This package aligns LC-HRMS metabolomics datasets acquired from biologically similar specimens analyzed under similar, but not necessarily identical, conditions. Peak-picked and simply aligned metabolomics feature tables (consisting of m/z, rt, and per-sample abundance measurements, plus optional identifiers & adduct annotations) are accepted as input. The package outputs a combined table of feature pair alignments, organized into groups of similar m/z, and ranked by a similarity score. Input tables are assumed to be acquired using similar (but not necessarily identical) analytical methods.

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-U74B\_probe\_tab.

This package applies several machine learning methods, including SVM, bagSVM, Random Forest and CART to RNA-Seq data.

Codelink UniSet Mouse 20k I Bioarray annotation data (chip m20kcod) assembled using data from public repositories.

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

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.

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 MOE430B\_probe\_tab.

Easily visualize and inspect microarrays for spatial artifacts.

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

It contains functions for estimating the DNA copy number profile using mBPCR with the aim of detecting regions with copy number changes.

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 miRNA-1\_0\_probe\_tab.

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

This package produces metagene plots to compare coverages of sequencing experiments at selected groups of genomic regions. It can be used for such analyses as assessing the binding of DNA-interacting proteins at promoter regions or surveying antisense transcription over the length of a gene. The metagene2 package can manage all aspects of the analysis, from normalization of coverages to plot facetting according to experimental metadata. Bootstraping analysis is used to provide confidence intervals of per-sample mean coverages.

This package provides a package containing an environment representing the miRNA-1_0_2Xgain.CDF file.

Our pipeline, MICSQTL, utilizes scRNA-seq reference and bulk transcriptomes to estimate cellular composition in the matched bulk proteomes. The expression of genes and proteins at either bulk level or cell type level can be integrated by Angle-based Joint and Individual Variation Explained (AJIVE) framework. Meanwhile, MICSQTL can perform cell-type-specic quantitative trait loci (QTL) mapping to proteins or transcripts based on the input of bulk expression data and the estimated cellular composition per molecule type, without the need for single cell sequencing. We use matched transcriptome-proteome from human brain frontal cortex tissue samples to demonstrate the input and output of our tool.

microbiomeDataSets is a collection of microbiome datasets loaded from Bioconductor'S ExperimentHub infrastructure. The datasets serve as reference for workflows and vignettes published adjacent to the microbiome analysis tools on Bioconductor. Additional datasets can be added overtime and additions from authors are welcome.

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-U74A\_probe\_tab.

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.

Affymetrix Affymetrix Mouse430_2 Array annotation data (chip mouse4302) assembled using data from public repositories.

This package was automatically created by package AnnotationForge version 1.7.17. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible.

MotifPeeker is used to compare and analyse datasets from epigenomic profiling methods with motif enrichment as the key benchmark. The package outputs an HTML report consisting of three sections: (1. General Metrics) Overview of peaks-related general metrics for the datasets (FRiP scores, peak widths and motif-summit distances). (2. Known Motif Enrichment Analysis) Statistics for the frequency of user-provided motifs enriched in the datasets. (3. De-Novo Motif Enrichment Analysis) Statistics for the frequency of de-novo discovered motifs enriched in the datasets and compared with known motifs.

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

Store minor allele frequency data from the Genome Aggregation Database (gnomAD exomes release 2.1) for the human genome version GRCh38.

Affymetrix Affymetrix MG_U74A Array annotation data (chip mgu74a) assembled using data from public repositories.