Files in waldronlab/curatedMetagenomicDataCuration
Curated Metagenomic Data of the Human Microbiome
.Rbuildignore
.github/.gitignore
.github/ISSUE_TEMPLATE/cMD_doi.yml
.github/ISSUE_TEMPLATE/cMD_paper_to_curate.yml
.github/workflows/curation.yml
.github/workflows/pkgdown.yaml
.gitignore
DESCRIPTION
NAMESPACE
R/PubMed-Class.R
R/PubMed.R
R/checkCuration.R
R/get_metadata.R
R/makeCombinedMetadata.R
R/metadata_long_form.R
README.md
curatedMetagenomicDataCuration.Rproj
inst/curated/ArtachoA_2021/ArtachoA_2021_metadata.tsv
inst/curated/AsnicarF_2017/AsnicarF_2017_metadata.tsv
inst/curated/AsnicarF_2017/add_lactating.py
inst/curated/AsnicarF_2021/AsnicarF_2021_metadata.tsv
inst/curated/AverinaOV_2020/AverinaOV_2020_metadata.tsv
inst/curated/BackhedF_2015/BackhedF_2015_metadata.tsv
inst/curated/BaiX_2021/BaiX_2021_metadata.tsv
inst/curated/BaruchEN_2021/BaruchEN_2021.tsv
inst/curated/BedarfJR_2017/BedarfJR_2017_metadata.tsv
inst/curated/Bengtsson-PalmeJ_2015/Bengtsson-PalmeJ_2015_metadata.tsv
inst/curated/BoktorJC_2023/BoktorJC_2023_metadata.tsv
inst/curated/BommanaS_2023/BommanaS_2023_metadata.tsv
inst/curated/BritoIL_2016/BritoIL_2016_metadata.tsv
inst/curated/BritoIL_2016/BritoIL_2016_notes.txt
inst/curated/BrooksB_2017/BrooksB_2017_metadata.tsv
inst/curated/Castro-NallarE_2015/Castro-NallarE_2015_metadata.tsv
inst/curated/Castro-NallarE_2015/Castro-NallarE_2015_notes.txt
inst/curated/ChengpingW_2017/ChengpingW_2017_metadata.tsv
inst/curated/ChngKR_2016/ChngKR_2016_metadata.tsv
inst/curated/ChngKR_2016/ChngKR_2016_notes.txt
inst/curated/ChuDM_2017/ChuDM_2017_metadata.tsv
inst/curated/ContevilleLC_2019/ContevilleLC_2019_metadata.tsv
inst/curated/CosteaPI_2017/CosteaPI_2017_metadata.tsv
inst/curated/DavarD_2021/DavarD_2021.tsv
inst/curated/DavidLA_2015/DavidLA_2015_metadata.tsv
inst/curated/DeFilippisF_2019/DeFilippisF_2019_metadata.tsv
inst/curated/DhakanDB_2019/DhakanDB_2019_metadata.tsv
inst/curated/FanY_2023/FanY_2023_metadata.tsv
inst/curated/FengQ_2015/FengQ_2015_metadata.tsv
inst/curated/FengQ_2015/FengQ_2015_notes.txt
inst/curated/FengQ_2015/remap.py
inst/curated/FerrettiP_2018/FerrettiP_2018_metadata.tsv
inst/curated/FrankelAE_2017/FrankelAE_2017_metadata.tsv
inst/curated/GhensiP_2019/GhensiP_2019_metadata.tsv
inst/curated/GopalakrishnanV_2018/GopalakrishnanV_2018_metadata.tsv
inst/curated/GunjurA_2024/GunjurA_2024_metadata.tsv
inst/curated/GuptaA_2019/GuptaA_2019_metadata.tsv
inst/curated/HMP_2012/HMP_2012_metadata.tsv
inst/curated/HMP_2012/correct_subjects.py
inst/curated/HMP_2019_ibdmdb/HMP_2019_ibdmdb_metadata.tsv
inst/curated/HMP_2019_t2d/HMP_2019_t2d_metadata.tsv
inst/curated/HallAB_2017/HallAB_2017_metadata.tsv
inst/curated/HanniganGD_2017/HanniganGD_2017_metadata.tsv
inst/curated/HansenLBS_2018/HansenLBS_2018_metadata.tsv
inst/curated/HeQ_2017/HeQ_2017_metadata.tsv
inst/curated/Heitz-BuschartA_2016/Heintz-BuschartA_2016_notes.txt
inst/curated/Heitz-BuschartA_2016/Heitz-BuschartA_2016_metadata.tsv
inst/curated/IaniroG_2022/IaniroG_2022_metadata.tsv
inst/curated/IjazUZ_2017/IjazUZ_2017_metadata.tsv
inst/curated/JacobsonDK_2021/JacobsonDK_2021_metadata.tsv
inst/curated/JieZ_2017/JieZ_2017_metadata.tsv
inst/curated/KarlssonFH_2013/KarlssonFH_2013_metadata.tsv
inst/curated/KarlssonFH_2013/KarlssonFH_2013_notes.txt
inst/curated/KarlssonFH_2013/disease
inst/curated/KarlssonFH_2013/setup.py
inst/curated/KartalE_2022/KartalE_2022_metadata.tsv
inst/curated/KaurK_2020/KaurK_2020_metadata.tsv
inst/curated/KeohaneDM_2020/KeohaneDM_2020_metadata.tsv
inst/curated/KieserS_2018/KieserS_2018_metadata.tsv
inst/curated/KosticAD_2015/KosticAD_2015_metadata.tsv
inst/curated/LassalleF_2017/LassalleF_2017_metadata.tsv
inst/curated/LeChatelierE_2013/LeChatelierE_2013_metadata.tsv
inst/curated/LeChatelierE_2013/asses.py
inst/curated/LeeKA_2022/LeeKA_2022_metadata.tsv
inst/curated/LiJ_2014/LiJ_2014_metadata.tsv
inst/curated/LiJ_2017/LiJ_2017_metadata.tsv
inst/curated/LiSS_2016/LiSS_2016_metadata.tsv
inst/curated/LifeLinesDeep_2016/LifeLinesDeep_2016_metadata.tsv
inst/curated/LiuW_2016/LiuW_2016_metadata.tsv
inst/curated/LiuW_2016/LiuW_2016_notes.txt
inst/curated/LiuW_2016/set.py
inst/curated/LokmerA_2019/LokmerA_2019_metadata.tsv
inst/curated/LomanNJ_2013/LomanNJ_2013_metadata.tsv
inst/curated/LoombaR_2017/LoombaR_2017_metadata.tsv
inst/curated/LouisS_2016/LouisS_2016_metadata.tsv
inst/curated/MaoL_2021/MaoL_2021_metadata.tsv
inst/curated/MatsonV_2018/MatsonV_2018_metadata.tsv
inst/curated/McCullochJA_2022/McCullochJA_2022_metadata.tsv
inst/curated/MehtaRS_2018/MehtaRS_2018_metadata.tsv
inst/curated/MejiaR_2020/MejiaR_2020_metadata.tsv
inst/curated/MetaCardis_2020_a/MetaCardis_2020_a_metadata.tsv
inst/curated/NagataN_2022/NagataN_2022_metadata.tsv
inst/curated/NagySzakalD_2017/NagySzakalD_2017_metadata.tsv
inst/curated/NayakRR_2021/NayakRR_2021_metadata.tsv
inst/curated/NielsenHB_2014/NielsenHB_2014_metadata.tsv
inst/curated/NielsenHB_2014/mapping.txt
inst/curated/NielsenHB_2014/set.py
inst/curated/Obregon-TitoAJ_2015/Obregon-TitoAJ_2015_metadata.tsv
inst/curated/Obregon-TitoAJ_2015/runs.txt
inst/curated/Obregon-TitoAJ_2015/set.py
inst/curated/OhJ_2014/OhJ_2014_metadata.tsv
inst/curated/OhJ_2014/map.py
inst/curated/OhJ_2014/mapping.txt
inst/curated/OhJ_2016/OhJ_2016_metadata.txt.nocheck
inst/curated/OhJ_2016/map.py
inst/curated/OhJ_2016/mapping.txt
inst/curated/OlmMR_2017/OlmMR_2017_metadata.tsv
inst/curated/OsakunorDNM_2020/OsakunorDNM_2020_metadata.tsv
inst/curated/PallejaA_2018/PallejaA_2018_metadata.tsv
inst/curated/PasolliE_2019/PasolliE_2019_metadata.tsv
inst/curated/PehrssonE_2016/PehrssonE_2016_metadata.tsv
inst/curated/PernigoniN_2021/PernigoniN_2021_metadata.tsv
inst/curated/PetersBA_2019/PetersBA_2019_metadata.tsv
inst/curated/QinJ_2012/QinJ_2012_metadata.tsv
inst/curated/QinN_2014/QinN_2014_metadata.tsv
inst/curated/QinN_2014/QinN_2015_notes.txt
inst/curated/QinN_2014/QinN_RUNS.txt
inst/curated/QinN_2014/addruns.py
inst/curated/README.md
inst/curated/RampelliS_2015/RampelliS_2015_metadata.tsv
inst/curated/RampelliS_2015/RampelliS_2015_notes.txt
inst/curated/RaymondF_2016/RaymondF_2016_metadata.tsv
inst/curated/RaymondF_2016/RaymondF_2016_notes.txt
inst/curated/RosaBA_2018/RosaBA_2018_metadata.tsv
inst/curated/RoutyB_2018/RoutyB_2018.tsv
inst/curated/RubelMA_2020/RubelMA_2020_metadata.tsv
inst/curated/SankaranarayananK_2015/SankaranarayananK_2015_metadata.tsv
inst/curated/SchirmerM_2016/SchirmerM_2016_metadata.tsv
inst/curated/SchirmerM_2016/SchirmerM_2016_notes.txt
inst/curated/ShaoY_2019/ShaoY_2019_metadata.tsv
inst/curated/ShiB_2015/ShiB_2015_metadata.tsv
inst/curated/SmitsSA_2017/SmitsSA_2017_metadata.tsv
inst/curated/Soto-GironMJ_2021/Soto-GironMJ_2021_metadata.tsv
inst/curated/SpencerCN_2021/SpencerCN_2021_metadata.tsv
inst/curated/TeeMZ_2022/TeeMZ_2022_metadata.tsv
inst/curated/TettAJ_2016/TettAJ_2016_metadata.tsv
inst/curated/TettAJ_2019_a/TettAJ_2019_a_metadata.tsv
inst/curated/TettAJ_2019_b/TettAJ_2019_b_metadata.tsv
inst/curated/TettAJ_2019_c/TettAJ_2019_c_metadata.tsv
inst/curated/ThomasAM_2018a/ThomasAM_2018a_metadata.tsv
inst/curated/ThomasAM_2018b/ThomasAM_2018b_metadata.tsv
inst/curated/ThomasAM_2019_c/ThomasAM_2019_c_metadata.tsv
inst/curated/Valles-ColomerM_2023_a/Valles-ColomerM_2023_a_metadata.tsv
inst/curated/Valles-ColomerM_2023_b/Valles-ColomerM_2023_b_metadata.tsv
inst/curated/Valles-ColomerM_2023_c/Valles-ColomerM_2023_c_metadata.tsv
inst/curated/Valles-ColomerM_2023_d/Valles-ColomerM_2023_d_metadata.tsv
inst/curated/Valles-ColomerM_2023_e/Valles-ColomerM_2023_e_metadata.tsv
inst/curated/VatanenT_2016/VatanenT_2016_metadata.tsv
inst/curated/VilaAV_2018/VilaAV_2018_metadata.tsv
inst/curated/VincentC_2016/VincentC_2016_metadata.tsv
inst/curated/VincentC_2016/VincentC_2016_notes.txt
inst/curated/VogtmannE_2016/VogtmannE_2016_metadata.tsv
inst/curated/VogtmannE_2016/adjust.py
inst/curated/WallenZD_2022/WallenZD_2022_metadata.tsv
inst/curated/WampachL_2018/WampachL_2018_metadata.tsv
inst/curated/WenC_2017/WenC_2017_metadata.tsv
inst/curated/WibowoMC_2021/WibowoMC_2021_metadata.tsv
inst/curated/WindTT_2020/WindTT_2020_metadata.tsv
inst/curated/WirbelJ_2018/WirbelJ_2018_metadata.tsv
inst/curated/XieH_2016/XieH_2016_metadata.tsv
inst/curated/XieH_2016/XieH_2016_notes.txt
inst/curated/XuQ_2021/XuQ_2021_metadata.tsv
inst/curated/YachidaS_2019/YachidaS_2019_metadata.tsv
inst/curated/YangJ_2020/YangJ_2020_metadata.tsv
inst/curated/YassourM_2016/YassourM_2016_metadata.tsv
inst/curated/YassourM_2018/YassourM_2018_metadata.tsv
inst/curated/YeZ_2018/YeZ_2018_metadata.tsv
inst/curated/YeZ_2020/YeZ_2020_metadata.tsv
inst/curated/YuJ_2015/YuJ_2015_metadata.tsv
inst/curated/ZeeviD_2015/ZeeviD_2015_metadata.tsv
inst/curated/ZellerG_2014/ZellerG_2014_metadata.tsv
inst/curated/ZellerG_2014/mapping
inst/curated/ZellerG_2014/msb145645-sup-0002-DatasetS1.xlsx
inst/curated/ZellerG_2014/msb145645-sup-0003-DatasetS2.xlsx
inst/curated/ZellerG_2014/remap.py
inst/curated/ZhangX_2015/ZhangX_2015_metadata.tsv
inst/curated/ZhouC_2020/ZhouC_2020_metadata.tsv
inst/curated/ZhuF_2020/ZhuF_2020_metadata.tsv
inst/curated/iMSMS_2022/iMSMS_2022_metadata.tsv
inst/extdata/README.md
inst/extdata/cMD_curated_metadata_release.csv
inst/extdata/cMD_data_dictionary.csv
man/PubMed-class.Rd
man/PubMed.Rd
man/checkCuration.Rd
man/get_metadata.Rd
man/makeCombinedMetadata.Rd
man/metadata_long_form.Rd
man/study_long_form.Rd
tests/testthat.R
tests/testthat/test-PubMed.R
tests/testthat/test-checkCuration.R
tests/testthat/test-get_metadata.R
vignettes/curatedMetagenomicDataCuration.Rmd
