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

This package provides tools for detecting drug-protein interactions and estimating IC50 values from chemoproteomics data. Implements semi-parametric isotonic regression, bootstrapping, and curve fitting to evaluate compound effects on protein abundance.

Affymetrix moex10 annotation data (chip moex10sttranscriptcluster) assembled using data from public repositories.

Extracted features from pathways derived from 8 different databases (KEGG, Reactome, Biocarta, etc.) can be used on transcriptomic, proteomic, and/or metabolomic level to calculate a combined GSEA-based enrichment score.

Base-level (i.e. cytosine-level) counts for a collection of public bisulfite-seq datasets (e.g., WGBS and RRBS), provided as SummarizedExperiment objects with sample- and base-level metadata.

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.

Analysis of de novo copy number variants in trios from high-dimensional genotyping platforms.

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

This package is a implementation of biclustering ensemble method MoSBi (Molecular signature Identification from Biclustering). MoSBi provides standardized interfaces for biclustering results and can combine their results with a multi-algorithm ensemble approach to compute robust ensemble biclusters on molecular omics data. This is done by computing similarity networks of biclusters and filtering for overlaps using a custom error model. After that, the louvain modularity it used to extract bicluster communities from the similarity network, which can then be converted to ensemble biclusters. Additionally, MoSBi includes several network visualization methods to give an intuitive and scalable overview of the results. MoSBi comes with several biclustering algorithms, but can be easily extended to new biclustering algorithms.

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.

Toolbox for larger-than-memory scientific computing and visualization, providing efficient out-of-core data structures using files or shared memory, for dense and sparse vectors, matrices, and arrays, with applications to nonuniformly sampled signals and images.

Example CDF data for the metaMS package.

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

Detect binding sites using motifs IUPAC sequence or bed coordinates and ChIP-seq experiments in bed or bam format. Combine/compare binding sites across experiments, tissues, or conditions. All normalization and differential steps are done using TMM-GLM method. Signal decomposition is done by setting motifs as the centers of the mixture of normal distribution curves.

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

Annotation package containing all available miRNA names from 22 versions (data from http://www.mirbase.org/).

Affymetrix nugomm1a520177 annotation data (chip nugomm1a520177) assembled using data from public repositories.

This package provides visualization functionality for untargeted LC-MS metabolomics research. Includes quality control visualizations, feature-wise visualizations and results visualizations.

Nucleolus is an important structure inside the nucleus in eukaryotic cells. It is the site for transcribing rDNA into rRNA and for assembling ribosomes, aka ribosome biogenesis. In addition, nucleoli are dynamic hubs through which numerous proteins shuttle and contact specific non-rDNA genomic loci. Deep sequencing analyses of DNA associated with isolated nucleoli (NAD- seq) have shown that specific loci, termed nucleolus- associated domains (NADs) form frequent three- dimensional associations with nucleoli. NAD-seq has been used to study the biological functions of NAD and the dynamics of NAD distribution during embryonic stem cell (ESC) differentiation. Here, we developed a Bioconductor package NADfinder for bioinformatic analysis of the NAD-seq data, including baseline correction, smoothing, normalization, peak calling, and annotation.

Perform non-parametric analysis of response curves as described by Childs, Bach, Franken et al. (2019): Non-parametric analysis of thermal proteome profiles reveals novel drug-binding proteins.

This package provides a model for semi-supervised prioritisation of genes integrating network data, phenotypes and additional prior knowledge about TP and TN gene labels from the literature or experts.

Takes as input an incomplete perturbation profile and differential gene expression in log odds and infers unobserved perturbations and augments observed ones. The inference is done by iteratively inferring a network from the perturbations and inferring perturbations from the network. The network inference is done by Nested Effects Models.

nuCpos, a derivative of NuPoP, is an R package for prediction of nucleosome positions. nuCpos calculates local and whole nucleosomal histone binding affinity (HBA) scores for a given 147-bp sequence. Note: This package was designed to demonstrate the use of chemical maps in prediction. As the parental package NuPoP now provides chemical-map-based prediction, the function for dHMM-based prediction was removed from this package. nuCpos continues to provide functions for HBA calculation.

This package provides methods and object classes for parsing FastQC reports and output summaries from other NGS tools into R. As well as parsing files, multiple plotting methods have been implemented for visualising the parsed data. Plots can be generated as static ggplot objects or interactive plotly objects.