curatedMetagenomicData-defunct: Defunct functions in package ‘curatedMetagenomicData’

In waldronlab/curatedMetagenomicData: Curated Metagenomic Data of the Human Microbiome

Defunct functions in package ‘curatedMetagenomicData’

Description

These functions are defunct and no longer available.

Details

The following functions (methods) are defunct:

• cmdValidVersions()

• getMetaphlanTree()

• ExpressionSet2MRexperiment()

• ExpressionSet2phyloseq()

The following functions (accessors) are defunct:

• AsnicarF_2017.genefamilies_relab.milk()

• AsnicarF_2017.genefamilies_relab.stool()

• AsnicarF_2017.marker_abundance.milk()

• AsnicarF_2017.marker_abundance.stool()

• AsnicarF_2017.marker_presence.milk()

• AsnicarF_2017.marker_presence.stool()

• AsnicarF_2017.metaphlan_bugs_list.milk()

• AsnicarF_2017.metaphlan_bugs_list.stool()

• AsnicarF_2017.pathabundance_relab.milk()

• AsnicarF_2017.pathabundance_relab.stool()

• AsnicarF_2017.pathcoverage.milk()

• AsnicarF_2017.pathcoverage.stool()

• BackhedF_2015.genefamilies_relab.stool()

• BackhedF_2015.marker_abundance.stool()

• BackhedF_2015.marker_presence.stool()

• BackhedF_2015.metaphlan_bugs_list.stool()

• BackhedF_2015.pathabundance_relab.stool()

• BackhedF_2015.pathcoverage.stool()

• Bengtsson-PalmeJ_2015.genefamilies_relab.stool()

• Bengtsson-PalmeJ_2015.marker_abundance.stool()

• Bengtsson-PalmeJ_2015.marker_presence.stool()

• Bengtsson-PalmeJ_2015.metaphlan_bugs_list.stool()

• Bengtsson-PalmeJ_2015.pathabundance_relab.stool()

• Bengtsson-PalmeJ_2015.pathcoverage.stool()

• BritoIL_2016.genefamilies_relab.oralcavity()

• BritoIL_2016.genefamilies_relab.stool()

• BritoIL_2016.marker_abundance.oralcavity()

• BritoIL_2016.marker_abundance.stool()

• BritoIL_2016.marker_presence.oralcavity()

• BritoIL_2016.marker_presence.stool()

• BritoIL_2016.metaphlan_bugs_list.oralcavity()

• BritoIL_2016.metaphlan_bugs_list.stool()

• BritoIL_2016.pathabundance_relab.oralcavity()

• BritoIL_2016.pathabundance_relab.stool()

• BritoIL_2016.pathcoverage.oralcavity()

• BritoIL_2016.pathcoverage.stool()

• Castro_NallarE_2015.genefamilies_relab.oralcavity()

• Castro_NallarE_2015.marker_abundance.oralcavity()

• Castro_NallarE_2015.marker_presence.oralcavity()

• Castro_NallarE_2015.metaphlan_bugs_list.oralcavity()

• Castro_NallarE_2015.pathabundance_relab.oralcavity()

• Castro_NallarE_2015.pathcoverage.oralcavity()

• Castro-NallarE_2015.genefamilies_relab.oralcavity()

• Castro-NallarE_2015.marker_abundance.oralcavity()

• Castro-NallarE_2015.marker_presence.oralcavity()

• Castro-NallarE_2015.metaphlan_bugs_list.oralcavity()

• Castro-NallarE_2015.pathabundance_relab.oralcavity()

• Castro-NallarE_2015.pathcoverage.oralcavity()

• ChengpingW_2017.genefamilies_relab.stool()

• ChengpingW_2017.marker_abundance.stool()

• ChengpingW_2017.marker_presence.stool()

• ChengpingW_2017.metaphlan_bugs_list.stool()

• ChengpingW_2017.pathabundance_relab.stool()

• ChengpingW_2017.pathcoverage.stool()

• ChngKR_2016.genefamilies_relab.skin()

• ChngKR_2016.marker_abundance.skin()

• ChngKR_2016.marker_presence.skin()

• ChngKR_2016.metaphlan_bugs_list.skin()

• ChngKR_2016.pathabundance_relab.skin()

• ChngKR_2016.pathcoverage.skin()

• CosteaPI_2017.genefamilies_relab.stool()

• CosteaPI_2017.marker_abundance.stool()

• CosteaPI_2017.marker_presence.stool()

• CosteaPI_2017.metaphlan_bugs_list.stool()

• CosteaPI_2017.pathabundance_relab.stool()

• CosteaPI_2017.pathcoverage.stool()

• DavidLA_2015.genefamilies_relab.stool()

• DavidLA_2015.marker_abundance.stool()

• DavidLA_2015.marker_presence.stool()

• DavidLA_2015.metaphlan_bugs_list.stool()

• DavidLA_2015.pathabundance_relab.stool()

• DavidLA_2015.pathcoverage.stool()

• DhakanDB_2019.genefamilies_relab.stool()

• DhakanDB_2019.marker_abundance.stool()

• DhakanDB_2019.marker_presence.stool()

• DhakanDB_2019.metaphlan_bugs_list.stool()

• DhakanDB_2019.pathabundance_relab.stool()

• DhakanDB_2019.pathcoverage.stool()

• FengQ_2015.genefamilies_relab.stool()

• FengQ_2015.marker_abundance.stool()

• FengQ_2015.marker_presence.stool()

• FengQ_2015.metaphlan_bugs_list.stool()

• FengQ_2015.pathabundance_relab.stool()

• FengQ_2015.pathcoverage.stool()

• FerrettiP_2018.genefamilies_relab.oralcavity()

• FerrettiP_2018.genefamilies_relab.skin()

• FerrettiP_2018.genefamilies_relab.stool()

• FerrettiP_2018.genefamilies_relab.vagina()

• FerrettiP_2018.marker_abundance.oralcavity()

• FerrettiP_2018.marker_abundance.skin()

• FerrettiP_2018.marker_abundance.stool()

• FerrettiP_2018.marker_abundance.vagina()

• FerrettiP_2018.marker_presence.oralcavity()

• FerrettiP_2018.marker_presence.skin()

• FerrettiP_2018.marker_presence.stool()

• FerrettiP_2018.marker_presence.vagina()

• FerrettiP_2018.metaphlan_bugs_list.oralcavity()

• FerrettiP_2018.metaphlan_bugs_list.skin()

• FerrettiP_2018.metaphlan_bugs_list.stool()

• FerrettiP_2018.metaphlan_bugs_list.vagina()

• FerrettiP_2018.pathabundance_relab.oralcavity()

• FerrettiP_2018.pathabundance_relab.skin()

• FerrettiP_2018.pathabundance_relab.stool()

• FerrettiP_2018.pathabundance_relab.vagina()

• FerrettiP_2018.pathcoverage.oralcavity()

• FerrettiP_2018.pathcoverage.skin()

• FerrettiP_2018.pathcoverage.stool()

• FerrettiP_2018.pathcoverage.vagina()

• GopalakrishnanV_2018.genefamilies_relab.stool()

• GopalakrishnanV_2018.marker_abundance.stool()

• GopalakrishnanV_2018.marker_presence.stool()

• GopalakrishnanV_2018.metaphlan_bugs_list.stool()

• GopalakrishnanV_2018.pathabundance_relab.stool()

• GopalakrishnanV_2018.pathcoverage.stool()

• HanniganGD_2017.genefamilies_relab.stool()

• HanniganGD_2017.marker_abundance.stool()

• HanniganGD_2017.marker_presence.stool()

• HanniganGD_2017.metaphlan_bugs_list.stool()

• HanniganGD_2017.pathabundance_relab.stool()

• HanniganGD_2017.pathcoverage.stool()

• HansenLBS_2018.genefamilies_relab.stool()

• HansenLBS_2018.marker_abundance.stool()

• HansenLBS_2018.marker_presence.stool()

• HansenLBS_2018.metaphlan_bugs_list.stool()

• HansenLBS_2018.pathabundance_relab.stool()

• HansenLBS_2018.pathcoverage.stool()

• Heitz_BuschartA_2016.genefamilies_relab.stool()

• Heitz_BuschartA_2016.marker_abundance.stool()

• Heitz_BuschartA_2016.marker_presence.stool()

• Heitz_BuschartA_2016.metaphlan_bugs_list.stool()

• Heitz_BuschartA_2016.pathabundance_relab.stool()

• Heitz_BuschartA_2016.pathcoverage.stool()

• Heitz-BuschartA_2016.genefamilies_relab.stool()

• Heitz-BuschartA_2016.marker_abundance.stool()

• Heitz-BuschartA_2016.marker_presence.stool()

• Heitz-BuschartA_2016.metaphlan_bugs_list.stool()

• Heitz-BuschartA_2016.pathabundance_relab.stool()

• Heitz-BuschartA_2016.pathcoverage.stool()

• HMP_2012.genefamilies_relab.nasalcavity()

• HMP_2012.genefamilies_relab.oralcavity()

• HMP_2012.genefamilies_relab.skin()

• HMP_2012.genefamilies_relab.stool()

• HMP_2012.genefamilies_relab.vagina()

• HMP_2012.marker_abundance.nasalcavity()

• HMP_2012.marker_abundance.oralcavity()

• HMP_2012.marker_abundance.skin()

• HMP_2012.marker_abundance.stool()

• HMP_2012.marker_abundance.vagina()

• HMP_2012.marker_presence.nasalcavity()

• HMP_2012.marker_presence.oralcavity()

• HMP_2012.marker_presence.skin()

• HMP_2012.marker_presence.stool()

• HMP_2012.marker_presence.vagina()

• HMP_2012.metaphlan_bugs_list.nasalcavity()

• HMP_2012.metaphlan_bugs_list.oralcavity()

• HMP_2012.metaphlan_bugs_list.skin()

• HMP_2012.metaphlan_bugs_list.stool()

• HMP_2012.metaphlan_bugs_list.vagina()

• HMP_2012.pathabundance_relab.nasalcavity()

• HMP_2012.pathabundance_relab.oralcavity()

• HMP_2012.pathabundance_relab.skin()

• HMP_2012.pathabundance_relab.stool()

• HMP_2012.pathabundance_relab.vagina()

• HMP_2012.pathcoverage.nasalcavity()

• HMP_2012.pathcoverage.oralcavity()

• HMP_2012.pathcoverage.skin()

• HMP_2012.pathcoverage.stool()

• HMP_2012.pathcoverage.vagina()

• JieZ_2017.genefamilies_relab.stool()

• JieZ_2017.marker_abundance.stool()

• JieZ_2017.marker_presence.stool()

• JieZ_2017.metaphlan_bugs_list.stool()

• JieZ_2017.pathabundance_relab.stool()

• JieZ_2017.pathcoverage.stool()

• KarlssonFH_2013.genefamilies_relab.stool()

• KarlssonFH_2013.marker_abundance.stool()

• KarlssonFH_2013.marker_presence.stool()

• KarlssonFH_2013.metaphlan_bugs_list.stool()

• KarlssonFH_2013.pathabundance_relab.stool()

• KarlssonFH_2013.pathcoverage.stool()

• KieserS_2018.genefamilies_relab.stool()

• KieserS_2018.marker_abundance.stool()

• KieserS_2018.marker_presence.stool()

• KieserS_2018.metaphlan_bugs_list.stool()

• KieserS_2018.pathabundance_relab.stool()

• KieserS_2018.pathcoverage.stool()

• KosticAD_2015.genefamilies_relab.stool()

• KosticAD_2015.marker_abundance.stool()

• KosticAD_2015.marker_presence.stool()

• KosticAD_2015.metaphlan_bugs_list.stool()

• KosticAD_2015.pathabundance_relab.stool()

• KosticAD_2015.pathcoverage.stool()

• LeChatelierE_2013.genefamilies_relab.stool()

• LeChatelierE_2013.marker_abundance.stool()

• LeChatelierE_2013.marker_presence.stool()

• LeChatelierE_2013.metaphlan_bugs_list.stool()

• LeChatelierE_2013.pathabundance_relab.stool()

• LeChatelierE_2013.pathcoverage.stool()

• LiJ_2014.genefamilies_relab.stool()

• LiJ_2014.marker_abundance.stool()

• LiJ_2014.marker_presence.stool()

• LiJ_2014.metaphlan_bugs_list.stool()

• LiJ_2014.pathabundance_relab.stool()

• LiJ_2014.pathcoverage.stool()

• LiJ_2017.genefamilies_relab.stool()

• LiJ_2017.marker_abundance.stool()

• LiJ_2017.marker_presence.stool()

• LiJ_2017.metaphlan_bugs_list.stool()

• LiJ_2017.pathabundance_relab.stool()

• LiJ_2017.pathcoverage.stool()

• LiSS_2016.genefamilies_relab.stool()

• LiSS_2016.marker_abundance.stool()

• LiSS_2016.marker_presence.stool()

• LiSS_2016.metaphlan_bugs_list.stool()

• LiSS_2016.pathabundance_relab.stool()

• LiSS_2016.pathcoverage.stool()

• LiuW_2016.genefamilies_relab.stool()

• LiuW_2016.marker_abundance.stool()

• LiuW_2016.marker_presence.stool()

• LiuW_2016.metaphlan_bugs_list.stool()

• LiuW_2016.pathabundance_relab.stool()

• LiuW_2016.pathcoverage.stool()

• LomanNJ_2013.genefamilies_relab.stool()

• LomanNJ_2013.marker_abundance.stool()

• LomanNJ_2013.marker_presence.stool()

• LomanNJ_2013.metaphlan_bugs_list.stool()

• LomanNJ_2013.pathabundance_relab.stool()

• LomanNJ_2013.pathcoverage.stool()

• LoombaR_2017.genefamilies_relab.stool()

• LoombaR_2017.marker_abundance.stool()

• LoombaR_2017.marker_presence.stool()

• LoombaR_2017.metaphlan_bugs_list.stool()

• LoombaR_2017.pathabundance_relab.stool()

• LoombaR_2017.pathcoverage.stool()

• LouisS_2016.genefamilies_relab.stool()

• LouisS_2016.marker_abundance.stool()

• LouisS_2016.marker_presence.stool()

• LouisS_2016.metaphlan_bugs_list.stool()

• LouisS_2016.pathabundance_relab.stool()

• LouisS_2016.pathcoverage.stool()

• MatsonV_2018.genefamilies_relab.stool()

• MatsonV_2018.marker_abundance.stool()

• MatsonV_2018.marker_presence.stool()

• MatsonV_2018.metaphlan_bugs_list.stool()

• MatsonV_2018.pathabundance_relab.stool()

• MatsonV_2018.pathcoverage.stool()

• NielsenHB_2014.genefamilies_relab.stool()

• NielsenHB_2014.marker_abundance.stool()

• NielsenHB_2014.marker_presence.stool()

• NielsenHB_2014.metaphlan_bugs_list.stool()

• NielsenHB_2014.pathabundance_relab.stool()

• NielsenHB_2014.pathcoverage.stool()

• Obregon_TitoAJ_2015.genefamilies_relab.stool()

• Obregon_TitoAJ_2015.marker_abundance.stool()

• Obregon_TitoAJ_2015.marker_presence.stool()

• Obregon_TitoAJ_2015.metaphlan_bugs_list.stool()

• Obregon_TitoAJ_2015.pathabundance_relab.stool()

• Obregon_TitoAJ_2015.pathcoverage.stool()

• Obregon-TitoAJ_2015.genefamilies_relab.stool()

• Obregon-TitoAJ_2015.marker_abundance.stool()

• Obregon-TitoAJ_2015.marker_presence.stool()

• Obregon-TitoAJ_2015.metaphlan_bugs_list.stool()

• Obregon-TitoAJ_2015.pathabundance_relab.stool()

• Obregon-TitoAJ_2015.pathcoverage.stool()

• OhJ_2014.genefamilies_relab.skin()

• OhJ_2014.marker_abundance.skin()

• OhJ_2014.marker_presence.skin()

• OhJ_2014.metaphlan_bugs_list.skin()

• OhJ_2014.pathabundance_relab.skin()

• OhJ_2014.pathcoverage.skin()

• OlmMR_2017.genefamilies_relab.oralcavity()

• OlmMR_2017.genefamilies_relab.skin()

• OlmMR_2017.genefamilies_relab.stool()

• OlmMR_2017.marker_abundance.oralcavity()

• OlmMR_2017.marker_abundance.skin()

• OlmMR_2017.marker_abundance.stool()

• OlmMR_2017.marker_presence.oralcavity()

• OlmMR_2017.marker_presence.skin()

• OlmMR_2017.marker_presence.stool()

• OlmMR_2017.metaphlan_bugs_list.oralcavity()

• OlmMR_2017.metaphlan_bugs_list.skin()

• OlmMR_2017.metaphlan_bugs_list.stool()

• OlmMR_2017.pathabundance_relab.oralcavity()

• OlmMR_2017.pathabundance_relab.skin()

• OlmMR_2017.pathabundance_relab.stool()

• OlmMR_2017.pathcoverage.oralcavity()

• OlmMR_2017.pathcoverage.skin()

• OlmMR_2017.pathcoverage.stool()

• PasolliE_2018.genefamilies_relab.stool()

• PasolliE_2018.marker_abundance.stool()

• PasolliE_2018.marker_presence.stool()

• PasolliE_2018.metaphlan_bugs_list.stool()

• PasolliE_2018.pathabundance_relab.stool()

• PasolliE_2018.pathcoverage.stool()

• PehrssonE_2016.genefamilies_relab.stool()

• PehrssonE_2016.marker_abundance.stool()

• PehrssonE_2016.marker_presence.stool()

• PehrssonE_2016.metaphlan_bugs_list.stool()

• PehrssonE_2016.pathabundance_relab.stool()

• PehrssonE_2016.pathcoverage.stool()

• QinJ_2012.genefamilies_relab.stool()

• QinJ_2012.marker_abundance.stool()

• QinJ_2012.marker_presence.stool()

• QinJ_2012.metaphlan_bugs_list.stool()

• QinJ_2012.pathabundance_relab.stool()

• QinJ_2012.pathcoverage.stool()

• QinN_2014.genefamilies_relab.stool()

• QinN_2014.marker_abundance.stool()

• QinN_2014.marker_presence.stool()

• QinN_2014.metaphlan_bugs_list.stool()

• QinN_2014.pathabundance_relab.stool()

• QinN_2014.pathcoverage.stool()

• RampelliS_2015.genefamilies_relab.stool()

• RampelliS_2015.marker_abundance.stool()

• RampelliS_2015.marker_presence.stool()

• RampelliS_2015.metaphlan_bugs_list.stool()

• RampelliS_2015.pathabundance_relab.stool()

• RampelliS_2015.pathcoverage.stool()

• RaymondF_2016.genefamilies_relab.stool()

• RaymondF_2016.marker_abundance.stool()

• RaymondF_2016.marker_presence.stool()

• RaymondF_2016.metaphlan_bugs_list.stool()

• RaymondF_2016.pathabundance_relab.stool()

• RaymondF_2016.pathcoverage.stool()

• SchirmerM_2016.genefamilies_relab.stool()

• SchirmerM_2016.marker_abundance.stool()

• SchirmerM_2016.marker_presence.stool()

• SchirmerM_2016.metaphlan_bugs_list.stool()

• SchirmerM_2016.pathabundance_relab.stool()

• SchirmerM_2016.pathcoverage.stool()

• ShiB_2015.genefamilies_relab.oralcavity()

• ShiB_2015.marker_abundance.oralcavity()

• ShiB_2015.marker_presence.oralcavity()

• ShiB_2015.metaphlan_bugs_list.oralcavity()

• ShiB_2015.pathabundance_relab.oralcavity()

• ShiB_2015.pathcoverage.oralcavity()

• SmitsSA_2017.genefamilies_relab.stool()

• SmitsSA_2017.marker_abundance.stool()

• SmitsSA_2017.marker_presence.stool()

• SmitsSA_2017.metaphlan_bugs_list.stool()

• SmitsSA_2017.pathabundance_relab.stool()

• SmitsSA_2017.pathcoverage.stool()

• TettAJ_2016.genefamilies_relab.skin()

• TettAJ_2016.marker_abundance.skin()

• TettAJ_2016.marker_presence.skin()

• TettAJ_2016.metaphlan_bugs_list.skin()

• TettAJ_2016.pathabundance_relab.skin()

• TettAJ_2016.pathcoverage.skin()

• TettAJ_2019_a.genefamilies_relab.stool()

• TettAJ_2019_a.marker_abundance.stool()

• TettAJ_2019_a.marker_presence.stool()

• TettAJ_2019_a.metaphlan_bugs_list.stool()

• TettAJ_2019_a.pathabundance_relab.stool()

• TettAJ_2019_a.pathcoverage.stool()

• TettAJ_2019_b.genefamilies_relab.stool()

• TettAJ_2019_b.marker_abundance.stool()

• TettAJ_2019_b.marker_presence.stool()

• TettAJ_2019_b.metaphlan_bugs_list.stool()

• TettAJ_2019_b.pathabundance_relab.stool()

• TettAJ_2019_b.pathcoverage.stool()

• TettAJ_2019_c.genefamilies_relab.stool()

• TettAJ_2019_c.marker_abundance.stool()

• TettAJ_2019_c.marker_presence.stool()

• TettAJ_2019_c.metaphlan_bugs_list.stool()

• TettAJ_2019_c.pathabundance_relab.stool()

• TettAJ_2019_c.pathcoverage.stool()

• ThomasAM_2018a.genefamilies_relab.stool()

• ThomasAM_2018a.marker_abundance.stool()

• ThomasAM_2018a.marker_presence.stool()

• ThomasAM_2018a.metaphlan_bugs_list.stool()

• ThomasAM_2018a.pathabundance_relab.stool()

• ThomasAM_2018a.pathcoverage.stool()

• ThomasAM_2018b.genefamilies_relab.stool()

• ThomasAM_2018b.marker_abundance.stool()

• ThomasAM_2018b.marker_presence.stool()

• ThomasAM_2018b.metaphlan_bugs_list.stool()

• ThomasAM_2018b.pathabundance_relab.stool()

• ThomasAM_2018b.pathcoverage.stool()

• VatanenT_2016.genefamilies_relab.stool()

• VatanenT_2016.marker_abundance.stool()

• VatanenT_2016.marker_presence.stool()

• VatanenT_2016.metaphlan_bugs_list.stool()

• VatanenT_2016.pathabundance_relab.stool()

• VatanenT_2016.pathcoverage.stool()

• VincentC_2016.genefamilies_relab.stool()

• VincentC_2016.marker_abundance.stool()

• VincentC_2016.marker_presence.stool()

• VincentC_2016.metaphlan_bugs_list.stool()

• VincentC_2016.pathabundance_relab.stool()

• VincentC_2016.pathcoverage.stool()

• VogtmannE_2016.genefamilies_relab.stool()

• VogtmannE_2016.marker_abundance.stool()

• VogtmannE_2016.marker_presence.stool()

• VogtmannE_2016.metaphlan_bugs_list.stool()

• VogtmannE_2016.pathabundance_relab.stool()

• VogtmannE_2016.pathcoverage.stool()

• XieH_2016.genefamilies_relab.stool()

• XieH_2016.marker_abundance.stool()

• XieH_2016.marker_presence.stool()

• XieH_2016.metaphlan_bugs_list.stool()

• XieH_2016.pathabundance_relab.stool()

• XieH_2016.pathcoverage.stool()

• YeZ_2018.genefamilies_relab.stool()

• YeZ_2018.marker_abundance.stool()

• YeZ_2018.marker_presence.stool()

• YeZ_2018.metaphlan_bugs_list.stool()

• YeZ_2018.pathabundance_relab.stool()

• YeZ_2018.pathcoverage.stool()

• YuJ_2015.genefamilies_relab.stool()

• YuJ_2015.marker_abundance.stool()

• YuJ_2015.marker_presence.stool()

• YuJ_2015.metaphlan_bugs_list.stool()

• YuJ_2015.pathabundance_relab.stool()

• YuJ_2015.pathcoverage.stool()

• ZeeviD_2015.genefamilies_relab.stool()

• ZeeviD_2015.marker_abundance.stool()

• ZeeviD_2015.marker_presence.stool()

• ZeeviD_2015.metaphlan_bugs_list.stool()

• ZeeviD_2015.pathabundance_relab.stool()

• ZeeviD_2015.pathcoverage.stool()

• ZellerG_2014.genefamilies_relab.stool()

• ZellerG_2014.marker_abundance.stool()

• ZellerG_2014.marker_presence.stool()

• ZellerG_2014.metaphlan_bugs_list.stool()

• ZellerG_2014.pathabundance_relab.stool()

• ZellerG_2014.pathcoverage.stool()

waldronlab/curatedMetagenomicData documentation built on Oct. 26, 2023, 6:32 a.m.