NEWS

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curatedMetagenomicData 3.16.1

• Updates to rownames = "short" due to downstream changes in mia (@TuomasBorman, #309)
• Use convertToPhyloseq in vignette instead of makePhyloseqFromTreeSummarizedExperiment (@cmirzayi, #310)
• Use rep_named instead of deprecated list_along (@LiNk-NY)

curatedMetagenomicData 3.6.0

• curatedMetagenomicData now contains 22,588 samples from 93 studies
• A total of 2,055 samples added since Bioconductor 3.15 (April 2022)
• Studies added since Bioconductor 3.15 (April 2022):
  • BedarfJR_2017 (59 samples)
  • IaniroG_2022 (165 samples)
  • MetaCardis_2020_a (1,831 samples)
• Both "short" and "NCBI" row names were re-validated against NCBI Taxonomy

curatedMetagenomicData 3.4.0

• curatedMetagenomicData now contains 20,533 samples from 90 studies
• A total of 251 samples added since Bioconductor 3.14 (October 2021)
• Studies added since Bioconductor 3.14 (October 2021):
  • FrankelAE_2017 (39 samples)
  • LeeKA_2022 (165 samples)
  • PetersBA_2019 (27 samples)
  • WindTT_2020 (20 samples)
• Both "short" and "NCBI" row names were re-validated against NCBI Taxonomy

curatedMetagenomicData 3.2.0

• 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 3.0.0

• 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:
  • cmdValidVersions()
  • getMetaphlanTree()
  • ExpressionSet2MRexperiment()
  • ExpressionSet2phyloseq()
• 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 1.16.0

• 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 1.14.0

• 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 1.12.0

• 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 1.10.0

• 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 1.8.0

• 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()

curatedMetagenomicData 1.6.0

• 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

curatedMetagenomicData 1.4.0

• Data updated to include accession numbers
• Minor updates to PaperFigures.Rmd vignette for reproducibility

curatedMetagenomicData 1.2.0

• 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

curatedMetagenomicData 1.0.4

• Fixed a bug related to ExperimentHub that caused checks to fail

curatedMetagenomicData 1.0.0

• 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)

curatedMetagenomicData 0.99.8

• 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)