The PLIER (Probe Logarithmic Error Intensity Estimate) method produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error at the appropriately at low and high signal values.

Platform Design Info for Affymetrix FelGene-1_0-st.

PWMEnrich pre-compiled background objects for H. sapiens (human) and MotifDb H. sapiens motifs.

Store UCSC phastCons mm39 conservation scores AnnotationHub Resource Metadata. Provide provenance and citation information for UCSC phastCons mm39 conservation score AnnotationHub resources. Illustrate in a vignette how to access those resources.

Platform Design Info for Affymetrix Clariom_S_Human.

Platform Design Info for NimbleGen 2006-07-18_hg18_refseq_promoter.

Platform Design Info for The Manufacturer's Name RN_U34.

Platform Design Info for Affymetrix Clariom_S_Rat.

Platform Design Info for The Manufacturer's Name U133_X3P.

Platform Design Info for NimbleGen feinberg_mm8_me_hx1.

Platform Design Info for The Manufacturer's Name Poplar.

This is a supplemental data package for the plotgardener package. Includes example datasets used in plotgardener vignettes and example raw data files. For details on how to use these datasets, see the plotgardener package vignettes.

Platform Design Info for The Manufacturer's Name Medicago.

In genomics, differential analysis enables the discovery of groups of genes implicating important biological processes such as cell differentiation and aging. Non-parametric tests of differential gene expression usually detect shifts in centrality (such as mean or median), and therefore suffer from diminished power against alternative hypotheses characterized by shifts in spread (such as variance). This package provides a flexible family of non-parametric two-sample tests and K-sample tests, which is based on theoretical work around non-parametric tests, spacing statistics and local asymptotic normality (Erdmann-Pham et al., 2022+ [arXiv:2008.06664v2]; Erdmann-Pham, 2023+ [arXiv:2209.14235v2]).

The package provides a framework for generic quality control of data. It permits to create, manage and visualise individual or sets of quality control metrics and generate quality control reports in various formats.

The package contains functions to perform normalization of high-throughput qPCR data. Basic functions for processing raw Ct data plus functions to generate diagnostic plots are also available.

The qmtools (quantitative metabolomics tools) package provides basic tools for processing quantitative metabolomics data with the standard SummarizedExperiment class. This includes functions for imputation, normalization, feature filtering, feature clustering, dimension-reduction, and visualization to help users prepare data for statistical analysis. This package also offers a convenient way to compute empirical Bayes statistics for which metabolic features are different between two sets of study samples. Several functions in this package could also be used in other types of omics data.

This package provides QDNAseq bin annotations for the human genome build hg19.

QuaternaryProd is an R package that performs causal reasoning on biological networks, including publicly available networks such as STRINGdb. QuaternaryProd is an open-source alternative to commercial products such as Inginuity Pathway Analysis. For a given a set of differentially expressed genes, QuaternaryProd computes the significance of upstream regulators in the network by performing causal reasoning using the Quaternary Dot Product Scoring Statistic (Quaternary Statistic), Ternary Dot product Scoring Statistic (Ternary Statistic) and Fisher's exact test (Enrichment test). The Quaternary Statistic handles signed, unsigned and ambiguous edges in the network. Ambiguity arises when the direction of causality is unknown, or when the source node (e.g., a protein) has edges with conflicting signs for the same target gene. On the other hand, the Ternary Statistic provides causal reasoning using the signed and unambiguous edges only. The Vignette provides more details on the Quaternary Statistic and illustrates an example of how to perform causal reasoning using STRINGdb.

Estimate gene and eQTL networks from high-throughput expression and genotyping assays.

This R package provides access to the Qtlizer web server. Qtlizer annotates lists of common small variants (mainly SNPs) and genes in humans with associated changes in gene expression using the most comprehensive database of published quantitative trait loci (QTLs).

This package provides tools for TMT based quantitative proteomics data analysis.

The data employed in the vignette of the QUBIC package. These data belong to Many Microbe Microarrays Database and STRING v10.

qPLEX-RIME and Full proteome TMT mass spectrometry datasets.