Implements a variety of methods for combining p-values in differential analyses of genome-scale datasets. Functions can combine p-values across different tests in the same analysis (e.g., genomic windows in ChIP-seq, exons in RNA-seq) or fo
中文简介正在准备中。当前显示原文说明。
查看安装方法安装前可以查看交给 AI 代理的指令内容。
Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
BiocManager::install("metapod")csaw) using grouped functions like groupedSimes.scran) using parallel functions like parallelSimes.summarizeParallelDirection or summarizeGroupedDirection.p.adjust instead because metapod is designed for hierarchical or multi-test aggregation.metapod operates strictly on p-values and their directions.grouped* functions) or a list of parallel numeric vectors of p-values (for parallel* functions).combineGroupedPValues (e.g., "simes", "holm-min").summarizeParallelDirection to only consider tests that contributed to the final p-value.parallelSimes or groupedSimes) when you expect dependencies between tests (e.g., overlapping genomic windows) as it is robust to such dependencies.log.p = TRUE when dealing with extremely small p-values to prevent underflow to zero during calculation.summarizeParallelDirection or summarizeGroupedDirection on the influential tests to avoid noise from non-significant tests when determining the consensus log-fold change direction.groupedFisher or parallelFisher) on highly correlated tests. Fix: Switch to Simes' method or the minimum Holm approach (groupedHolmMin), which do not require independence.log.p = TRUE.countParallelDirection without understanding that it applies Benjamini-Hochberg or Holm corrections internally. Fix: Read the documentation for countParallelDirection carefully, or use summarizeParallelDirection for a simpler consensus.This skill is the knowledge layer — when, why, and how to use metapod. To run this analysis on your own data with managed compute, automated QC, and reproducible outputs, use BioMate — free to start.
还没有评价。欢迎分享你的使用感受。
无需登录即可发表。欢迎分享使用感受、提问，或说明在哪些环境下无法运行。
还没有评论。来写第一条吧。
The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.
中文简介正在准备中。当前显示原文说明。
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
中文简介正在准备中。当前显示原文说明。
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
中文简介正在准备中。当前显示原文说明。
apeglm provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients.
中文简介正在准备中。当前显示原文说明。
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).
中文简介正在准备中。当前显示原文说明。
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
中文简介正在准备中。当前显示原文说明。