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101-120 of 141 ARTICLES
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https://doi.org/10.12688/f1000research.14361.1
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freesurfer: Connecting the Freesurfer software with R
[version 1; peer review: 2 approved]
John Muschelli, Elizabeth Sweeney, Ciprian M. Crainiceanu
Peer Reviewers Seth T. Lirette; Pierre Lafaye de Micheaux
  • Funder
  • National Institutes of Health
PUBLISHED 16 May 2018
https://doi.org/10.12688/f1000research.14217.1
Software Tool Article metrics
ShinyDiversity - Understanding Alpha and Beta Diversity through Interactive Visualizations
[version 1; peer review: 1 approved, 1 approved with reservations]
Eric T. Leung, Roshan Noronha, Ali Mirza, Reva Shenwai, Asterios Mpatziakas
Peer Reviewers Jianguo Xia; Richard E. Isaacson
  • Funder
  • U.S. National Library of Medicine
PUBLISHED 20 Apr 2018
https://doi.org/10.12688/f1000research.13049.2
Software Tool Article metrics
Revised
RSEQREP: RNA-Seq Reports, an open-source cloud-enabled framework for reproducible RNA-Seq data processing, analysis, and result reporting
[version 2; peer review: 2 approved]
Travis L. Jensen, Michael Frasketi, Kevin Conway, Leigh Villarroel, Heather Hill, Konstantinos Krampis, Johannes B. Goll
Peer Reviewers Anup Mahurkar; Ben Busby
  • Funders
  • Emmes Corporation
  • National Institutes of Health
LATEST VERSION PUBLISHED 13 Apr 2018
https://doi.org/10.12688/f1000research.14197.1
Software Tool Article metrics
TCGAbiolinksGUI: A graphical user interface to analyze cancer molecular and clinical data
[version 1; peer review: 1 approved, 1 approved with reservations]
Tiago Chedraoui Silva, Antonio Colaprico, Catharina Olsen, Tathiane M Malta, Gianluca Bontempi, Michele Ceccarelli, Benjamin P Berman, Houtan Noushmehr
Peer Reviewers Zuguang Gu; Michael Lawrence
  • Funders
  • Fonds De La Recherche Scientifique - FNRS
  • National Cancer Institute
  • Fundação de Amparo à Pesquisa do Estado de São Paulo
  • Henry Ford Hospital
  • Innoviris
PUBLISHED 10 Apr 2018
https://doi.org/10.12688/f1000research.12947.3
Software Tool Article metrics
Revised
PPInfer: a Bioconductor package for inferring functionally related proteins using protein interaction networks
[version 3; peer review: 1 approved, 1 approved with reservations]
Dongmin Jung, Xijin Ge
Peer Reviewers Cathy H. Wu and Karen E. Ross; Helen V. Cook
  • Funder
  • National Science Foundation
LATEST VERSION PUBLISHED 12 Mar 2018
https://doi.org/10.12688/f1000research.13577.2
Method Article metrics
Revised
Using regulatory genomics data to interpret the function of disease variants and prioritise genes from expression studies
[version 2; peer review: 2 approved]
Enrico Ferrero
Peer Reviewers Aaron T. L. Lun; Vincent J. Carey
LATEST VERSION PUBLISHED 23 Feb 2018
https://doi.org/10.12688/f1000research.11840.4
Software Tool Article metrics
Revised
GAC: Gene Associations with Clinical, a web based application
[version 4; peer review: 2 approved, 1 approved with reservations]
Xinyan Zhang, Manali Rupji, Jeanne Kowalski
Peer Reviewers Shengjie Yang; Matthew N. McCall; Cedric Simillion
  • Funders
  • Winship Cancer Institute of Emory University
  • National Cancer Institute
LATEST VERSION PUBLISHED 15 Feb 2018
https://doi.org/10.12688/f1000research.13541.1
Software Tool Article metrics
archiDART v3.0: A new data analysis pipeline allowing the topological analysis of plant root systems
[version 1; peer review: 2 approved, 1 approved with reservations]
Benjamin M. Delory, Mao Li, Christopher N. Topp, Guillaume Lobet
Peer Reviewers Magdalena M. Julkowska; Alexander Bucksch; Nathan D. Miller
  • Funder
  • Leuphana University
PUBLISHED 08 Jan 2018
https://doi.org/10.12688/f1000research.9893.2
Software Tool Article metrics
Revised
exprso: an R-package for the rapid implementation of machine learning algorithms
[version 2; peer review: 2 approved]
Thomas Quinn, Daniel Tylee, Stephen Glatt
Peer Reviewers Dariusz Plewczynski and Julian Zubek; Henry Löffler-Wirth
LATEST VERSION PUBLISHED 06 Dec 2017
https://doi.org/10.12688/f1000research.13098.1
Software Tool Article metrics
miRcomp-Shiny: Interactive assessment of qPCR-based microRNA quantification and quality control algorithms
[version 1; peer review: 3 approved with reservations]
Lauren Kemperman, Matthew N. McCall
Peer Reviewers Levi Waldron; Simina M. Boca; Elana J. Fertig
  • Funder
  • National Institutes of Health
PUBLISHED 23 Nov 2017
https://doi.org/10.12688/f1000research.12512.1
Software Tool Article metrics
lakemorpho: Calculating lake morphometry metrics in R
[version 1; peer review: 2 approved]
Jeffrey Hollister, Jemma Stachelek
Peer Reviewers Samantha K. Oliver; Luke A. Winslow
PUBLISHED 21 Sep 2017
https://doi.org/10.12688/f1000research.11830.2
Software Tool Article metrics
Revised
CASAS: Cancer Survival Analysis Suite, a web based application
[version 2; peer review: 2 approved]
Manali Rupji, Xinyan Zhang, Jeanne Kowalski
Peer Reviewers Gang Han; Seon-Young Kim
  • Funders
  • Winship Cancer Institute of Emory University
  • National Cancer Institute
LATEST VERSION PUBLISHED 31 Jul 2017
https://doi.org/10.12688/f1000research.9259.2
Software Tool Article metrics
Revised
GeneBreak: detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes
[version 2; peer review: 2 approved]
Evert van den Broek, Stef van Lieshout, Christian Rausch, Bauke Ylstra, Mark A. van de Wiel, Gerrit A. Meijer, Remond J.A. Fijneman, Sanne Abeln
Peer Reviewers Tobias Marschall; Angel Rubio
LATEST VERSION PUBLISHED 06 Jul 2017
https://doi.org/10.12688/f1000research.11997.1
Software Tool Article metrics
valr: Reproducible genome interval analysis in R
[version 1; peer review: 2 approved]
Kent A. Riemondy, Ryan M. Sheridan, Austin Gillen, Yinni Yu, Christopher G. Bennett, Jay R. Hesselberth
Peer Reviewers Robert A. Amezquita; Ryan K. Dale
  • Funders
  • U.S. National Library of Medicine
  • National Institutes of Health
  • Colorado Office of Economic Development and International Trade
  • BioFrontiers Institute, University of Colorado Boulder
  • University of Colorado
PUBLISHED 29 Jun 2017
https://doi.org/10.12688/f1000research.11317.1
Software Tool Article metrics
ogttMetrics: Data structures and algorithms for oral glucose tolerance tests
[version 1; peer review: 1 approved with reservations]
Benjamin J. Stubbs, Keith Frankston, Marcel Ramos, Nancy Laranjo, Frank M. Sacks, Vincent J. Carey
Peer Reviewers Antti Honkela
  • Funders
  • National Institute of Diabetes and Digestive and Kidney Diseases
  • National Cancer Institute
PUBLISHED 16 May 2017
https://doi.org/10.12688/f1000research.10742.2
Software Tool Article metrics
Revised
haploR: an R package for querying web-based annotation tools
[version 2; peer review: 3 approved]
Ilya Y. Zhbannikov, Konstantin Arbeev, Svetlana Ukraintseva, Anatoliy I. Yashin
Peer Reviewers Garrett M. Dancik; Claudia Vitolo and Estibaliz Gascon; Stephanie M. Gogarten
  • Funder
  • National Institute on Aging
LATEST VERSION PUBLISHED 15 May 2017
https://doi.org/10.12688/f1000research.9742.2
Software Tool Article metrics
Revised
whoishRisk – an R package to calculate WHO/ISH cardiovascular risk scores for all epidemiological subregions of the world
[version 2; peer review: 3 approved]
Dylan Collins, Joseph Lee, Niklas Bobrovitz, Constantinos Koshiaris, Alison Ward, Carl J. Heneghan
Peer Reviewers Raivo Kolde; Scott A. Chamberlain; Maria Suarez-Diez
LATEST VERSION PUBLISHED 08 Mar 2017
https://doi.org/10.12688/f1000research.7312.2
Research Article metrics
Revised
An adaptable toolkit to assess commercial fishery costs and benefits related to marine protected area network design
[version 2; peer review: 2 approved]
Rémi M. Daigle, Cristián J. Monaco, Ashley K. Elgin
Peer Reviewers Pedro Peres-Neto; Marco Andrello
LATEST VERSION PUBLISHED 22 Feb 2017
https://doi.org/10.12688/f1000research.9582.2
Software Tool Article metrics
Revised
Building pathway graphs from BioPAX data in R
[version 2; peer review: 3 approved, 1 approved with reservations]
Nirupama Benis, Dirkjan Schokker, Frank Kramer, Mari A. Smits, Maria Suarez-Diez
Peer Reviewers Lynn Fink; Stephen N. Floor; Hilary Ann Coller; Kyle Ellrott
LATEST VERSION PUBLISHED 12 Dec 2016
https://doi.org/10.12688/f1000research.8900.2
Method Article metrics
Revised
DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics
[version 2; peer review: 2 approved]
Malgorzata Nowicka, Mark D. Robinson
Peer Reviewers Alejandro Reyes; Robert Castelo
LATEST VERSION PUBLISHED 06 Dec 2016
101-120 of 141 ARTICLES
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