• The curatedMetagenomicData() function now has a rownames argument:
    • "long", the default character string derived from MetaPhlAn3
    • "short", the NCBI Taxonomy species name from the CHOCOPhlAn database
      • "short" row names are validated against NCBI Taxonomy with taxize
    • "NCBI", the NCBI Taxonomy ID from the CHOCOPhlAn database
      • "NCBI" row names are validated against NCBI Taxonomy with taxize
      • rowData becomes NCBI Taxonomy ID numbers instead of taxa names
  • The sparse matrix data structure was switched from dgTMatrix to dgCMatrix
  • A few studies were reprocessed because of a minor error related to MetaPhlAn3
  • Changes inside the package were made to address bugs discovered by users
  • The combined_metadata object has been removed
  • curatedMetagenomicData now contains 20,282 samples from 86 studies
  • A total of 10,083 samples added since Bioconductor 3.10 (October 2019)
  • Studies added since Bioconductor 3.10 (October 2019):
    • AsnicarF_2021 (1098 samples)
    • BrooksB_2017 (408 samples)
    • ChuDM_2017 (86 samples)
    • DeFilippisF_2019 (97 samples)
    • GhensiP_2019 (113 samples)
    • GuptaA_2019 (60 samples)
    • HallAB_2017 (259 samples)
    • HMP_2019_ibdmdb (1627 samples)
    • HMP_2019_t2d (296 samples)
    • IjazUZ_2017 (94 samples)
    • KaurK_2020 (31 samples)
    • KeohaneDM_2020 (117 samples)
    • LassalleF_2017 (23 samples)
    • LifeLinesDeep_2016 (1135 samples)
    • LokmerA_2019 (57 samples)
    • MehtaRS_2018 (928 samples)
    • NagySzakalD_2017 (100 samples)
    • PasolliE_2019 (112 samples)
    • RosaBA_2018 (24 samples)
    • RubelMA_2020 (175 samples)
    • SankaranarayananK_2015 (37 samples)
    • ShaoY_2019 (1644 samples)
    • ThomasAM_2019_c (80 samples)
    • VilaAV_2018 (355 samples)
    • WampachL_2018 (63 samples)
    • WirbelJ_2018 (125 samples)
    • YachidaS_2019 (616 samples)
    • YassourM_2016 (36 samples)
    • YassourM_2018 (271 samples)
    • ZhuF_2020 (171 samples)
  • All raw data has been reprocessed with MetaPhlAn3 (v3.0.0) & HUMAnN3 (v3.0.0.alpha.3)
  • The curatedMetagenomicData() function has been refactored for efficiency
    • It now returns SummarizedExperiment/TreeSummarizedExperiment objects
    • Sample metadata always stays up to date and is updated weekly
    • It is now the primary (and only) means to access data
  • The mergeData() function has been refactored for accuracy and efficiency
  • The returnSamples() function has been added for returns across studies
  • The sampleMetadata object replaces the combined_metadata object
  • The combined_metadata object will be removed in the next release
  • A number of functions have moved directly to defunct status:
  • All named accessors (e.g. HMP_2012.pathcoverage.stool()) have become defunct
    • These were very hard to maintain and document; the package is now simpler
    • The curatedMetagenomicData() function replaces all named accessors
  • curatedMetagenomicData now contains 10,199 samples from 57 studies
  • A total of 2,209 samples added since Bioconductor 3.9 (April 2019)
  • Datasets added since Bioconductor 3.9 (April 2019):
    • DhakanDB_2019 (110 samples)
    • GopalakrishnanV_2018 (25 samples)
    • HansenLBS_2018 (208 samples)
    • JieZ_2017 (385 samples)
    • KieserS_2018 (27 samples)
    • MatsonV_2018 (39 samples)
    • PehrssonE_2016 (191 samples)
    • TettAJ_2019_a (68 samples)
    • TettAJ_2019_b (44 samples)
    • TettAJ_2019_c (50 samples)
    • YeZ_2018 (65 samples)
    • ZeeviD_2015 (900 samples)
  • curatedMetagenomicData now contains 8,087 samples from 45 studies
  • A total of 935 samples added since Bioconductor 3.8 (October 2018)
  • Datasets added since Bioconductor 3.8 (October 2018):
    • BackhedF_2015 (381 samples)
    • CosteaPI_2017 (279 samples)
    • FerrettiP_2018 (215 samples)
    • ThomasAM_2018b (60 samples)
  • Fixed an error in the metadata for HMP_2012 where posterior fornix samples were incorrectly tagged as ‘oralcavity’
  • Removed metadata from HMP_2012 attributing the study to Federal Urdu University… Karachi, Pakistan
  • WenC_2017 has been renamed ChengpingW_2017
  • WenC_2017 is deprecated and will be removed in the next release
  • curatedMetagenomicData now contains 7,152 samples from 41 studies
  • A total of 766 samples added since Bioconductor 3.7 (May 2018) relaese
  • Datasets added since Bioconductor 3.7 (May 2018) release:
    • Bengtsson-PalmeJ_2015 (70 samples)
    • DavidLA_2015 (49 samples)
    • KosticAD_2015 (124 samples)
    • LiSS_2016 (55 samples)
    • LoombaR_2017 (86 samples)
    • OlmMR_2017 (45 samples)
    • PasolliE_2018 (112 samples)
    • ShiB_2015 (48 samples)
    • ThomasAM_2018a (80 samples)
    • WenC_2017 (97 samples)
  • Fixed a bug in expressionset names where “-”s would be replaced with “_”
  • As a result of this fix, the following datasets are deprecated and will be removed in the next release:
    • Bengtsson_PalmeJ_2015
    • Castro_NallarE_2015
    • Heitz_BuschartA_2016
    • Obregon_TitoAJ_2015
  • curatedMetagenomicData now contains 6386 samples from 31 studies : )
  • A total of 328 samples added since Bioconductor 3.6 (October, 2017) release
  • Datasets added since Bioconductor 3.6 (October, 2017) release
    • LiJ_2017 (196 samples)
    • LouisS_2016 (92 samples)
    • SmitsSA_2017 (40 samples)
  • A curator field has been added to metadata to credit the work of curators
  • curatedMetagenomicData is currently on a diet and being refactored:
    • The docs directory used to build the github pages site has been moved to a branch, making the R package smaller
    • All code used for processing of raw data in R is moving to a seperate GitHub repository curatedMetagenomicDataPipeline
    • Curation takes place in the curatedMetagenomicDataCuration repository and curation is automatically checked; contributions are welcomed
    • All code used for processing of raw data beyond R is moving to a seperate GitHub repository curatedMetagenomicDataHighLoad
  • All data has been reprocessed to ensure updated and correct curation
  • curatedMetagenomicData now contains 6058 samples from 28 studies : )
  • A total of 3,152 samples added since Bioconductor 3.5 (April, 2017) release
  • Datasets added since Bioconductor 3.5 (April, 2017) release
    • HanniganGD_2017 (82 samples)
    • LiJ_2014 (260 samples)
    • AsnicarF_2017 (26 samples)
    • BritoIL_2016 (312 samples)
    • Castro-NallarE_2015 (32 samples)
    • ChngKR_2016 (78 samples)
    • FengQ_2015 (154 samples)
    • Heitz-BuschartA_2016 (53 samples)
    • LiuW_2016 (110 samples)
    • RaymondF_2016 (72 samples)
    • SchirmerM_2016 (471 samples)
    • VatanenT_2016 (785 samples)
    • VincentC_2016 (229 samples)
    • VogtmannE_2016 (110 samples)
    • XieH_2016 (250 samples)
    • YuJ_2015 (128 samples)
  • The cmdversion argument was removed from the curatedMetagenomicData() function
  • Calls to curatedMetagenomicData() simply return the newest version of the data
  • Older versions of datasets are accessible by using the named functions
  • Added phylogenetictree = TRUE argument to ExpressionSet2phyloseq()
  • doubled the number of samples to over 5,700
  • made naming of metadata more complete and strict, see inst/extdata/template.csv
  • mergeData() function for convenient merging of datasets
  • combined_metadata table providing all sample information for all studies
  • Data updated to include accession numbers
  • Minor updates to PaperFigures.Rmd vignette for reproducibility
  • Vast improvements to documentation, now more informative and compact
  • New function to coerce data to an MRexperiment class
  • New workhorse function to access data with wildcard search
  • Fun intro message for developers
  • Fixed a bug related to ExperimentHub that caused checks to fail
  • Fixed a bug related to ExperimentHub that caused checks to fail
  • Package vignette is updated to reflect in the intended use of ExperimentHub
  • Object level documentation is update for completeness and aliased
  • Minor description file changes to ensure collation order
  • Version bumped to reflect latest y version of Bioconductor
  • All data is reprocessed in R (v3.3.2)
  • Codebase is completely refactored to ExperimentHub specifications
  • Package vignette is updated to Rmd syntax and uses BiocStyle
  • New parallel functions allow for faster data processing
  • Documentation updated to use roxygen2
  • All data is reprocessed in R (v3.3.1)
  • All raw data is reprocessed with MetaPhlAn2 (v2.2.0) & HUMAnN2 (v0.7.0)