MetaboCoreUtils defines metabolomics-related core functionality provided as low-level functions to allow a data structure-independent usage across various R packages. This includes functions to calculate between ion (adduct) and compound ma
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Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
BiocManager::install("MetaboCoreUtils")mass2mz and mz2mass.standardizeFormula), adding/subtracting elements (addElements, subtractElements), and calculating exact masses (calculateMass).fit_lm and adjust_lm.calculateKmd and calculateRkmd.xcms instead because MetaboCoreUtils only provides low-level utility functions.fit_lm is designed for simple linear drift adjustments."C6H12O6"), numeric vectors for masses or $m/z$ values, and matrices for feature abundances.data.frame containing retention times and corresponding index values is required for indexRtime and correctRindex.data.frame of covariates (e.g., injection index)."[M+H]+" or "[M+Na]+") for mass conversions.data.frame containing the covariates (e.g., injection_index) passed to fit_lm and adjust_lm.fit_lm.fit_lm.adjust_lm to correct the data.standardizeFormula before comparing them or counting elements (countElements) to ensure consistent formatting.adductNames to view the exact spelling of all supported ESI ion adduct definitions before performing $m/z$ conversions.fit_lm) exclusively on QC samples to ensure the estimated drift is independent of biological covariates.adjust_lm.minVals parameter in fit_lm to require a strict minimum of non-missing QC values.adjust_lm to all features can introduce noise to features without true signal drift; Fix: Filter the list of models returned by fit_lm to remove fits with poor p-values before adjustment.adductNames() to verify the exact string format (e.g., "[M+H]+").This skill is the knowledge layer — when, why, and how to use metabocoreutils. To run this analysis on your own data with managed compute, automated QC, and reproducible outputs, use BioMate — free to start.
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The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.
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This tool uses the label-tree function from HyPhy to annotate a phylogenetic tree. It allows users to select a subset of leaves using either a regular expression or a list of sequence names, and then apply a specified label to these selecte
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This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, En
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apeglm provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients.
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ASURAT is a software for single-cell data analysis. Using ASURAT, one can simultaneously perform unsupervised clustering and biological interpretation in terms of cell type, disease, biological process, and signaling pathway activity. Inputting a single-cell RNA-seq data and knowledge-based databases, such as Cell Ontology, Gene Ontology, KEGG, etc., ASURAT transforms gene expression tables into original multivariate tables, termed sign-by-sample matrices (SSMs).
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AUCell allows to identify cells with active gene sets (e.g. signatures, gene modules...) in single-cell RNA-seq data. AUCell uses the "Area Under the Curve" (AUC) to calculate whether a critical subset of the input gene set is enriched with
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