Changes in version 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() method 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() method has been refactored for accuracy and efficiency - The returnSamples() method 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 methods 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() method replaces all named accessors Changes in version 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) Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 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() Changes in version 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 Changes in version 1.4.0 - Data updated to include accession numbers - Minor updates to PaperFigures.Rmd vignette for reproducibility Changes in version 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 Changes in version 1.0.4 - Fixed a bug related to ExperimentHub that caused checks to fail Changes in version 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) Changes in version 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)