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Original article:

Nuno Saraiva-Agostinho and Nuno L. Barbosa-Morais (2019). psichomics: graphical application for alternative splicing quantification and analysis. Nucleic Acids Research. 47(2), e7.

Interactive R package with an intuitive Shiny-based graphical interface for alternative splicing quantification and integrative analyses of alternative splicing and gene expression based on The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression (GTEx) project, Sequence Read Archive (SRA) and user-provided data.

psichomics interactively performs: - Dimensionality reduction - Median- and variance-based differential splicing and gene expression analyses - Survival analysis - Correlation analysis - Grouping by clinical and molecular features (such as tumour stage or survival) - Genomic mapping and functional annotation of alternative splicing events and genes

Differential splicing analysis in *psichomics*

Table of Contents

Install and start running

To install the package from Bioconductor, type the following in RStudio or in an R console:



The following case studies and tutorials are available and were based on our original article:

Another tutorial was published as part of the Methods in Molecular Biology book series (the code for performing the analysis can be found here):

Nuno Saraiva-Agostinho and Nuno L. Barbosa-Morais (2020). Interactive Alternative Splicing Analysis of Human Stem Cells Using psichomics. In: Kidder B. (eds) Stem Cell Transcriptional Networks. Methods in Molecular Biology, vol 2117. Humana, New York, NY


Data input

Automatic retrieval and loading of pre-processed data from the following sources:

Other SRA, VAST-TOOLS and user-provided data can also be manually loaded. Please read Loading SRA, VAST-TOOLS and user-provided RNA-seq data for more information.

Alternative splicing quantification

The quantification of each alternative splicing event is based on the proportion of junction reads that support the inclusion isoform, known as percent spliced-in or PSI (Wang et al., 2008).

An estimate of this value is obtained based on the the proportion of reads supporting the inclusion of an exon over the reads supporting both the inclusion and exclusion of that exon. To measure this estimate, we require:

  1. Alternative splicing annotation: human annotation is provided and custom annotations can be prepared for use in psichomics.
  2. Quantification of RNA-Seq reads aligning to exon-exon splice junctions (exon-exon junction quantification), either user-provided or retrieved from TCGA, GTEx and SRA.

Gene expression processing

Gene expression can be normalised, filtered and log2-transformed in-app or provided by the user.

Data grouping

Molecular and clinical sample-associated attributes allow to establish groups that can be explored in data analyses.

For instance, TCGA data can be analysed based on smoking history, gender and race, among other attributes. Groups can also be manipulated (e.g. merged, intersected, etc.), allowing for complex attribute combinations. Groups can also be saved and loaded between different sessions.

Data Analyses

Feedback and support

Please send any feedback and questions on psichomics to:

Nuno Saraiva-Agostinho (

Disease Transcriptomics Lab, Instituto de Medicina Molecular (Portugal)


Wang, E. T., R. Sandberg, S. Luo, I. Khrebtukova, L. Zhang, C. Mayr, S. F. Kingsmore, G. P. Schroth, and C. B. Burge. 2008. Alternative isoform regulation in human tissue transcriptomes. Nature 456 (7221): 470–76.

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psichomics documentation built on Nov. 8, 2020, 5:44 p.m.