This package allows to estimate missing values in DNA methylation data. methyLImp method is based on linear regression since methylation levels show a high degree of inter-sample correlation. Implementation is parallelised over chromosomes since probes on different chromosomes are usually independent. Mini-batch approach to reduce the runtime in case of large number of samples is available.

This package was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0.

MyGene.Info_ provides simple-to-use REST web services to query/retrieve gene annotation data. It's designed with simplicity and performance emphasized. *mygene*, is an easy-to-use R wrapper to access MyGene.Info_ services.

msqrob2 provides a robust linear mixed model framework for assessing differential abundance in MS-based Quantitative proteomics experiments. Our workflows can start from raw peptide intensities or summarised protein expression values. The model parameter estimates can be stabilized by ridge regression, empirical Bayes variance estimation and robust M-estimation. msqrob2's hurde workflow can handle missing data without having to rely on hard-to-verify imputation assumptions, and, outcompetes state-of-the-art methods with and without imputation for both high and low missingness. It builds on QFeature infrastructure for quantitative mass spectrometry data to store the model results together with the raw data and preprocessed data.

Identification of differentially expressed genes and false discovery rate (FDR) calculation by Multiple Comparison test.

Useful functions to work with sequence motifs in the analysis of genomics data. These include methods to annotate genomic regions or sequences with predicted motif hits and to identify motifs that drive observed changes in accessibility or expression. Functions to produce informative visualizations of the obtained results are also provided.

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.

This package provides a package containing an environment representing the MOE430A.CDF file.

This package provides a collection of tools for doing various analyses of multi-state QTL data, with a focus on visualization and interpretation. The package multistateQTL contains functions which can remove or impute missing data, identify significant associations, as well as categorise features into global, multi-state or unique. The analysis results are stored in a QTLExperiment object, which is based on the SummarisedExperiment framework.

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MG-U74Bv2\_probe\_tab.

Agilent "Mouse Genome, Whole" annotation data (chip mgug4122a) assembled using data from public repositories.

FHCRC Genomics Shared Resource Mu15v1 Annotation Data (Mu15v1) assembled using data from public repositories.

The `miaTime` package provides tools for microbiome time series analysis based on (Tree)SummarizedExperiment infrastructure.

MUSCLE performs multiple sequence alignments of nucleotide or amino acid sequences.

Affymetrix Affymetrix MG_U74B Array annotation data (chip mgu74b) assembled using data from public repositories.

Store minor allele frequency data from the Exome Aggregation Consortium (ExAC release 1.0 subset of nonTCGA exomes) for the human genome version GRCh38.

Codelink Mouse Whole Genome Bioarray (~36 000 mouse gene targets) annotation data (chip mwgcod) assembled using data from public repositories.

The Molecular Degree of Perturbation webtool quantifies the heterogeneity of samples. It takes a data.frame of omic data that contains at least two classes (control and test) and assigns a score to all samples based on how perturbed they are compared to the controls. It is based on the Molecular Distance to Health (Pankla et al. 2009), and expands on this algorithm by adding the options to calculate the z-score using the modified z-score (using median absolute deviation), change the z-score zeroing threshold, and look at genes that are most perturbed in the test versus control classes.

This package provides functions for fitting MOSAiCS and MOSAiCS-HMM, a statistical framework to analyze one-sample or two-sample ChIP-seq data of transcription factor binding and histone modification.

Simulate a multigeneration methylation case versus control experiment with inheritance relation using a real control dataset.

High level functions to assist in annotation of (metabolomics) data sets. These include functions to perform simple tentative annotations based on mass matching but also functions to consider m/z and retention times for annotation of LC-MS features given that respective reference values are available. In addition, the function provides high-level functions to simplify matching of LC-MS/MS spectra against spectral libraries and objects and functionality to represent and manage such matched data.

This package provides a package containing an environment representing the MoGene-1_0-st-v1.cdf file.

Affymetrix Affymetrix Mu19KsubB Array annotation data (chip mu19ksubb) assembled using data from public repositories.

Subsampled Hi-C in HEK cells expressing the NHA9 fusion with an F to S mutated IDR ("FS") or without any mutations to the IDR ("Wildtype" or "WT"). These files are used for testing mariner functions and some examples.