ArticlePloS one2017
shinyheatmap: Ultra fast low memory heatmap web interface for big data genomics.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 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
65 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Decreased sphingomyelin (t34:1) is a candidate predictor for lung squamous cell carcinoma recurrence after radical surgery: a case-control study.BMC cancer · 2021Pooled it
- Clock pathway inhibitor overcomes tumor immune-exclusion via regulation of fibrocyte differentiation.NPJ precision oncology · 2025Article
- The Proposed Categorization of Vitiligo Lesions on the Hands.Pigment cell & melanoma research · 2025Article
- Loss of mitochondrial pyruvate transport initiates cardiac glycogen accumulation and heart failure.bioRxiv : the preprint server for biology · 2025Article
- Molecular similarity: Theory, applications, and perspectives.Artificial intelligence chemistry · 2024Article
- Cryptosporidium life cycle small molecule probing implicates translational repression and an Apetala 2 transcription factor in macrogamont differentiation.PLoS pathogens · 2024Article
- TCMNPAS: a comprehensive analysis platform integrating network formulaology and network pharmacology for exploring traditional Chinese medicine.Chinese medicine · 2024Article
- Characteristics of MicroRNA Expression Depending on the Presence or Absence of Meningioma in Patients with Neurofibromatosis Type 2: A Secondary Analysis.Neurologia medico-chirurgica · 2024Article
- Cotton Meristem Transcriptomes: Constructing an RNA-Seq Pipeline to Explore Crop Architecture Regulation.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Anthropogenic fertilization influences a shift in barley rhizosphere microbial communities.PeerJ · 2024Article
- Altered Caveolin-1 Dynamics Result in Divergent Mineralization Responses in Bone and Vascular Calcification.Cellular and molecular bioengineering · 2023Article
- Altered expression of SELF-PRUNING disrupts homeostasis and facilitates signal delivery to meristems.Plant physiology · 2023Article
- Effect of oral cannabis administration on the fat depots of obese and streptozotocin-induced diabetic rats.Phytotherapy research : PTR · 2023Article
- Article
- Machine learning classifiers predict key genomic and evolutionary traits across the kingdoms of life.Scientific reports · 2023Article
- Plasminogen Activator Inhibitor-1 Potentiates Neutrophil Infiltration and Tissue Injury in Colitis.International journal of biological sciences · 2023Article
- Article
- Maize rhizosphere modulates the microbiome diversity and community structure to enhance plant health.Saudi journal of biological sciences · 2023Article
- KLF15 controls brown adipose tissue transcriptional flexibility and metabolism in response to various energetic demands.iScience · 2022Article
- Hippo signaling pathway activation during SARS-CoV-2 infection contributes to host antiviral response.PLoS biology · 2022Article
5 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
3 authors.
Funding
Abstract
backgroundTranscriptomics, metabolomics, metagenomics, and other various next-generation sequencing (-omics) fields are known for their production of large datasets, especially across single-cell sequencing studies. Visualizing such big data has posed technical challenges in biology, both in terms of available computational resources as well as programming acumen. Since heatmaps are used to depict high-dimensional numerical data as a colored grid of cells, efficiency and speed have often proven to be critical considerations in the process of successfully converting data into graphics. For example, rendering interactive heatmaps from large input datasets (e.g., 100k+ rows) has been computationally infeasible on both desktop computers and web browsers. In addition to memory requirements, programming skills and knowledge have frequently been barriers-to-entry for creating highly customizable heatmaps.
resultsWe propose shinyheatmap: an advanced user-friendly heatmap software suite capable of efficiently creating highly customizable static and interactive biological heatmaps in a web browser. shinyheatmap is a low memory footprint program, making it particularly well-suited for the interactive visualization of extremely large datasets that cannot typically be computed in-memory due to size restrictions. Also, shinyheatmap features a built-in high performance web plug-in, fastheatmap, for rapidly plotting interactive heatmaps of datasets as large as 105-107 rows within seconds, effectively shattering previous performance benchmarks of heatmap rendering speed.
conclusionsshinyheatmap is hosted online as a freely available web server with an intuitive graphical user interface: http://shinyheatmap.com. The methods are implemented in R, and are available as part of the shinyheatmap project at: https://github.com/Bohdan-Khomtchouk/shinyheatmap. Users can access fastheatmap directly from within the shinyheatmap web interface, and all source code has been made publicly available on Github: https://github.com/Bohdan-Khomtchouk/fastheatmap.
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.