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https://doi.org/10.12688/f1000research.27262.1
Method Article metrics
A pipeline to analyse time-course gene expression data
[version 1; peer review: 2 approved with reservations]
Nelle Varoquaux, Elizabeth Purdom
Peer Reviewers Michael I. Love; Rodolphe Thiébaut
  • Funders
  • U.S. Department of Energy
  • École Normale Supérieure
  • Gordon and Betty Moore Foundation
  • Alfred P. Sloan Foundation
PUBLISHED 11 Dec 2020
https://doi.org/10.12688/f1000research.27893.1
Method Article metrics
A guide to creating design matrices for gene expression experiments
[version 1; peer review: 2 approved]
Charity W. Law, Kathleen Zeglinski, Xueyi Dong, Monther Alhamdoosh, Gordon K. Smyth, Matthew E. Ritchie
Peer Reviewers Federico Marini; Jenny Drnevich
  • Funders
  • National Health and Medical Research Council
  • Chan Zuckerberg Initiative
PUBLISHED 10 Dec 2020
https://doi.org/10.12688/f1000research.24435.2
Software Tool Article metrics
Revised
iMutSig: a web application to identify the most similar mutational signature using shiny
[version 2; peer review: 2 approved]
Zhi Yang, Priyatama Pandey, Paul Marjoram, Kimberly D. Siegmund
Peer Reviewers Adrian Baez-Ortega; Vittorio Perduca
  • Funders
  • National Institute of Environmental Health Sciences
  • National Cancer Institute
LATEST VERSION PUBLISHED 19 Nov 2020
https://doi.org/10.12688/f1000research.24187.2
Software Tool Article metrics
Revised
ExploreModelMatrix: Interactive exploration for improved understanding of design matrices and linear models in R
[version 2; peer review: 3 approved]
Charlotte Soneson, Federico Marini, Florian Geier, Michael I. Love, Michael B. Stadler
Peer Reviewers Jean Fan; Lucy D'Agostino McGowan; Matthew Ritchie
  • Funders
  • National Institutes of Health
  • German Federal Ministry of Education and Research
LATEST VERSION PUBLISHED 16 Sep 2020
https://doi.org/10.12688/f1000research.21201.1
Review metrics
Fear conditioning and the basolateral amygdala
[version 1; peer review: 3 approved]
Yajie Sun, Helen Gooch, Pankaj Sah
Peer Reviewers Nathan M Holmes; Roger L Clem; Benedetto Sacchetti
  • Funders
  • National Health and Medical Research Council
  • Australian Research Council
PUBLISHED 28 Jan 2020
https://doi.org/10.12688/f1000research.21307.1
Review metrics
Recent advances in understanding regulation of the Arabidopsis circadian clock by local cellular environment
[version 1; peer review: 3 approved]
Timothy J. Hearn, Alex A.R. Webb
Peer Reviewers Motomu Endo; Ke-Qiang Wu; C Robertson McClung
PUBLISHED 27 Jan 2020
https://doi.org/10.12688/f1000research.21900.1
Method Article metrics PEER REVIEW DISCONTINUED
Using the “Uniform Scale” to facilitate meta-analysis where exposure variables are qualitative and vary between studies – methodology, examples and software
[version 1; peer review: 1 approved with reservations]
Peter N Lee, Jan Hamling, John S Fry, Sonja Vandyke, Rolf Weitkunat
Peer Reviewers Chang Xu
  • Funder
  • Philip Morris International
PUBLISHED 22 Jan 2020
https://doi.org/10.12688/f1000research.21586.1
Research Article metrics
Invariance in ecological pattern
[version 1; peer review: 2 approved]
Steven A. Frank, Jordi Bascompte
Peer Reviewers David Alonso; Neil McRoberts
  • Funders
  • Swiss National Science Foundation
  • Donald Bren Foundation
PUBLISHED 12 Dec 2019
https://doi.org/10.12688/f1000research.20210.2
Software Tool Article metrics
Revised
HDCytoData: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats
[version 2; peer review: 2 approved]
Lukas M. Weber, Charlotte Soneson
Peer Reviewers Shila Ghazanfar; Laurent Gatto
  • Funder
  • Universität Zürich
LATEST VERSION PUBLISHED 04 Dec 2019
https://doi.org/10.12688/f1000research.20887.3
Software Tool Article metrics
Revised
RCy3: Network biology using Cytoscape from within R
[version 3; peer review: 3 approved]
Julia A. Gustavsen, Shraddha Pai, Ruth Isserlin, Barry Demchak, Alexander R. Pico
Peer Reviewers James Denvir; Krithika Bhuvaneshwar; Ludwig Geistlinger
  • Funders
  • Google
  • National Institute of General Medical Sciences
LATEST VERSION PUBLISHED 04 Dec 2019
https://doi.org/10.12688/f1000research.20072.2
Method Article metrics
Revised
A new statistical method to analyze Morris Water Maze data using Dirichlet distribution
[version 2; peer review: 2 approved]
Marianne Maugard, Cyrille Doux, Gilles Bonvento
Peer Reviewers Richard GM Morris; Avgoustinos Vouros, Luca Manneschi and Eleni Vasilaki
  • Funders
  • Association France Alzheimer
  • Fondation de France
  • Fondation Plan Alzheimer
LATEST VERSION PUBLISHED 28 Oct 2019
https://doi.org/10.12688/f1000research.20843.1
Software Tool Article metrics
Creating and sharing reproducible research code the workflowr way
[version 1; peer review: 3 approved]
John D. Blischak, Peter Carbonetto, Matthew Stephens
Peer Reviewers Peter F. Hickey; Przemysław Biecek; Peter Baker
  • Funder
  • Gordon and Betty Moore Foundation
PUBLISHED 14 Oct 2019
https://doi.org/10.12688/f1000research.16216.2
Software Tool Article metrics
Revised
Feature selection with the R package MXM
[version 2; peer review: 2 approved]
Michail Tsagris, Ioannis Tsamardinos
Peer Reviewers Thodoris Kypraios; Huitong Qiu
  • Funder
  • Seventh Framework Programme
LATEST VERSION PUBLISHED 30 Sep 2019
https://doi.org/10.12688/f1000research.18310.2
Research Note metrics
Revised
Causes of reporting bias: a theoretical framework
[version 2; peer review: 2 approved]
Jenny T van der Steen, Gerben ter Riet, Cornelis A van den Bogert, Lex M Bouter
Peer Reviewers Ksenija Bazdaric; Arnaud Vaganay
  • Funders
  • Netherlands Organisation for Scientific Research (NWO)
  • H2020 European Research Council
  • Leiden University Medical Center, Leiden, The Netherlands
LATEST VERSION PUBLISHED 17 Jul 2019
https://doi.org/10.12688/f1000research.19557.1
Research Article metrics PEER REVIEW DISCONTINUED
Climate change in the UAE: Modeling air temperature using ARIMA and STI across four bio-climatic zones
[version 1; peer review: peer review discontinued]
Taoufik Saleh Ksiksi, Latifa Saeed Al-Blooshi
Peer Reviewers Invited
  • Funder
  • United Arab Emirates University
PUBLISHED 26 Jun 2019
https://doi.org/10.12688/f1000research.19375.1
Research Article metrics
Accumulation Bias in meta-analysis: the need to consider time in error control
[version 1; peer review: 2 approved]
Judith ter Schure, Peter Grünwald
Peer Reviewers Steven P. Ellis; Joanna IntHout
  • Funder
  • Nederlandse Organisatie voor Wetenschappelijk Onderzoek
PUBLISHED 25 Jun 2019
https://doi.org/10.12688/f1000research.19661.1
Research Article metrics
Towards a new model for producing evidence-based guidelines: a qualitative study of current approaches and opportunities for innovation among Australian guideline developers
[version 1; peer review: 2 approved]
Steve McDonald, Julian H. Elliott, Sally Green, Tari Turner
Peer Reviewers Tracy Merlin; Amanda Leach
  • Funders
  • Cochrane
  • National Health and Medical Research Council
PUBLISHED 24 Jun 2019
https://doi.org/10.12688/f1000research.13490.5
Research Article metrics
Revised
Does evidence support the high expectations placed in precision medicine? A bibliographic review
[version 5; peer review: 2 approved, 1 approved with reservations, 3 not approved]
Jordi Cortés, José Antonio González, María Nuncia Medina, Markus Vogler, Marta Vilaró, Matt Elmore, Stephen John Senn, Michael Campbell, Erik Cobo
Peer Reviewers Ian White; Erica E.M. Moodie; Saskia le Cessie; Richard Stevens and David Nunan; Vance W. Berger; Dennis W. Lendrem
  • Funders
  • Departament d'Economia i Coneixement de la Generalitat de Catalunya
  • Ministerio de Economía y Competitividad
  • H2020 Marie Skłodowska-Curie Actions
LATEST VERSION PUBLISHED 10 Jun 2019
https://doi.org/10.12688/f1000research.15512.3
Research Article metrics
Revised
Factors influencing malignant mesothelioma survival: a retrospective review of the National Mesothelioma Virtual Bank cohort
[version 3; peer review: 2 approved, 1 approved with reservations]
Waqas Amin, Faina Linkov, Douglas P. Landsittel, Jonathan C. Silverstein, Wiam Bshara, Carmelo Gaudioso, Michael D. Feldman, Harvey I. Pass, Jonathan Melamed, Joseph S. Friedberg, Michael J. Becich
Peer Reviewers Nico van Zandwijk; Michele Carbone; Tobias Peikert
  • Funders
  • Centers for Disease Control and Prevention
  • National Institute for Occupational Safety and Health
LATEST VERSION PUBLISHED 03 Jun 2019
https://doi.org/10.12688/f1000research.19310.1
Software Tool Article metrics
A new method for detecting abrupt shifts in time series
[version 1; peer review: 2 approved with reservations]
Chris A. Boulton, Timothy M. Lenton
Peer Reviewers Valerie N. Livina; Sonia Kéfi
  • Funder
  • Natural Environment Research Council
PUBLISHED 28 May 2019
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