Installing and starting the program | Quick reference of psichomics functions | Exploration of clinically-relevant, differentially spliced events in breast cancer | Downloading and loading TCGA data | Filtering and normalising gene expression | Quantifying alternative splicing | Data grouping | Principal component analysis (PCA) | NUMB exon 12 inclusion and correlation with QKI gene expression | Differential inclusion of NUMB exon 12 | Correlation between NUMB exon 12 inclusion and QKI expression | Differential splicing analysis | Performing multiple survival analysis | Differential gene expression | UHRF2 exon 10 inclusion | Survival analysis | Differential expression | Literature support and external database information | Interpretation | Loading data from other sources | Load GTEx data | Load SRA project data using recount | Load user-provided data | Feedback | References

Installing and starting the program | Exploration of clinically-relevant, differentially spliced events in breast cancer | Downloading and loading TCGA data | Filtering and normalising gene expression | Quantifying alternative splicing | Data grouping | Principal component analysis (PCA) | PCA performance | PCA plotting | NUMB exon 12 inclusion and correlation with QKI gene expression | Differential inclusion of NUMB exon 12 | Correlation between NUMB exon 12 inclusion and QKI expression | Differential splicing analysis | Filtering alternative splicing events | Performing multiple survival analysis | Differential gene expression | UHRF2 exon 10 inclusion | Survival analysis | Differential expression | Literature support and external database information | Interpretation | Exploring alternative splicing changes between human isogenic stem cells and fibroblasts | Load SRA and user-provided local files | Feedback | References

Supported file formats | Prepare SRA Run Selector data | Prepare tables based on RNA-seq data using STAR | Download FASTQ files (optional) | Align RNA-seq data to quantify splice junctions | Index the genome using STAR | Align against genome index using STAR | Prepare output for psichomics | Prepare VAST-TOOLS data | Prepare FireBrowse data | Prepare GTEx data | Prepare data from any source | Sample information | Subject information | Gene expression | Exon-exon junction quantification | Alternative splicing quantification (also known as inclusion levels) | Load user-provided data into psichomics | Load using the visual interface | Load using the command-line interface (CLI) | Feedback | References

Creating custom alternative splicing annotation | SUPPA annotation | rMATS annotation | MISO annotation | VAST-TOOLS annotation | Combining annotation from different sources | Quantifying alternative splicing using the custom annotation | Feedback

Introduction | Getting started | Load ENCODE RNA-seq data and perform differential gene expression analysis | Load CMap perturbation data | Comparison with CMap perturbations | Information on perturbations | Relationship plots | Predict targeting drugs | Molecular descriptor enrichment analysis | Contact information