# 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)