mikemc/speedyseq

Issues

• phyloseq breaks (?) after using speedyseq?

  #80 opened 22 days ago by gabrielet
  6

• Clustering ASVs to OTUs

  #78 opened 22 days ago by ConstanceBtd
  3

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

  #79 opened 6 months ago by pickyseok
  5

• `glimpse()` does not return the original object type

  #77 opened 8 months ago by mikemc
  0

• `print()` fails with error on otu tables

  #76 opened 8 months ago by mikemc
  0

• tax_glom add sample names

  #75 opened 3 years ago by g-antonello
  2

• Add a function to convert a melted data frame to a phyloseq object

  #67 opened 4 years ago by mikemc
  2

• Add support for groups in mutate and transmute methods

  #74 opened 3 years ago by mikemc
  0

• Add method to facilitate using dplyr::count on tax tables and sample data

  #73 opened 4 years ago by mikemc
  0

• Add `ps_tibble()` functions for coercing phyloseq components to tibbles

  #64 opened 4 years ago by mikemc
  2

• Add joining functions for taxonomy tables and sample data

  #72 opened 4 years ago by mikemc
  1

• Create additional otu-table transformation methods

  #49 opened 4 years ago by mikemc
  0

• Add functions to rename taxa and samples

  #68 opened 4 years ago by mikemc
  1

• Update and organize function reference page

  #66 opened 4 years ago by mikemc
  1

• Add better handling of name conflicts in internal methods

  #51 opened 4 years ago by mikemc
  2

• Create dplyr verb functions for sample data and tax tables

  #69 opened 4 years ago by mikemc
  2

• add `transform_sample_data(physeq)` function to facilitate modifying sample data in pipes

  #33 opened 4 years ago by mikemc
  3

• Allow specification of abundance-summarizing function to be used when merging samples

  #47 opened 4 years ago by mikemc
  1

• Case where `merge_samples2()` fails on creating new sample data

  #71 opened 4 years ago by mikemc
  2

• Allow `tax_glom()` to accept unquoted rank names

  #70 opened 4 years ago by mikemc
  0

• Allow definition of new names in `merge_taxa_vec()`

  #46 opened 4 years ago by mikemc
  0

• `merge_samples2()` - Add column to sample data with number of merged samples

  #48 opened 4 years ago by mikemc
  0

• Allow criteria other than abundance when merging taxa

  #58 opened 4 years ago by bobthacker
  2

• Add version of `sweep()` that works on phyloseq and otu_table objects

  #62 opened 4 years ago by mikemc
  0

• Migrate from travis-ci.org to travis-ci.com

  #65 opened 4 years ago by mikemc
  1

• Fix CMD check errors and warnings

  #63 opened 4 years ago by mikemc
  1

• Replace `rlang::scoped_options()` with function from withr in `tibble_print()`

  #55 opened 4 years ago by mikemc
  0

• `as_tibble()` is masked when tibble is loaded after speedyseq

  #61 opened 4 years ago by mikemc
  1

• taxa and sample names don't print correctly in component print methods

  #60 opened 4 years ago by mikemc
  1

• Segfault memory issue on cluster

  #59 opened 4 years ago by ptpell77
  6

• Revamp constructors

  #57 opened 4 years ago by mikemc
  0

• Counting and formatting errors in `print()` output

  #56 opened 4 years ago by mikemc
  0

• Give messages when samples or taxa are dropped

  #36 opened 4 years ago by mikemc
  1

• Add option to `psmelt()` to choose between data.frame, data.table, and tibble output format

  #38 opened 4 years ago by mikemc
  0

• `merge_samples2()` fails when `group` values are numbers

  #52 opened 4 years ago by mikemc
  2

• Apply consistent rules about allowed sample names?

  #53 opened 4 years ago by mikemc
  2

• Add checks to `subset_*()` commands

  #54 opened 4 years ago by mikemc
  0

• `merge_taxa_vec()` fails when there is only one tax rank

  #50 opened 4 years ago by mikemc
  1

• Make argument names in `transform_sample_counts()` and `filter_taxa*()` match phyloseq's?

  #41 opened 4 years ago by mikemc
  1

• Output whether taxa are rows when print/showing phyloseq objects

  #40 opened 4 years ago by mikemc
  0

• Create function to enforce otu-table orientation

  #42 opened 4 years ago by mikemc
  0

• Adjust otu-table sample names to match sample data when subsetting duplicate samples

  #45 opened 4 years ago by mikemc
  0

• Add `tax_glom()` option to merge NA taxa into an "Unknown" category

  #44 opened 4 years ago by mikemc
  0

• Add "taxa are rows" or "taxa are columns" to `print(physeq)`

  #43 opened 4 years ago by mikemc
  1

• Improve error messages when an operation results in 0 samples or taxa

  #39 opened 4 years ago by mikemc
  0

• Add optional parameter to `psmelt()` to set column names

  #37 opened 4 years ago by mikemc
  0

• Give message/warning when subset_*() functions drop items due to NAs

  #35 opened 4 years ago by mikemc
  0

• Change `prune_taxa()` to never change taxon order

  #34 opened 5 years ago by mikemc
  0

• `tax_glom()` behaves incorrectly if a tax table or matrix named `new_tax_mat` exists

  #31 opened 5 years ago by mikemc
  2

• Check that (optional) named arguments are used in function calls

  #32 opened 5 years ago by mikemc
  0