curatedMetagenomicData - Curated Metagenomic Data of the Human Microbiome
The curatedMetagenomicData package provides standardized, curated human microbiome data for novel analyses. It includes gene families, marker abundance, marker presence, pathway abundance, pathway coverage, and relative abundance for samples collected from different body sites. The bacterial, fungal, and archaeal taxonomic abundances for each sample were calculated with MetaPhlAn3, and metabolic functional potential was calculated with HUMAnN3. The manually curated sample metadata and standardized metagenomic data are available as (Tree)SummarizedExperiment objects.
Last updated
experimenthubhomo_sapiens_datamicrobiomedatareproducibleresearchbioconductorbioconductor-packager01ca230551
9.62 score 160 stars 437 scriptscuratedMetagenomicData - Curated Metagenomic Data of the Human Microbiome
The curatedMetagenomicData package provides standardized, curated human microbiome data for novel analyses. It includes gene families, marker abundance, marker presence, pathway abundance, pathway coverage, and relative abundance for samples collected from different body sites. The bacterial, fungal, and archaeal taxonomic abundances for each sample were calculated with MetaPhlAn3, and metabolic functional potential was calculated with HUMAnN3. The manually curated sample metadata and standardized metagenomic data are available as (Tree)SummarizedExperiment objects.
Last updated
experimenthubhomo_sapiens_datamicrobiomedatareproducibleresearchbioconductorbioconductor-packager01ca230551datapkg
8.24 score 160 stars 430 scriptsHMP16SData - 16S rRNA Sequencing Data from the Human Microbiome Project
HMP16SData is a Bioconductor ExperimentData package of the Human Microbiome Project (HMP) 16S rRNA sequencing data for variable regions 1–3 and 3–5. Raw data files are provided in the package as downloaded from the HMP Data Analysis and Coordination Center. Processed data is provided as SummarizedExperiment class objects via ExperimentHub.
Last updated
experimentdataexperimenthubhomo_sapiens_datamicrobiomedatareproducibleresearchsequencingdatabioconductorbioconductor-packagehmpr01ca230551datapkg
6.73 score 11 stars 46 scriptsHMP16SData - 16S rRNA Sequencing Data from the Human Microbiome Project
HMP16SData is a Bioconductor ExperimentData package of the Human Microbiome Project (HMP) 16S rRNA sequencing data for variable regions 1–3 and 3–5. Raw data files are provided in the package as downloaded from the HMP Data Analysis and Coordination Center. Processed data is provided as SummarizedExperiment class objects via ExperimentHub.
Last updated
experimentdataexperimenthubhomo_sapiens_datamicrobiomedatareproducibleresearchsequencingdatabioconductorbioconductor-packagehmpr01ca230551
6.73 score 11 stars 46 scripts
tuberculosis - Tuberculosis Gene Expression Data for Machine Learning
The tuberculosis R/Bioconductor package features tuberculosis gene expression data for machine learning. All human samples from GEO that did not come from cell lines, were not taken postmortem, and did not feature recombination have been included. The package has more than 10,000 samples from both microarray and sequencing studies that have been processed from raw data through a hyper-standardized, reproducible pipeline.
Last updated
experimenthubexpressiondatahomo_sapiens_datamicroarraydatasequencingdatareproducibleresearchbioconductorbioconductor-packagedatapkg
5.26 score 4 stars 4 scriptsMultimodalExperiment - Integrative Bulk and Single-Cell Experiment Container
MultimodalExperiment is an S4 class that integrates bulk and single-cell experiment data; it is optimally storage-efficient, and its methods are exceptionally fast. It effortlessly represents multimodal data of any nature and features normalized experiment, subject, sample, and cell annotations, which are related to underlying biological experiments through maps. Its coordination methods are opt-in and employ database-like join operations internally to deliver fast and flexible management of multimodal data.
Last updated
datarepresentationinfrastructuresinglecell
4.00 score 8 scripts 392 downloads