ArticleBMC genomics2023
plotnineSeqSuite: a Python package for visualizing sequence data using ggplot2 style.
Article in BMC genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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.
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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.
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Who cites it
42 citing papers in PubMed.
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- Mitochondrial-related biomarkers as the diagnostic markers in sepsis induced acute respiratory distress syndrome.European journal of medical research · 2026Article
- Screening and Preliminary Validation of Parthanatos-Related Key Genes in Asthma Using Transcriptomic and Machine Learning Approaches.Journal of inflammation research · 2026Article
- Glycosylation-Related Gene Signature Identifies MFNG as a Key Driver of Proliferation and Metastasis in Colorectal Cancer.OncoTargets and therapy · 2026Article
- Article
- Prognostic Relevance of Neddylation-Related Genes in Hepatocellular Carcinoma.Journal of hepatocellular carcinoma · 2026Article
- Dysregulated fibroblast-immune crosstalk drives statin-associated erectile dysfunction: integrative evidence from pharmacovigilance and single-cell transcriptomics.Frontiers in pharmacology · 2026Article
- Identification of a prognostic signature based on ammonia metabolism-related genes in clear cell renal cell carcinoma: an integrated analysis of bulk and single-cell transcriptomics.Frontiers in immunology · 2026Article
- Identifying Immunological Biomarkers for Major Depressive Disorder: Insights From Machine Learning, Single-Nucleus Bioinformatics, and Experimental Validation.BioMed research international · 2026Article
- Exploring the mechanism of Yi Qi Huo Xue compound prescription in treating chronic heart failure based on integrated network pharmacology and transcriptomics.Frontiers in cardiovascular medicine · 2026Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
backgroundThe visual sequence logo has been a hot area in the development of bioinformatics tools. ggseqlogo written in R language has been the most popular API since it was published. With the popularity of artificial intelligence and deep learning, Python is currently the most popular programming language. The programming language used by bioinformaticians began to shift to Python. Providing APIs in Python that are similar to those in R can reduce the learning cost of relearning a programming language. And compared to ggplot2 in R, drawing framework is not as easy to use in Python. The appearance of plotnine (ggplot2 in Python version) makes it possible to unify the programming methods of bioinformatics visualization tools between R and Python.
resultsHere, we introduce plotnineSeqSuite, a new plotnine-based Python package provides a ggseqlogo-like API for programmatic drawing of sequence logos, sequence alignment diagrams and sequence histograms. To be more precise, it supports custom letters, color themes, and fonts. Moreover, the class for drawing layers is based on object-oriented design so that users can easily encapsulate and extend it.
conclusionsplotnineSeqSuite is the first ggplot2-style package to implement visualization of sequence -related graphs in Python. It enhances the uniformity of programmatic plotting between R and Python. Compared with tools appeared already, the categories supported by plotnineSeqSuite are much more complete. The source code of plotnineSeqSuite can be obtained on GitHub ( https://github.com/caotianze/plotnineseqsuite ) and PyPI ( https://pypi.org/project/plotnineseqsuite ), and the documentation homepage is freely available on GitHub at ( https://caotianze.github.io/plotnineseqsuite/ ).
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What Socratic 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 Socratic graph.