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https://doi.org/10.12688/f1000research.10232.1
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Approaches to R education in Canadian universities
[version 1; peer review: 1 approved, 2 approved with reservations]
Michael A. Carson, Nathan Basiliko
Peer Reviewers Colin W. Rundel; Eliezer Gurarie; Luc F. Bussiere
PUBLISHED 30 Nov 2016
https://doi.org/10.12688/f1000research.9821.1
Software Tool Article metrics
A guide and best practices for R/Bioconductor tool integration in Galaxy
[version 1; peer review: 1 approved, 1 approved with reservations]
Nitesh Turaga, Mallory A. Freeberg, Dannon Baker, John Chilton, Galaxy Team, Anton Nekrutenko, James Taylor
Peer Reviewers Paul A. Stewart and Dekai Rohlsen; Houtan Noushmehr and Tiago Silva
PUBLISHED 24 Nov 2016
https://doi.org/10.12688/f1000research.7082.3
Software Tool Article metrics
Revised
EvolQG - An R package for evolutionary quantitative genetics
[version 3; peer review: 2 approved, 1 approved with reservations]
Diogo Melo, Guilherme Garcia, Alex Hubbe, Ana Paula Assis, Gabriel Marroig
Peer Reviewers Mark Grabowsky; David Houle; Charles Roseman
LATEST VERSION PUBLISHED 08 Nov 2016
https://doi.org/10.12688/f1000research.9357.2
Software Tool Article metrics
Revised
Genomic variant annotation workflow for clinical applications
[version 2; peer review: 2 approved]
Thomas Thurnherr, Franziska Singer, Daniel J. Stekhoven, Niko Beerenwinkel
Peer Reviewers Christopher Southan; Ankush Sharma and Md. Sahidul Islam
LATEST VERSION PUBLISHED 24 Oct 2016
https://doi.org/10.12688/f1000research.6379.2
Software Tool Article metrics
Revised
regionReport: Interactive reports for region-level and feature-level genomic analyses
[version 2; peer review: 2 approved, 1 approved with reservations]
Leonardo Collado-Torres, Andrew E. Jaffe, Jeffrey T. Leek
Peer Reviewers Timothy J. Triche Jr; Karthik Ram; David Robinson
LATEST VERSION PUBLISHED 29 Jun 2016
https://doi.org/10.12688/f1000research.8759.2
Software Tool Article metrics
Revised
Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments
[version 2; peer review: 2 approved]
Aaron T. L. Lun, Malcolm Perry, Elizabeth Ing-Simmons
Peer Reviewers Douglas Phanstiel; Nicolas Servant
LATEST VERSION PUBLISHED 28 Jun 2016
https://doi.org/10.12688/f1000research.9022.1
Software Tool Article metrics
ddpcr: an R package and web application for analysis of droplet digital PCR data
[version 1; peer review: 2 approved]
Dean Attali, Roza Bidshahri, Charles Haynes, Jennifer Bryan
Peer Reviewers Timothy J. Triche Jr; Stephanie L. Hazlitt and Andy Teucher
PUBLISHED 17 Jun 2016
https://doi.org/10.12688/f1000research.8964.1
Software Tool Article metrics
RiboProfiling: a Bioconductor package for standard Ribo-seq pipeline processing
[version 1; peer review: 3 approved]
Alexandra Popa, Kevin Lebrigand, Agnes Paquet, Nicolas Nottet, Karine Robbe-Sermesant, Rainer Waldmann, Pascal Barbry
Peer Reviewers Olivier Namy and Pierre Bertin; Audrey M Michel; Ghislain Bidaut
PUBLISHED 09 Jun 2016
https://doi.org/10.12688/f1000research.8918.1
Research Note metrics
Decomposition of mutational context signatures using quadratic programming methods
[version 1; peer review: 1 approved, 1 approved with reservations]
Andy G. Lynch
Peer Reviewers Mohamed Helmy; Miguel Vazquez
PUBLISHED 07 Jun 2016
https://doi.org/10.12688/f1000research.8694.1
Software Tool Article metrics
IncucyteDRC: An R package for the dose response analysis of live cell imaging data
[version 1; peer review: 2 approved]
Philip J. Chapman, Dominic I. James, Amanda J. Watson, Gemma V. Hopkins, Ian D. Waddell, Donald J. Ogilvie
Peer Reviewers Guillaume Devailly; Clara Alsinet-Armengol
PUBLISHED 23 May 2016
https://doi.org/10.12688/f1000research.7563.2
Method Article metrics
Revised
Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences
[version 2; peer review: 2 approved]
Charlotte Soneson, Michael I. Love, Mark D. Robinson
Peer Reviewers Stephen N. Floor; Rob Patro
LATEST VERSION PUBLISHED 29 Feb 2016
https://doi.org/10.12688/f1000research.7453.1
Software Tool Article metrics
Crambled: A Shiny application to enable intuitive resolution of conflicting cellularity estimates
[version 1; peer review: 2 approved]
Andy G. Lynch
Peer Reviewers Jan Oosting; Ingrid Lönnstedt
PUBLISHED 07 Dec 2015
https://doi.org/10.12688/f1000research.6030.2
Software Tool Article metrics
Revised
AGA: Interactive pipeline for reproducible gene expression and DNA methylation data analyses
[version 2; peer review: 2 approved]
Michael Considine, Hilary Parker, Yingying Wei, Xaio Xia, Leslie Cope, Michael Ochs, Elana Fertig
Peer Reviewers Subha Madhavan; Matthew McCall
LATEST VERSION PUBLISHED 21 Oct 2015
https://doi.org/10.12688/f1000research.6925.1
Software Tool Article metrics
GOsummaries: an R Package for Visual Functional Annotation of Experimental Data
[version 1; peer review: 2 approved]
Raivo Kolde, Jaak Vilo
Peer Reviewers Shaillay Dogra; Hilary Ann Coller
PUBLISHED 18 Aug 2015
https://doi.org/10.12688/f1000research.3928.2
Software Tool Article metrics
Update
edgeR: a versatile tool for the analysis of shRNA-seq and CRISPR-Cas9 genetic screens
[version 2; peer review: 3 approved]
Zhiyin Dai, Julie M. Sheridan, Linden J. Gearing, Darcy L. Moore, Shian Su, Sam Wormald, Stephen Wilcox, Liam O'Connor, Ross A. Dickins, Marnie E. Blewitt, Matthew E. Ritchie
Peer Reviewers James W. MacDonald; Ross Lazarus; Sumit Deswal
LATEST VERSION PUBLISHED 21 Oct 2014
https://doi.org/10.12688/f1000research.4680.2
Software Tool Article metrics
Revised
shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R
[version 2; peer review: 2 approved]
Jean-Philippe Fortin, Elana Fertig, Kasper Hansen
Peer Reviewers Timothy J. Triche; Tiffany J. Morris
LATEST VERSION PUBLISHED 19 Sep 2014
https://doi.org/10.12688/f1000research.4831.1
Software Tool Article metrics
FALCON: a software package for analysis of nestedness in bipartite networks
[version 1; peer review: 2 approved]
Stephen J. Beckett, Chris A. Boulton, Hywel T. P. Williams
Peer Reviewers C. Patrick Doncaster; Justin R. Meyer
PUBLISHED 06 Aug 2014
https://doi.org/10.12688/f1000research.4784.1
Software Tool Article metrics
dendsort: modular leaf ordering methods for dendrogram representations in R
[version 1; peer review: 2 approved]
Ryo Sakai, Raf Winand, Toni Verbeiren, Andrew Vande Moere, Jan Aerts
Peer Reviewers Eamonn Maguire and Rodrigo Santamaria; Jan Oosting
PUBLISHED 30 Jul 2014
https://doi.org/10.12688/f1000research.2-192.v2
Software Tool Article metrics
Revised
Cyrface: An interface from Cytoscape to R that provides a user interface to R packages
[version 2; peer review: 3 approved]
Emanuel Gonçalves, Franz Mirlach, Julio Saez-Rodriguez
Peer Reviewers Nikolaus Schultz and B. Arman Aksoy; Ghislain Bidaut; Paul T. Shannon
LATEST VERSION PUBLISHED 01 Jul 2014
https://doi.org/10.12688/f1000research.2-264.v1
Software Tool Article metrics
illuminaio: An open source IDAT parsing tool for Illumina microarrays
[version 1; peer review: 2 approved]
Mike L Smith, Keith A. Baggerly, Henrik Bengtsson, Matthew E. Ritchie, Kasper D. Hansen
Peer Reviewers Jan Oosting; Tiffany J. Morris
PUBLISHED 04 Dec 2013
121-140 of 141 ARTICLES
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