mikemc / speedyseq

Speedy versions of phyloseq functions

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

mikemc/speedyseq Issues

tax_glom add sample names
Updated 2 years ago2
Add a function to convert a melted data frame to a phyloseq object
Updated 3 years ago2
Enable choosing to install stable or development version
Updated 3 years ago3
Add support for groups in mutate and transmute methods
Updated 3 years ago
Add method to facilitate using dplyr::count on tax tables and sample data
Updated 3 years ago
Add `ps_tibble()` functions for coercing phyloseq components to tibbles
Closed 3 years ago2
Add joining functions for taxonomy tables and sample data
Closed 3 years ago1
Create additional otu-table transformation methods
Updated 3 years ago
Add functions to rename taxa and samples
Closed 3 years ago1
Update and organize function reference page
Closed 3 years ago1
Add better handling of name conflicts in internal methods
Updated 3 years ago2
Create dplyr verb functions for sample data and tax tables
Closed 3 years ago2
add `transform_sample_data(physeq)` function to facilitate modifying sample data in pipes
Closed 3 years ago3
Allow specification of abundance-summarizing function to be used when merging samples
Closed 3 years ago1
Case where `merge_samples2()` fails on creating new sample data
Updated 3 years ago2
Allow `tax_glom()` to accept unquoted rank names
Updated 3 years ago
Allow definition of new names in `merge_taxa_vec()`
Updated 3 years ago
`merge_samples2()` - Add column to sample data with number of merged samples
Updated 3 years ago
Allow criteria other than abundance when merging taxa
Updated 3 years ago2
Add version of `sweep()` that works on phyloseq and otu_table objects
Updated 3 years ago
Migrate from travis-ci.org to travis-ci.com
Closed 3 years ago1
Fix CMD check errors and warnings
Closed 3 years ago1
Replace `rlang::scoped_options()` with function from withr in `tibble_print()`
Updated 3 years ago
`as_tibble()` is masked when tibble is loaded after speedyseq
Closed 3 years ago1
taxa and sample names don't print correctly in component print methods
Closed 3 years ago1
Segfault memory issue on cluster
Closed 3 years ago6
Revamp constructors
Updated 4 years ago
Counting and formatting errors in `print()` output
Updated 4 years ago
Give messages when samples or taxa are dropped
Updated 4 years ago1
Add option to `psmelt()` to choose between data.frame, data.table, and tibble output format
Closed 4 years ago
`merge_samples2()` fails when `group` values are numbers
Closed 4 years ago2
Apply consistent rules about allowed sample names?
Updated 4 years ago2
Add checks to `subset_*()` commands
Updated 4 years ago
`merge_taxa_vec()` fails when there is only one tax rank
Closed 4 years ago1
Make argument names in `transform_sample_counts()` and `filter_taxa*()` match phyloseq's?
Closed 4 years ago1
Output whether taxa are rows when print/showing phyloseq objects
Closed 4 years ago
Create function to enforce otu-table orientation
Closed 4 years ago
Adjust otu-table sample names to match sample data when subsetting duplicate samples
Updated 4 years ago
Add `tax_glom()` option to merge NA taxa into an "Unknown" category
Updated 4 years ago
Add "taxa are rows" or "taxa are columns" to `print(physeq)`
Closed 4 years ago1
Improve error messages when an operation results in 0 samples or taxa
Updated 4 years ago
Add `bad_empty` argument to `merge_taxa_vec()`
Updated 4 years ago
Add optional parameter to `psmelt()` to set column names
Updated 4 years ago
Give message/warning when subset_*() functions drop items due to NAs
Updated 4 years ago
Add more non-speed enhancements?
Closed 4 years ago1
Change `prune_taxa()` to never change taxon order
Updated 4 years ago
`tax_glom()` behaves incorrectly if a tax table or matrix named `new_tax_mat` exists
Closed 4 years ago2
Check that (optional) named arguments are used in function calls
Updated 4 years ago
Create a method for testing equivalence between phyloseq objects
Updated 4 years ago1
Package Download Issue
Closed 4 years ago3