CuratedAtlasQueryR

This is a collection of utility functions that allow to perform exploration of and calculations to RNA sequencing data, in a modular, pipe-friendly and tidy fashion.

The tidyomics ecosystem is a set of packages for ’omic data analysis that work together in harmony; they share common data representations and API design, consistent with the tidyverse ecosystem. The tidyomics package is designed to make it easy to install and load core packages from the tidyomics ecosystem with a single command.

The tidySummarizedExperiment package provides a set of tools for creating and manipulating tidy data representations of SummarizedExperiment objects. SummarizedExperiment is a widely used data structure in bioinformatics for storing high-throughput genomic data, such as gene expression or DNA sequencing data. The tidySummarizedExperiment package introduces a tidy framework for working with SummarizedExperiment objects. It allows users to convert their data into a tidy format, where each observation is a row and each variable is a column. This tidy representation simplifies data manipulation, integration with other tidyverse packages, and enables seamless integration with the broader ecosystem of tidy tools for data analysis.

Differential expression analysis of sequence count data. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models, quasi-likelihood, and gene set enrichment. Can perform differential analyses of any type of omics data that produces read counts, including RNA-seq, ChIP-seq, ATAC-seq, Bisulfite-seq, SAGE, CAGE, metabolomics, or proteomics spectral counts. RNA-seq analyses can be conducted at the gene or isoform level, and tests can be conducted for differential exon or transcript usage.

This package implements a variety of functions useful for gene set analysis using rotations to approximate the null distribution. It contributes with the implementation of seven test statistic scores that can be used with different goals and interpretations. Several functions are available to complement the statistical results with graphical representations.

'tidySingleCellExperiment' is an adapter that abstracts the 'SingleCellExperiment' container in the form of a 'tibble'. This allows *tidy* data manipulation, nesting, and plotting. For example, a 'tidySingleCellExperiment' is directly compatible with functions from 'tidyverse' packages `dplyr` and `tidyr`, as well as plotting with `ggplot2` and `plotly`. In addition, the package provides various utility functions specific to single-cell omics data analysis (e.g., aggregation of cell-level data to pseudobulks).