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

FHCRC Genomics Shared Resource Mu22v3 Annotation Data (Mu22v3) assembled using data from public repositories.

This package provides functionality for processing and statistical analysis of multiplexed assays of variant effect (MAVE) and similar data. The package contains functions covering the full workflow from raw FASTQ files to publication-ready visualizations. A broad range of library designs can be processed with a single, unified interface.

This package finds optimal sets of genes that seperate samples into two or more classes.

Store minor allele frequency data from NHLBI TOPMed for the human genome version hg19.

MEDIPS was developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, MEDIPS provides functionalities for the analysis of any kind of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential coverage between groups of samples and saturation and correlation analysis.

Classification of pediatric tumors into biologically defined subtypes is challenging and multifaceted approaches are needed. For this aim, we developed a diagnostic classifier based on DNA methylation profiles. We offer MethPed as an easy-to-use toolbox that allows researchers and clinical diagnosticians to test single samples as well as large cohorts for subclass prediction of pediatric brain tumors. The current version of MethPed can classify the following tumor diagnoses/subgroups: Diffuse Intrinsic Pontine Glioma (DIPG), Ependymoma, Embryonal tumors with multilayered rosettes (ETMR), Glioblastoma (GBM), Medulloblastoma (MB) - Group 3 (MB_Gr3), Group 4 (MB_Gr3), Group WNT (MB_WNT), Group SHH (MB_SHH) and Pilocytic Astrocytoma (PiloAstro).

This package provides a package containing an environment representing the Mu19KsubB.CDF file.

MicrobiotaProcess is an R package for analysis, visualization and biomarker discovery of microbial datasets. It introduces MPSE class, this make it more interoperable with the existing computing ecosystem. Moreover, it introduces a tidy microbiome data structure paradigm and analysis grammar. It provides a wide variety of microbiome data analysis procedures under the unified and common framework (tidy-like framework).

Affymetrix Affymetrix MOE430B Array annotation data (chip moe430b) assembled using data from public repositories.

This package estimates epigenetic age in skeletal muscle, using DNA methylation data generated with the Illumina Infinium technology (HM27, HM450 and HMEPIC).

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

Custom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.

MetNet contains functionality to infer metabolic network topologies from quantitative data and high-resolution mass/charge information. Using statistical models (including correlation, mutual information, regression and Bayes statistics) and quantitative data (intensity values of features) adjacency matrices are inferred that can be combined to a consensus matrix. Mass differences calculated between mass/charge values of features will be matched against a data frame of supplied mass/charge differences referring to transformations of enzymatic activities. In a third step, the two levels of information are combined to form a adjacency matrix inferred from both quantitative and structure information.

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.

Data used by the barcode package for microarrays of type mouse4302.

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

Affymetrix mogene21 annotation data (chip mogene21stprobeset) assembled using data from public repositories.

The functions in this package return optimized parameter estimates and log likelihoods for mixture models of truncated data with normal or lognormal distributions.

Store minor allele frequency data from the Exome Aggregation Consortium (ExAC release 1.0 subset of nonTCGA exomes) for the human genome version hs37d5.

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 MoGene-1\_0-st-v1\_probe\_tab.

The package is designed to detect marker genes from Microarray gene expression data sets.

This package fits a model to the pattern of dropouts in single-cell RNASeq data. This model is used as a null to identify significantly variable (i.e. differentially expressed) genes for use in downstream analysis, such as clustering cells. Also includes an method for calculating exact Pearson residuals in UMI-tagged data using a library-size aware negative binomial model.

This package provides a package containing an environment representing the Mouse430_2.cdf file.