ArticleNucleic acids research2019
psichomics: graphical application for alternative splicing quantification and analysis.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 1 of them a synthesis that pooled it.
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Who cites it
31 citing papers in PubMed, 1 synthesis or guideline pooled it, 48 citations in OpenAlex.
- HIV-1 Infection Transcriptomics: Meta-Analysis of CD4+ T Cells Gene Expression Profiles.Viruses · 2021Pooled it
- Integrating single-cell sQTL mapping with deep-learning splicing prediction identifies causal variants under influenza infection.Genome biology · 2026Article
- Exon 7 splicing of ERα predicts poor prognosis and increases phenotypic heterogeneity in luminal a subtype breast cancer.FEBS open bio · 2026Article
- Causal splicing variants revealed by deep-learning integration of single-cell sQTL mapping under influenza infection.Research square · 2026Article
- Aberrant Splicing Burden Predicts Immune Infiltration and Prognosis in Head and Neck Squamous Cell Carcinomas.Head & neck · 2026Article
- Deep indel mutagenesis reveals the regulatory and modulatory architecture of alternative exon splicing.Nature communications · 2025Article
- Alternative Splicing in Tumorigenesis and Cancer Therapy.Biomolecules · 2025Review
- Establishment of an alternative splicing prognostic risk model and identification of FN1 as a potential biomarker in glioblastoma multiforme.Scientific reports · 2025Article
- Unravelling genotype-phenotype correlations in Stargardt disease using patient-derived retinal organoids.Cell death & disease · 2025Article
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- betAS: intuitive analysis and visualization of differential alternative splicing using beta distributions.RNA (New York, N.Y.) · 2024Article
- A-Z of Epigenetic Readers: Targeting Alternative Splicing and Histone Modification Variants in Cancer.Cancers · 2024Review
- An alternative splicing signature defines the basal-like phenotype and predicts worse clinical outcome in pancreatic cancer.Cell reports. Medicine · 2024Article
- Dysregulation of RNA splicing in early non-alcoholic fatty liver disease through hepatocellular carcinoma.Scientific reports · 2024Article
- OutSplice: A Novel Tool for the Identification of Tumor-Specific Alternative Splicing Events.BioMedInformatics · 2023Article
- FOXA1 regulates alternative splicing in prostate cancer.Cell reports · 2022Article
- Hepatocyte Deletion of IGF2 Prevents DNA Damage and Tumor Formation in Hepatocellular Carcinoma.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022Article
- Effects of alternative splicing events and transcriptome changes on kidney stone formation.Urolithiasis · 2022Article
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Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alternative pre-mRNA splicing generates functionally distinct transcripts from the same gene and is involved in the control of multiple cellular processes, with its dysregulation being associated with a variety of pathologies. The advent of next-generation sequencing has enabled global studies of alternative splicing in different physiological and disease contexts. However, current bioinformatics tools for alternative splicing analysis from RNA-seq data are not user-friendly, disregard available exon-exon junction quantification or have limited downstream analysis features. To overcome such limitations, we have developed psichomics, an R package with an intuitive graphical interface for alternative splicing quantification and downstream dimensionality reduction, differential splicing and gene expression and survival analyses based on The Cancer Genome Atlas, the Genotype-Tissue Expression project, the Sequence Read Archive project and user-provided data. These integrative analyses can also incorporate clinical and molecular sample-associated features. We successfully used psichomics in a laptop to reveal alternative splicing signatures specific to stage I breast cancer and associated novel putative prognostic factors.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.