MethylSig is a package for testing for differentially methylated cytosines (DMCs) or regions (DMRs) in whole-genome bisulfite sequencing (WGBS) or reduced representation bisulfite sequencing (RRBS) experiments. MethylSig uses a beta binomial model to test for significant differences between groups of samples. Several options exist for either site-specific or sliding window tests, and variance estimation.

Agilent annotation data (chip mgug4120a) assembled using data from public repositories.

This package provides a collection of datasets to accompany the R package MOFA and illustrate running and analysing MOFA models.

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 MOE430A\_probe\_tab.

This package provides a package containing an environment representing the Mouse430A_2.cdf file.

MEDME allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments.

This package provides a package containing an environment representing the MG_U74Cv2.CDF file.

magrene allows the identification and analysis of graph motifs in (duplicated) gene regulatory networks (GRNs), including lambda, V, PPI V, delta, and bifan motifs. GRNs can be tested for motif enrichment by comparing motif frequencies to a null distribution generated from degree-preserving simulated GRNs. Motif frequencies can be analyzed in the context of gene duplications to explore the impact of small-scale and whole-genome duplications on gene regulatory networks. Finally, users can calculate interaction similarity for gene pairs based on the Sorensen-Dice similarity index.

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.

Provide functions for performing abundance and compositional based binning on metagenomic samples, directly from FASTA or FASTQ files. Functions are implemented in Java and called via rJava. Parallel implementation that operates directly on input FASTA/FASTQ files for fast execution.

Agilent Chips that use Agilent design number 026655 annotation data (chip MmAgilentDesign026655) assembled using data from public repositories.

This package provides a package containing an environment representing the miRNA-1_0.CDF file.

Bedgraph files generated by Bisulfite pipelines often come in various flavors. Critical downstream step requires summarization of these files into methylation/coverage matrices. This step of data aggregation is done by Methrix, including many other useful downstream functions.

This package provides functions for the analysis of data generated by the multiplex substrate profiling by mass spectrometry for proteases (MSP-MS) method. Data exported from upstream proteomics software is accepted as input and subsequently processed for analysis. Tools for statistical analysis, visualization, and interpretation of the data are provided.

Topological pathway analysis tool able to integrate multi-omics data. It finds survival-associated modules or significant modules for two-class analysis. This tool have two main methods: pathway tests and module tests. The latter method allows the user to dig inside the pathways itself.

This package provides a package containing an environment representing the MG_U74B.cdf file.

This package provides tools for augmenting signaling pathways to perform pathway analysis of microRNA and mRNA expression levels.

This package provides a package containing an environment representing the Mu6500subD.CDF file.

affy and illumina raw data for assessing outlier detector performance.

This package provides a package containing an environment representing the MG_U74Av2.CDF file.

Annotation data file for mouseCHRLOC assembled using data from public data repositories.

This package provides a model-based background correction method, which incorporates the negative control beads to pre-process Illumina BeadArray data.

MAPFX is an end-to-end toolbox that pre-processes the raw data from MPC experiments (e.g., BioLegend's LEGENDScreen and BD Lyoplates assays), and further imputes the ‘missing’ infinity markers in the wells without those measurements. The pipeline starts by performing background correction on raw intensities to remove the noise from electronic baseline restoration and fluorescence compensation by adapting a normal-exponential convolution model. Unwanted technical variation, from sources such as well effects, is then removed using a log-normal model with plate, column, and row factors, after which infinity markers are imputed using the informative backbone markers as predictors. The completed dataset can then be used for clustering and other statistical analyses. Additionally, MAPFX can be used to normalise data from FFC assays as well.

R objects describing the MEEBO set.