Evidence map›Paper›PMID 39457368›Full record

ArticleGenes2024

Visual Integration of Genome-Wide Association Studies and Differential Expression Results with the Hidecan R Package.

Olivia Angelin-Bonnet, Matthieu Vignes, Patrick J Biggs, Samantha Baldwin, Susan Thomson

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genes, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from 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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Olivia Angelin-BonnetThe New Zealand Institute for Plant and Food Research Limited, Palmerston North 4442, New Zealand.ORCID 0000-0002-7708-2919
Matthieu VignesSchool of Mathematical and Computational Sciences, Massey University, Palmerston North 4442, New Zealand.ORCID 0000-0001-8929-2975
Patrick J BiggsSchool of Food Technology and Natural Sciences, Massey University, Palmerston North 4442, New Zealand.ORCID 0000-0002-0285-4101
Samantha BaldwinThe New Zealand Institute for Plant and Food Research Limited, Christchurch 8140, New Zealand.ORCID 0000-0002-8151-8850
Susan ThomsonThe New Zealand Institute for Plant and Food Research Limited, Christchurch 8140, New Zealand.ORCID 0000-0001-7127-9414

Funding

Crown Research Institutes NA
6 · The paper itself

Abstract

BACKGROUND/

objectivesWe present hidecan, an R package for generating visualisations that summarise the results of one or more genome-wide association studies (GWAS) and differential expression analyses, as well as manually curated candidate genes, e.g., extracted from the literature. This tool is applicable to all ploidy levels; we notably provide functionalities to facilitate the visualisation of GWAS results obtained for autotetraploid organisms with the GWASpoly package.

resultsWe illustrate the capabilities of hidecan with examples from two autotetraploid potato datasets.

conclusionsThe hidecan package is implemented in R and is publicly available on the CRAN repository and on GitHub. A description of the package, as well as a detailed tutorial, is made available alongside the package. It is also part of the VIEWpoly tool for the visualisation and exploration of results from polyploids computational tools.

Indexed as

Genome-Wide Association StudySoftwareSolanum tuberosumComputational BiologyHumansautotetraploiddifferential expressiongenome-wide association studiesR packagevisualisation

Identifiers

PMID39457368
PMCPMC11506992

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.