Shiny apps

R packages

psichomics

Graphical application for alternative splicing quantification and analysis

psichomics is an 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), Genotype-Tissue Expression (GTEx) project, Sequence Read Archive (SRA) and user-provided data.

psichomics interactively performs survival, dimensionality reduction and median- and variance-based differential splicing and gene expression analyses that benefit from the incorporation of clinical and molecular sample-associated features (such as tumour stage or survival). Interactive visual access to genomic mapping and functional annotation of selected alternative splicing events is also included.

Tutorial: Interactive Alternative Splicing Analysis of Human Stem Cells Using psichomics

Saraiva-Agostinho N, Barbosa-Morais NL (2019). “psichomics: graphical application for alternative splicing quantification and analysis.” Nucleic Acids Research, 47(2), e7. https://doi.org/10.1093/nar/gky888.

cTRAP

Identification of candidate causal perturbations from differential gene expression data

cTRAP is an R package designed to compare differential gene expression results with those from known cellular perturbations (such as gene knockdown, overexpression or small molecules) derived from the Connectivity Map (CMap; Subramanian et al., Cell 2017). Such analyses allow not only to infer the molecular causes of the observed difference in gene expression but also to identify small molecules that could drive or revert specific transcriptomic alterations.

Tutorial: identifying candidate causal perturbations from differential gene expression data

de Almeida BP, Saraiva-Agostinho N, Barbosa-Morais NL (2020). cTRAP: Identification of candidate causal perturbations from differential gene expression data. R package version 1.6.0, https://github.com/nuno-agostinho/cTRAP.