mikemc speedyseq issues

mikemc / speedyseq

Speedy versions of phyloseq functions

https://mikemc.github.io/speedyseq/

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issues

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Errors in calling phyloseq object after using filter_sample_data(), filter_tax_table()

#79 pickyseok closed 2 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 4 months ago
0
`print()` fails with error on otu tables

#76 mikemc closed 4 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