RbcBook1

Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports various annotation graphics.

Scalable genomic analysis.

Using single-cell RNA-Seq expression to visualize CNV in cells.

The aim of TCGAbiolinks is : i) facilitate the GDC open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses and iv) to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.

bambu is a R package for multi-sample transcript discovery and quantification using long read RNA-Seq data. You can use bambu after read alignment to obtain expression estimates for known and novel transcripts and genes. The output from bambu can directly be used for visualisation and downstream analysis such as differential gene expression or transcript usage.

`muscat` provides various methods and visualization tools for DS analysis in multi-sample, multi-group, multi-(cell-)subpopulation scRNA-seq data, including cell-level mixed models and methods based on aggregated “pseudobulk” data, as well as a flexible simulation platform that mimics both single and multi-sample scRNA-seq data.