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mikemc
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speedyseq
Speedy versions of phyloseq functions
https://mikemc.github.io/speedyseq/
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Errors in calling phyloseq object after using filter_sample_data(), filter_tax_table()
#79
pickyseok
closed
3 months ago
5
Clustering ASVs to OTUs
#78
ConstanceBtd
opened
4 months ago
1
`glimpse()` does not return the original object type
#77
mikemc
closed
5 months ago
0
`print()` fails with error on otu tables
#76
mikemc
closed
5 months ago
0
tax_glom add sample names
#75
g-antonello
opened
2 years ago
2
Add support for groups in mutate and transmute methods
#74
mikemc
opened
3 years ago
0
Add method to facilitate using dplyr::count on tax tables and sample data
#73
mikemc
opened
3 years ago
0
Add joining functions for taxonomy tables and sample data
#72
mikemc
closed
3 years ago
1
Case where `merge_samples2()` fails on creating new sample data
#71
mikemc
opened
3 years ago
2
Allow `tax_glom()` to accept unquoted rank names
#70
mikemc
opened
3 years ago
0
Create dplyr verb functions for sample data and tax tables
#69
mikemc
closed
3 years ago
2
Add functions to rename taxa and samples
#68
mikemc
closed
3 years ago
1
Add a function to convert a melted data frame to a phyloseq object
#67
mikemc
opened
3 years ago
2
Update and organize function reference page
#66
mikemc
closed
3 years ago
1
Migrate from travis-ci.org to travis-ci.com
#65
mikemc
closed
3 years ago
1
Add `ps_tibble()` functions for coercing phyloseq components to tibbles
#64
mikemc
closed
3 years ago
2
Fix CMD check errors and warnings
#63
mikemc
closed
3 years ago
1
Add version of `sweep()` that works on phyloseq and otu_table objects
#62
mikemc
opened
3 years ago
0
`as_tibble()` is masked when tibble is loaded after speedyseq
#61
mikemc
closed
3 years ago
1
taxa and sample names don't print correctly in component print methods
#60
mikemc
closed
3 years ago
1
Segfault memory issue on cluster
#59
ptpell77
closed
3 years ago
6
Allow criteria other than abundance when merging taxa
#58
bobthacker
opened
3 years ago
2
Revamp constructors
#57
mikemc
opened
3 years ago
0
Counting and formatting errors in `print()` output
#56
mikemc
opened
3 years ago
0
Replace `rlang::scoped_options()` with function from withr in `tibble_print()`
#55
mikemc
opened
3 years ago
0
Add checks to `subset_*()` commands
#54
mikemc
opened
4 years ago
0
Apply consistent rules about allowed sample names?
#53
mikemc
opened
4 years ago
2
`merge_samples2()` fails when `group` values are numbers
#52
mikemc
closed
3 years ago
2
Add better handling of name conflicts in internal methods
#51
mikemc
opened
4 years ago
2
`merge_taxa_vec()` fails when there is only one tax rank
#50
mikemc
closed
4 years ago
1
Create additional otu-table transformation methods
#49
mikemc
opened
4 years ago
0
`merge_samples2()` - Add column to sample data with number of merged samples
#48
mikemc
opened
4 years ago
0
Allow specification of abundance-summarizing function to be used when merging samples
#47
mikemc
closed
3 years ago
1
Allow definition of new names in `merge_taxa_vec()`
#46
mikemc
opened
4 years ago
0
Adjust otu-table sample names to match sample data when subsetting duplicate samples
#45
mikemc
opened
4 years ago
0
Add `tax_glom()` option to merge NA taxa into an "Unknown" category
#44
mikemc
opened
4 years ago
0
Add "taxa are rows" or "taxa are columns" to `print(physeq)`
#43
mikemc
closed
4 years ago
1
Create function to enforce otu-table orientation
#42
mikemc
closed
4 years ago
0
Make argument names in `transform_sample_counts()` and `filter_taxa*()` match phyloseq's?
#41
mikemc
closed
4 years ago
1
Output whether taxa are rows when print/showing phyloseq objects
#40
mikemc
closed
4 years ago
0
Improve error messages when an operation results in 0 samples or taxa
#39
mikemc
opened
4 years ago
0
Add option to `psmelt()` to choose between data.frame, data.table, and tibble output format
#38
mikemc
closed
3 years ago
0
Add optional parameter to `psmelt()` to set column names
#37
mikemc
opened
4 years ago
0
Give messages when samples or taxa are dropped
#36
mikemc
opened
4 years ago
1
Give message/warning when subset_*() functions drop items due to NAs
#35
mikemc
opened
4 years ago
0
Change `prune_taxa()` to never change taxon order
#34
mikemc
opened
4 years ago
0
add `transform_sample_data(physeq)` function to facilitate modifying sample data in pipes
#33
mikemc
closed
3 years ago
3
Check that (optional) named arguments are used in function calls
#32
mikemc
opened
4 years ago
0
`tax_glom()` behaves incorrectly if a tax table or matrix named `new_tax_mat` exists
#31
mikemc
closed
4 years ago
2
Create a method for testing equivalence between phyloseq objects
#30
mikemc
opened
4 years ago
1
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