Artifacts using Cowplot (25)

'ggplot2' is an excellent and flexible package for elegant data visualization in R. However the default generated plots requires some formatting before we can send them for publication. Furthermore, to customize a 'ggplot', the syntax is opaque and this raises the level of difficulty for researchers with no advanced R programming skills. 'ggpubr' provides some easy-to-use functions for creating and customizing 'ggplot2'- based publication ready plots.

'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics. 'ggtree' is designed for visualization and annotation of phylogenetic trees with their covariates and other associated data.

Convert plot function call (using expression or formula) to 'grob' or 'ggplot' object that compatible to the 'grid' and 'ggplot2' ecosystem. With this package, we are able to e.g. using 'cowplot' to align plots produced by 'base' graphics, 'grid', 'lattice', 'vcd' etc. by converting them to 'ggplot' objects.

The BPRMeth package is a probabilistic method to quantify explicit features of methylation profiles, in a way that would make it easier to formally use such profiles in downstream modelling efforts, such as predicting gene expression levels or clustering genomic regions according to their methylation profiles.

This package conveniently wraps all functions needed to reproduce the figures in the IHW preprint, available on biorXiv under http://biorxiv.org/content/early/2016/03/30/034330. Thus it is a companion package to the Bioconductor IHW package.

Provides functions for creating an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. Particular attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results.

This package perform weighted-pvalue based multiple hypothesis test and provides corresponding information such as ranking probability, weight, significant tests, etc . To conduct this testing procedure, the testing method apply a probabilistic relationship between the test rank and the corresponding test effect size.

The pbcmc package characterizes uncertainty assessment on gene expression classifiers, a. k. a. molecular signatures, based on a permutation test. In order to achieve this goal, synthetic simulated subjects are obtained by permutations of gene labels. Then, each synthetic subject is tested against the corresponding subtype classifier to build the null distribution. Thus, classification confidence measurement can be provided for each subject, to assist physician therapy choice. At present, it is only ...

An R implementation of the correlation-based method developed in the Joshi laboratory to analyse and filter processed single-cell RNAseq data. It returns a filtered version of the data containing only genes expression values unaffected by systematic noise.

Provides useful functions for visualizing sequence recombination and virus reassortment events.