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Invited Commentary: Improving the Accessibility of Human Microbiome Project Data Through Integration With R/Bioconductor

https://doi.org/10.1093/aje/kwz007
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/j.gendis.2017.06.001openalex-snapshot
Hypothesis testing and statistical analysis of microbiome
inferredcites →https://doi.org/10.1038/nature08821openalex-snapshot
A human gut microbial gene catalogue established by metagenomic sequencing
inferredcites →https://doi.org/10.1038/nature11234openalex-snapshot
Structure, function and diversity of the healthy human microbiome
inferredcites →https://doi.org/10.1038/nbt.3981openalex-snapshot
Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium
inferredcites →https://doi.org/10.1038/nmeth.2658openalex-snapshot
Differential abundance analysis for microbial marker-gene surveys
inferredcites →https://doi.org/10.1038/nmeth.3252openalex-snapshot
Orchestrating high-throughput genomic analysis with Bioconductor
inferredcites →https://doi.org/10.1038/nmeth.3869openalex-snapshot
DADA2: High-resolution sample inference from Illumina amplicon data
inferredcites →https://doi.org/10.1038/nmeth.4468openalex-snapshot
Accessible, curated metagenomic data through ExperimentHub
inferredcites →https://doi.org/10.1038/nmeth.f.303openalex-snapshot
QIIME allows analysis of high-throughput community sequencing data
inferredcites →https://doi.org/10.1038/nrmicro3344openalex-snapshot
The gut microbiota, bacterial metabolites and colorectal cancer
inferredcites →https://doi.org/10.1038/nrrheum.2011.121openalex-snapshot
The microbiome and rheumatoid arthritis
inferredcites →https://doi.org/10.1093/aje/kwz006openalex-snapshot
HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor
inferredcites →https://doi.org/10.1093/bioinformatics/btp616openalex-snapshot
edgeR : a Bioconductor package for differential expression analysis of digital gene expression data
inferredcites →https://doi.org/10.1101/gr.131029.111openalex-snapshot
Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis
inferredcites →https://doi.org/10.1128/aem.01541-09openalex-snapshot
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
inferredcites →https://doi.org/10.1128/mbio.01012-14openalex-snapshot
Metatranscriptomics of the Human Oral Microbiome during Health and Disease
inferredcites →https://doi.org/10.1128/msystems.00191-16openalex-snapshot
Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
inferredcites →https://doi.org/10.1136/gutjnl-2016-312580openalex-snapshot
Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study
inferredcites →https://doi.org/10.1146/annurev-micro-092611-150157openalex-snapshot
Vaginal Microbiome: Rethinking Health and Disease
inferredcites →https://doi.org/10.1186/1471-2105-12-38openalex-snapshot
Removing Noise From Pyrosequenced Amplicons
inferredcites →https://doi.org/10.1186/gb-2012-13-9-r79openalex-snapshot
Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment
inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
inferredcites →https://doi.org/10.1371/journal.pone.0030087openalex-snapshot
Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community DNA Sample
inferredcites →https://doi.org/10.1371/journal.pone.0039315openalex-snapshot
Evaluation of 16S rDNA-Based Community Profiling for Human Microbiome Research
inferredcites →https://doi.org/10.1371/journal.pone.0061217openalex-snapshot
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
inferredcites →https://doi.org/10.1371/journal.ppat.1004436openalex-snapshot
The Skin Microbiome: A Focus on Pathogens and Their Association with Skin Disease
inferredcites →https://doi.org/10.2337/dc14-0769openalex-snapshot
Insights Into the Role of the Microbiome in Obesity and Type 2 Diabetes
inferredcites →https://doi.org/10.7287/peerj.preprints.27295v1openalex-snapshot
QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science
inferredcites →https://doi.org/10.7717/peerj.5364openalex-snapshot
Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.2139/ssrn.4694107openalex-extracted
Population Genomics Analysis Reveals Footprints of Selective Breeding in a Rapid-Growth Variety of Paulownia Fortunei with Apical Dominance
inferred← citeshttps://doi.org/10.1016/b978-0-443-40483-2.00053-4openalex-snapshot
Definition and importance of the human microbiome
inferred← citeshttps://doi.org/10.1016/j.ygeno.2024.110849openalex-snapshot
Population genomics analysis reveals footprints of selective breeding in a rapid-growth variety of Paulownia fortunei with apical dominance
inferred← citeshttps://doi.org/10.1093/aje/kwz008openalex-snapshot
Waldron et al. Reply to “Commentary on the HMP16SData Bioconductor Package”
inferred← citeshttps://doi.org/10.17116/rosakush20202006176openalex-snapshot
Vaginal dysbiosis as a risk factor for the chronic endometritis development
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.