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61-80 of 130 ARTICLES
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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.16032.3
Software Tool Article metrics
Revised
epiflows: an R package for risk assessment of travel-related spread of disease
[version 3; peer review: 2 approved]
Paula Moraga, Ilaria Dorigatti, Zhian N. Kamvar, Pawel Piatkowski, Salla E. Toikkanen, VP Nagraj, Christl A. Donnelly, Thibaut Jombart
Peer Reviewers Noam Ross; Jon Zelner
  • Funders
  • National Institute for Health Research
  • UK Medical Research Council
  • Imperial College Junior Research Fellowship
LATEST VERSION PUBLISHED 12 Sep 2019
https://doi.org/10.12688/f1000research.16200.2
Research Article metrics
Revised
Predicting transcription factor binding using ensemble random forest models
[version 2; peer review: 2 approved]
Fatemeh Behjati Ardakani, Florian Schmidt, Marcel H. Schulz
Peer Reviewers Jan Grau; Gary D Stormo
  • Funder
  • Cluster of Excellence on Multimodal Computing and Interaction (DFG)
LATEST VERSION PUBLISHED 02 Sep 2019
https://doi.org/10.12688/f1000research.16083.2
Software Tool Article metrics
Revised
seqCAT: a Bioconductor R-package for variant analysis of high throughput sequencing data
[version 2; peer review: 1 approved, 1 not approved]
Erik Fasterius, Cristina Al-Khalili Szigyarto
Peer Reviewers Matej Lexa; Jean Fan
  • Funder
  • European Community 7th Framework Program
LATEST VERSION PUBLISHED 12 Aug 2019
https://doi.org/10.12688/f1000research.20027.1
Software Tool Article metrics
ChIPdig: a comprehensive user-friendly tool for mining multi-sample ChIP-seq data
[version 1; peer review: 3 approved with reservations]
Ruben Esse
Peer Reviewers Tao Liu; Hinrich Gronemeyer and Marco Antonio Mendoza-Parra; Thomas Carroll
  • Funder
  • National Institutes of Health
PUBLISHED 31 Jul 2019
https://doi.org/10.12688/f1000research.17824.2
Method Article metrics
Revised
Enhancing gene set enrichment using networks
[version 2; peer review: 2 approved, 2 approved with reservations]
Michael Prummer
Peer Reviewers Kimberly Glass; Monther Alhamdoosh; Jill P. Mesirov and Alexander Wenzel; Rita Casadio
LATEST VERSION PUBLISHED 16 Jul 2019
https://doi.org/10.12688/f1000research.18952.1
Software Tool Article metrics
Detection and mitigation of spurious antisense expression with RoSA
[version 1; peer review: 2 approved with reservations]
Kira Mourão, Nicholas J. Schurch, Radek Lucoszek, Kimon Froussios, Katarzyna MacKinnon, Céline Duc, Gordon Simpson, Geoffrey J. Barton
Peer Reviewers Ian Sudbery; John Casement and Andreas Werner
  • Funder
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 07 Jun 2019
https://doi.org/10.12688/f1000research.19410.1
Software Tool Article metrics
BiocPkgTools: Toolkit for mining the Bioconductor package ecosystem
[version 1; peer review: 2 approved, 1 approved with reservations]
Shian Su, Vincent J. Carey, Lori Shepherd, Matthew E. Ritchie, Martin T. Morgan, Sean Davis
Peer Reviewers Simina M. Boca; Mike Smith; Henrik Bengtsson
  • Funders
  • EU H2020 Personalizing Health and Care Program
  • Intramural Research Program, National Institutes of Health
  • National Cancer Institute
  • National Human Genome Research Institute
PUBLISHED 29 May 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
https://doi.org/10.12688/f1000research.18636.1
Method Article metrics
A Bioconductor workflow for the Bayesian analysis of spatial proteomics
[version 1; peer review: 1 approved, 2 approved with reservations]
Oliver M. Crook, Lisa M. Breckels, Kathryn S. Lilley, Paul D.W. Kirk, Laurent Gatto
Peer Reviewers Pierre M. Jean Beltran; Susan Holmes; Angus Lamond and Alejandro Brenes Murillo
  • Funders
  • Medical Research Council
  • Wellcome Trust
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 11 Apr 2019
https://doi.org/10.12688/f1000research.17548.2
Software Tool Article metrics
Revised
Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python
[version 2; peer review: 2 approved]
Klara Kaleb, Alex Warwick Vesztrocy, Adrian M. Altenhoff, Christophe Dessimoz
Peer Reviewers Bastian Greshake Tzovaras and Ngoc-Vinh Tran; Laurent Gatto
  • Funders
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
  • University College London
  • Swiss State Secretariat for Education
  • Biotechnology and Biological Sciences Research Council
LATEST VERSION PUBLISHED 29 Mar 2019
https://doi.org/10.12688/f1000research.17139.3
Software Tool Article metrics
Revised
Radtools: R utilities for convenient extraction of medical image metadata
[version 3; peer review: 2 approved]
Pamela H. Russell, Debashis Ghosh
Peer Reviewers Andrey Fedorov; Volker Schmid
  • Funder
  • Cancer Center, University of Colorado
LATEST VERSION PUBLISHED 25 Mar 2019
https://doi.org/10.12688/f1000research.16198.2
Software Tool Article metrics
Revised
scClustViz – Single-cell RNAseq cluster assessment and visualization
[version 2; peer review: 2 approved]
Brendan T. Innes, Gary D. Bader
Peer Reviewers Martin Hemberg and Tallulah Andrews; Michael Steinbaugh
  • Funder
  • Canada First Research Excellence Fund
LATEST VERSION PUBLISHED 12 Mar 2019
https://doi.org/10.12688/f1000research.17669.1
Software Tool Article metrics
shiny-pred: a server for the prediction of protein disordered regions
[version 1; peer review: 1 approved with reservations, 1 not approved]
Mauricio Oberti, Iosif Vaisman
Peer Reviewers Jinbo Xu; Appadurai Rajeswari and Anand Srivastava
PUBLISHED 28 Feb 2019
https://doi.org/10.12688/f1000research.15949.2
Software Tool Article metrics
Revised
The Mega2R package: R tools for accessing and processing genetic data in common formats
[version 2; peer review: 3 approved]
Robert V. Baron, Justin R. Stickel, Daniel E. Weeks
Peer Reviewers Dajiang J. Lui; Alejandro Q. Nato, Jr.; Derek Gordon
  • Funders
  • The University of Pittsburgh
  • National Institutes of Health
LATEST VERSION PUBLISHED 25 Feb 2019
https://doi.org/10.12688/f1000research.17916.1
Method Article metrics
Relative Abundance of Transcripts (RATs): Identifying differential isoform abundance from RNA-seq
[version 1; peer review: 1 approved, 2 approved with reservations]
Kimon Froussios, Kira Mourão, Gordon Simpson, Geoffrey J. Barton, Nicholas Schurch
Peer Reviewers Sophie Shaw; James P. B. Lloyd; Michael I. Love
  • Funders
  • Wellcome Trust
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 24 Feb 2019
https://doi.org/10.12688/f1000research.18002.1
Software Tool Article metrics
Epidemic curves made easy using the R package incidence
[version 1; peer review: 1 approved, 2 approved with reservations]
Zhian N. Kamvar, Jun Cai, Juliet R.C. Pulliam, Jakob Schumacher, Thibaut Jombart
Peer Reviewers Benjamin M. Bolker; Quirine ten Bosch; Bertrand Sudre
  • Funders
  • Global Challenges Research Fund (GCRF)
  • United Kingdom Department of Health and Social Care
  • National Institute for Health Research - Health Protection Research Unit for Modelling Methodology
PUBLISHED 31 Jan 2019
https://doi.org/10.12688/f1000research.16409.2
Software Tool Article metrics
Revised
gganatogram: An R package for modular visualisation of anatograms and tissues based on ggplot2
[version 2; peer review: 2 approved]
Jesper L.V. Maag
Peer Reviewers Helder I. Nakaya; Saskia Freytag
LATEST VERSION PUBLISHED 20 Nov 2018
https://doi.org/10.12688/f1000research.16680.1
Software Tool Article metrics
ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations
[version 1; peer review: 1 approved, 2 approved with reservations]
Gaurav S. Kandlikar, Zachary J. Gold, Madeline C. Cowen, Rachel S. Meyer, Amanda C. Freise, Nathan J.B. Kraft, Jordan Moberg-Parker, Joshua Sprague, David J. Kushner, Emily E. Curd
Peer Reviewers Tristan Cordier; Holly M. Bik; Niklaus J. Grünwald and Zach Foster
  • Funders
  • University of California President’s Research Catalyst Awards
  • National Science Foundation
PUBLISHED 01 Nov 2018
https://doi.org/10.12688/f1000research.14492.2
Software Tool Article metrics
Revised
epicontacts: Handling, visualisation and analysis of epidemiological contacts
[version 2; peer review: 2 approved, 1 approved with reservations]
VP Nagraj, Nistara Randhawa, Finlay Campbell, Thomas Crellen, Bertrand Sudre, Thibaut Jombart
Peer Reviewers Melissa A. Rolfes; Peter Adebayo Adewuyi; Josie Athens
LATEST VERSION PUBLISHED 11 Oct 2018
61-80 of 130 ARTICLES
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