in GFF files
#60
qisun2
closed
1 year ago
6
roary_2_pagoo Error: subscript contains invalid names
#59
jhcuarta
closed
1 year ago
35
Is there a function pagoo_2_roary ?
#58
diaspj
opened
2 years ago
4
panaroo to pagoo, support for bakta annos
#57
herber4
closed
2 years ago
29
Failed with error: ‘package ‘S4Vectors’ required by ‘pagoo’ could not be found’
#56
MauriAndresMU1313
closed
1 year ago
14
Cluster annotations do not match cluster names
#55
eam12
closed
2 years ago
5
Remove metadata option
#54
g1o
opened
2 years ago
3
panaroo_2_pagoo error
#53
hayleyjaywilson
closed
3 years ago
6
Add Willenbrock et al. 2007 coregenome fit function
#52
iferres
opened
3 years ago
0
Bug when `$add_metadata()` with missing key at the end
#51
iferres
closed
3 years ago
0
Develop
#50
iferres
closed
3 years ago
1
Improve internal ggplot2 functions handling
#49
iferres
opened
3 years ago
0
load_pangenomeRDS() fails with old third party objects
#48
iferres
closed
3 years ago
1
Implement $drop(hard = TRUE)
#47
iferres
opened
3 years ago
1
Re-assign genes to other clusters
#46
iferres
opened
3 years ago
0
Add `phylo` object as metadata
#45
iferres
opened
3 years ago
5
$add_metadata() should override columns with same name
#44
iferres
closed
3 years ago
2
Code coverage - shiny on tests
#43
iferres
opened
3 years ago
0
added more recipes: ML phylogeny and nuc div vs distance
#42
iferres
closed
4 years ago
1
Develop
#41
iferres
closed
4 years ago
0
Develop
#40
iferres
closed
4 years ago
1
Develop
#39
iferres
closed
4 years ago
1
Develop
#38
iferres
closed
4 years ago
0
develop
#37
iferres
closed
4 years ago
0
Fixed most notes and warnings.
#36
iferres
closed
4 years ago
1
fixed core_seqs_4_phylo() and more tests (methods and plots)
#35
iferres
closed
4 years ago
0
add codecov badge
#34
iferres
closed
4 years ago
0
Add tests and covr workflow
#33
iferres
closed
4 years ago
0
bugfix
#32
iferres
closed
4 years ago
0
bugfix
#31
iferres
closed
4 years ago
0
Develop
#30
iferres
closed
4 years ago
0
Develop
#29
iferres
closed
4 years ago
0
Develop
#28
iferres
closed
4 years ago
0
Fixes vignettes. Add index.md different from README.md for pkgdown
#27
iferres
closed
4 years ago
0
New pkgdown site on docs/
#26
iferres
closed
4 years ago
0
Develop
#25
iferres
closed
4 years ago
0
bug fix. removed dep readr
#24
iferres
closed
4 years ago
0
Develop
#23
iferres
closed
4 years ago
0
Shiny
#22
iferres
closed
4 years ago
0
Develop
#21
iferres
closed
5 years ago
0
Develop
#20
iferres
closed
5 years ago
0
bump version to 0.2.0
#19
iferres
closed
5 years ago
0
Develop
#18
iferres
closed
5 years ago
1
drop = F on subsetted data frames
#17
iferres
closed
5 years ago
0
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