ArticleBMC bioinformatics2019
pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components.
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 177 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
177 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of gonadal transcriptome provides novel insights into sex change mechanism across protogynous fishes.Genes to cells : devoted to molecular & cellular mechanisms · 2024Pooled it
- Multi-omics analysis reveals COVID-19 vaccine induced attenuation of inflammatory responses during breakthrough disease.Nature communications · 2024Trial
- Vitamin D3 and deconvoluting a rash.JCI insight · 2023Trial
- Large-scale and innervated functional human gut tissues for transplantation via transient spheroid confinement.Nature biomedical engineering · 2026Article
- Population-Associated Molecular Variation in Histologically Normal Breast Tissue Is Associated with Distinct Baseline Transcriptional States.International journal of molecular sciences · 2026Article
- Plasma membrane order maps functional diversity in immune cells.Nature chemical biology · 2026Article
- Elimination of myotonia improves myopathy in a muscleblind-like knockout model of myotonic dystrophy.Nature communications · 2026Article
- Inhibition of AXL receptor tyrosine kinase increases osteoblast function and bone mass.Bone research · 2026Article
- Alveolar macrophage subtypes express cholesterol and inflammation genes in cystic fibrosis.Life science alliance · 2026Article
- Deletion of CEACAM1 does not affect retinal and choroidal morphology or transcriptome.Cell and tissue research · 2026Article
- Newly identified invasion drivers define the tumor front in oral squamous cell carcinoma.Cell death discovery · 2026Article
- Differential Immune Priming Effects of Banana Extracellular Self-DNA Derived from Bananas with Varying Disease Severities AgainstJournal of fungi (Basel, Switzerland) · 2026Article
- Wnt/β-catenin signaling regulates fibrotic atrophy of intra-articular adipose tissue in post-traumatic osteoarthritis.bioRxiv : the preprint server for biology · 2026Article
- USP2 is an androgen-repressed survival factor that stabilises oncoproteins to facilitate therapy resistance in prostate cancer.Cell death & disease · 2026Article
- Aldh3a1-mediated detoxification of reactive aldehydes contributes to distinct muscle responses to amyotrophic lateral sclerosis progression.Free radical biology & medicine · 2026Article
- Highly Aggressive and Metastatic MDA-MB-231 and Mel Z Cancer Cells Have Common Sets of Down- and Upregulated Genes During Formation of the Vasculogenic Mimicry Phenotype.International journal of molecular sciences · 2026Article
- The MYB-related transcription factor MYPOP acts as a selective regulator of cancer cell growth.Communications biology · 2026Article
- Transcriptome profiling of bovine preantral follicles during early folliculogenesis.Journal of animal science and biotechnology · 2026Article
- HER2-driven mammary tumorigenesis enhances bioenergetics despite reductions in mitochondrial content.eLife · 2026Article
- Histone methylation defines c-Jun/Sox2/Hif1α axis that controls stemness and tumor progression in squamous cell carcinoma.Nature communications · 2026Article
117 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
backgroundPrincipal component analysis (PCA) is frequently used in genomics applications for quality assessment and exploratory analysis in high-dimensional data, such as RNA sequencing (RNA-seq) gene expression assays. Despite the availability of many software packages developed for this purpose, an interactive and comprehensive interface for performing these operations is lacking.
resultsWe developed the pcaExplorer software package to enhance commonly performed analysis steps with an interactive and user-friendly application, which provides state saving as well as the automated creation of reproducible reports. pcaExplorer is implemented in R using the Shiny framework and exploits data structures from the open-source Bioconductor project. Users can easily generate a wide variety of publication-ready graphs, while assessing the expression data in the different modules available, including a general overview, dimension reduction on samples and genes, as well as functional interpretation of the principal components.
conclusionpcaExplorer is distributed as an R package in the Bioconductor project ( http://bioconductor.org/packages/pcaExplorer/ ), and is designed to assist a broad range of researchers in the critical step of interactive data exploration.
Indexed as
Identifiers
What OpenQuestion holds
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.