All pull requests

Pull requests

• [fix] ggplot2::aes_string() wasdeprecated

  #1799·CedricMidoux opened Jun 24, 2026·

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• Add sample name to OTU table for single sample with import_biom()

  #1797·AnthonyPiot91 opened Mar 25, 2026·

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• Update plot-methods.R

  #1779·ssohail1 opened Feb 20, 2025·

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• Fix tables and Bioconductor build

  #1777·TuomasBorman opened Jan 15, 2025·

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• plot_tree: Added ggplot code to fix ugly legend "a"s

  #1748·stephanbitterwolf opened Apr 29, 2024·

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• New feature: allow merge_taxa to keep recored of merged (and inextension tax_glom).

  #1707·derele opened Oct 13, 2023·

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• Fixed paste error in rarefy_even_dept & improved efficiency

  #1630·salix-d opened Oct 23, 2022·

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• fisher.alpha(x, se=TRUE) is defunct since Dec 2013: can cause error

  #1582·jarioksa opened Apr 17, 2022·

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• Fix issues with plot_tree function

  #1445·ycl6 opened Feb 26, 2021·

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• Fix minor message formatting

  #1395·erictleung opened Sep 27, 2020·

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• Make logo in README smaller for ease of seeing

  #1340·erictleung opened Jun 4, 2020·

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• fixed plot_phyloseq checking for wrong slots ...

  #1330·FelixErnst opened May 13, 2020·

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• Fix formatting and remove trailing spaces

  #1289·erictleung opened Jan 1, 2020·

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• import_qiime couldn't parse the otu table of "taxonomy" column name

  #1253·xiangpin opened Oct 23, 2019·

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• Fix typo in plot ordination documentation

  #1246·erictleung opened Oct 12, 2019·

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• Update phyloseq_to_metagenomeSeq function

  #1216·jordiestelle opened Aug 23, 2019·

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• Update almostAllAccessors.R

  #1091·cedwardson4 opened Mar 10, 2019·

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• add label_size parameter for plot_network function

  #907·CedricMidoux opened Mar 28, 2018·

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• merge_samples checks for single value before coercing to numeric

  #893·benjjneb opened Mar 5, 2018Contributor·

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• Fix species richness for non-integer data (e.g., OTU proportions)

  #891·vmikk opened Mar 1, 2018·

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• Add missing whitespace in rarefy_even_depth message

  #875·vmikk opened Feb 1, 2018·

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• Added a SILVA parseFunction.

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  #854·grabear opened Dec 4, 2017·

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  14

• Added na.rm option to taxa_sums.

  #733·antagomir opened Mar 25, 2017·

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• ENH: add evenness metrics

  #575·colinbrislawn opened Jan 27, 2016·

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• Support for generalized UniFrac (again)

  #528·fangly opened Sep 19, 2015·

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  2