Package to retrieve and visualize data from the Comparative Toxicogenomics Database (http://ctdbase.org/). The downloaded data is formated as DataFrames for further downstream analyses.

Biological studies often consist of multiple conditions which are examined with different laboratory set ups like RNA-sequencing or ChIP-sequencing. To get an overview about the whole resulting data set, Cogito provides an automated, complete, reproducible and clear report about all samples and basic comparisons between all different samples. This report can be used as documentation about the data set or as starting point for further custom analysis.

Base annotation databases for canine, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.

This package is for analysis of SILAC labeled complexome profiling data. It uses peptide table in tab-delimited format as an input and produces ready-to-use tables and plots.

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 Cotton\_probe\_tab.

CaMutQC is able to filter false positive mutations generated due to technical issues, as well as to select candidate cancer mutations through a series of well-structured functions by labeling mutations with various flags. And a detailed and vivid filter report will be offered after completing a whole filtration or selection section. Also, CaMutQC integrates serveral methods and gene panels for Tumor Mutational Burden (TMB) estimation.

Base annotation databases for chicken, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.

This package provides functions to reconstruct case and control AFs from summary statistics. One function uses OR, NCase, NControl, and SE(log(OR)). The second function uses OR, NCase, NControl, and AF for the whole sample.

The cfTools R package provides methods for cell-free DNA (cfDNA) methylation data analysis to facilitate cfDNA-based studies. Given the methylation sequencing data of a cfDNA sample, for each cancer marker or tissue marker, we deconvolve the tumor-derived or tissue-specific reads from all reads falling in the marker region. Our read-based deconvolution algorithm exploits the pervasiveness of DNA methylation for signal enhancement, therefore can sensitively identify a trace amount of tumor-specific or tissue-specific cfDNA in plasma. cfTools provides functions for (1) cancer detection: sensitively detect tumor-derived cfDNA and estimate the tumor-derived cfDNA fraction (tumor burden); (2) tissue deconvolution: infer the tissue type composition and the cfDNA fraction of multiple tissue types for a plasma cfDNA sample. These functions can serve as foundations for more advanced cfDNA-based studies, including cancer diagnosis and disease monitoring.

This package provides an interface to access pre-trained models for on-target and off-target gRNA activity prediction algorithms implemented in the crisprScore package. Pre-trained model data are stored in the ExperimentHub database. Users should consider using the crisprScore package directly to use and load the pre-trained models.

This package provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data.

Data package which provides default drug profiles for the DrugVsDisease package as well as associated gene lists and data clusters used by the DrugVsDisease package.

COCOA is a method for understanding epigenetic variation among samples. COCOA can be used with epigenetic data that includes genomic coordinates and an epigenetic signal, such as DNA methylation and chromatin accessibility data. To describe the method on a high level, COCOA quantifies inter-sample variation with either a supervised or unsupervised technique then uses a database of "region sets" to annotate the variation among samples. A region set is a set of genomic regions that share a biological annotation, for instance transcription factor (TF) binding regions, histone modification regions, or open chromatin regions. COCOA can identify region sets that are associated with epigenetic variation between samples and increase understanding of variation in your data.

CBN2Path package provides a unifying interface to facilitate CBN-based quantification, analysis and visualization of cancer progression pathways.

This explorative ordination method combines quasi-likelihood estimation, compositional regression models and latent variable models for integrative visualization of several omics datasets. Both unconstrained and constrained integration are available. The results are shown as interpretable, compositional multiplots.

This package does optimisation of boolean logic networks of signalling pathways based on a previous knowledge network and a set of data upon perturbation of the nodes in the network.

This package can be used to estimate the number of clusters in a set of microarray data, as well as test the stability of these clusters.

The curatedBladderData package provides relevant functions and data for gene expression analysis in patients with bladder cancer.

Coralysis is an R package featuring a multi-level integration algorithm for sensitive integration, reference-mapping, and cell-state identification in single-cell data. The multi-level integration algorithm is inspired by the process of assembling a puzzle - where one begins by grouping pieces based on low-to high-level features, such as color and shading, before looking into shape and patterns. This approach progressively blends the batch effects and separates cell types across multiple rounds of divisive clustering.

This package is desgined to perform statistical analysis to identify statistically significant differentially bound regions between multiple groups of ChIP-seq dataset.

This package implements classes and methods for large-scale SNP association studies.

This package serves as a query interface for important community collections of small molecules, while also allowing users to include custom compound collections.

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

Store University of Washington CADD v1.6 hg38 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for University of Washington CADD v1.6 hg38 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those resources.