Evidence map›Paper›PMID 40160449›Full record

ArticleArXiv2025

Learning and teaching biological data science in the Bioconductor community.

Jenny Drnevich, Frederick J Tan, Fabricio Almeida-Silva, Robert Castelo, Aedin C Culhane, Sean Davis, Maria A Doyle, Ludwig Geistlinger, Andrew R Ghazi, Susan Holmes and 8 more

Abstract readPreprint
PubMed Full text at PMC
In one paragraph

Article in ArXiv, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

18 authors.

Jenny DrnevichRoy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Illinois, USA.
Frederick J TanJohns Hopkins University, Department of Biology, Baltimore, Maryland, USA.
Fabricio Almeida-SilvaDepartment of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
Robert CasteloDepartment of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
Aedin C CulhaneLimerick Digital Cancer Research Centre, School of Medicine, University of Limerick, Ireland.
Sean DavisUniversity of Colorado Anschutz School of Medicine, Denver, Colorado, USA.
Maria A DoyleLimerick Digital Cancer Research Centre, School of Medicine, University of Limerick, Ireland.
Ludwig GeistlingerCore for Computational Biomedicine, Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA.
Andrew R GhaziCore for Computational Biomedicine, Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA.
Susan HolmesStatistics Department, Stanford University, Stanford, California, USA.
Leo LahtiDepartment of Computing, University of Turku, Finland.
Alexandru MahmoudChanning Division of Network Medicine, Harvard Medical School, Boston, Massachusetts , USA.
Kozo NishidaRIKEN Center for Biosystems Dynamics Research, 6-7-1 Minatojima Minamimachi, Chuoku, Kobe, Hyogo, Japan.
Marcel RamosDepartment of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, New York, USA.
Kevin Rue-AlbrechtMRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
David Jh ShihSchool of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
Laurent GattoComputational Biology and Bioinformatics Unit, de Duve Institute, UCLouvain, Brussels, Belgium.
Charlotte SonesonFriedrich Miescher Institute for Biomedical Research, Basel, Switzerland.

Funding

Supplement: Enhancing Community Contributions to Bioconductor With Build System Containerization and a GPU for TestingU24HG004059 · NHGRI · DANA-FARBER CANCER INST · PI VINCENT JAMES CAREY, Rafael Angel Irizarry · 2021 to 2026
$7.3M
Cancer Genomics:Integrative and Scalable Solutions in R / BioconductorU24CA180996 · NCI · ROSWELL PARK CANCER INSTITUTE CORP · PI MORGAN, MARTIN T, WALDRON, LEVI · 2014 to 2023
$6.9M
Cancer Genomics: Integrative and Scalable Solutions in R/BioconductorU24CA289073 · NCI · GRADUATE SCHOOL OF PUBLIC HEALTH AND HEALTH POLICY · PI Sean Davis, Levi Waldron · 2024 to 2026
$3.2M
NCI NIH HHS U24 CA180996NCI NIH HHS U24 CA289073NHGRI NIH HHS U24 HG004059
6 · The paper itself

Abstract

Modern biological research is increasingly data-intensive, leading to a growing demand for effective training in biological data science. In this article, we provide an overview of key resources and best practices available within the Bioconductor project - an open-source software community focused on omics data analysis. This guide serves as a valuable reference for both learners and educators in the field.

Identifiers

PMID40160449
PMCPMC11952580

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.