ArticleBMC genomics2022
GenomicDistributions: fast analysis of genomic intervals with Bioconductor.
Article in BMC genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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.
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
19 citing papers in PubMed, 27 citations in OpenAlex.
- Multimodal atlas of human atherosclerosis links granular vascular cell states to coronary artery disease risk.medRxiv : the preprint server for health sciences · 2026Article
- mNature communications · 2026Article
- Plasma extrachromosomal circular DNA as a biomarker in EGFR-targeted therapy of non-small cell lung cancer.Molecular oncology · 2026Article
- Histone variant H2BE controls activity-dependent gene expression and homeostatic scaling.Cell reports · 2026Article
- Age- and cell-type-specific effects of histone variant H2BE in the brain.Cell reports · 2025Article
- Dna methylation dynamics associated with visual system remodeling during flatfish metamorphosis.Epigenetics & chromatin · 2025Article
- PoreMeth2 for decoding the evolution of methylome alterations with nanopore sequencing.Genome research · 2025Article
- Episodic and Ongoing Mechanisms Drive Plastid-Derived Nuclear DNA Evolution in Angiosperms.Genome biology and evolution · 2025Article
- Ribosomal RNA transcription regulates splicing through ribosomal protein RPL22.Cell chemical biology · 2025Article
- Intracellular protein editing enables incorporation of noncanonical residues in endogenous proteins.Science (New York, N.Y.) · 2025Article
- Article
- Utility of Plasma Cell-free Chromatin Immunoprecipitation to Detect Cardiac Allograft Rejection.medRxiv : the preprint server for health sciences · 2025Article
- Expanding the BonnMu sequence-indexed repository of transposon induced maize (Zea mays L.) mutations in dent and flint germplasm.The Plant journal : for cell and molecular biology · 2024Article
- Histone variant H2BE enhances chromatin accessibility in neurons to promote synaptic gene expression and long-term memory.Molecular cell · 2024Article
- Histone variant H2BE enhances chromatin accessibility in neurons to promote synaptic gene expression and long-term memory.bioRxiv : the preprint server for biology · 2024Article
- Plastid DNA is a major source of nuclear genome complexity and of RNA genes in the orphan crop moringa.BMC plant biology · 2024Article
- PML modulates epigenetic composition of chromatin to regulate expression of pro-metastatic genes in triple-negative breast cancer.Nucleic acids research · 2023Article
- Globally elevated levels of histone H3 lysine 9 trimethylation in early infancy are associated with poor growth trajectory in Bangladeshi children.Clinical epigenetics · 2023Article
- Histone H3 lysine 27 acetylation profile undergoes two global shifts in undernourished children and suggests altered one-carbon metabolism.Clinical epigenetics · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundEpigenome analysis relies on defined sets of genomic regions output by widely used assays such as ChIP-seq and ATAC-seq. Statistical analysis and visualization of genomic region sets is essential to answer biological questions in gene regulation. As the epigenomics community continues generating data, there will be an increasing need for software tools that can efficiently deal with more abundant and larger genomic region sets. Here, we introduce GenomicDistributions, an R package for fast and easy summarization and visualization of genomic region data.
resultsGenomicDistributions offers a broad selection of functions to calculate properties of genomic region sets, such as feature distances, genomic partition overlaps, and more. GenomicDistributions functions are meticulously optimized for best-in-class speed and generally outperform comparable functions in existing R packages. GenomicDistributions also offers plotting functions that produce editable ggplot objects. All GenomicDistributions functions follow a uniform naming scheme and can handle either single or multiple region set inputs.
conclusionsGenomicDistributions offers a fast and scalable tool for exploratory genomic region set analysis and visualization. GenomicDistributions excels in user-friendliness, flexibility of outputs, breadth of functions, and computational performance. GenomicDistributions is available from Bioconductor ( https://bioconductor.org/packages/release/bioc/html/GenomicDistributions.html ).
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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.