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https://doi.org/10.12688/f1000research.16301.2
Software Tool Article metrics
Revised
Increasing workflow development speed and reproducibility with Vectools
[version 2; peer review: 2 approved]
Tyler Weirick, Raphael Müller, Shizuka Uchida
Peer Reviewers Yutaka Saito; Dimitar Vassilev
  • Funders
  • Deutsche Forschungsgemeinschaft
  • Gheens Foundation
  • University of Louisville
LATEST VERSION PUBLISHED 23 Oct 2018
https://doi.org/10.12688/f1000research.16453.1
Software Tool Article metrics
DataViz: visualization of high-dimensional data in virtual reality
[version 1; peer review: 1 not approved]
Eric Feng, Xijin Ge
Peer Reviewers David R. Glowacki and Michael O'Connor
  • Funder
  • National Science Foundation
PUBLISHED 23 Oct 2018
https://doi.org/10.12688/f1000research.16516.1
Method Article metrics
Orchestrating a community-developed computational workshop and accompanying training materials
[version 1; peer review: 2 approved]
Sean Davis, Marcel Ramos, Lori Shepherd, Nitesh Turaga, Ludwig Geistlinger, Martin T. Morgan, Benjamin Haibe-Kains, Levi Waldron
Peer Reviewers Ewy Mathe; Kevin Blighe
  • Funders
  • Horizon 2020
  • National Cancer Institute
  • National Human Genome Research Institute
PUBLISHED 17 Oct 2018
https://doi.org/10.12688/f1000research.16605.1
Software Tool Article metrics
KnetMaps: a BioJS component to visualize biological knowledge networks
[version 1; peer review: 3 approved, 1 approved with reservations]
Ajit Singh, Christopher J. Rawlings, Keywan Hassani-Pak
Peer Reviewers Ian Dunham and Gareth Peat; Chia-Yi Cheng; Nicholas J. Provart; Ramil Mauleon
  • Funder
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 17 Oct 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
https://doi.org/10.12688/f1000research.13196.2
Method Article metrics
Revised
Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR
[version 2; peer review: 2 approved, 1 approved with reservations]
Yunshun Chen, Bhupinder Pal, Jane E. Visvader, Gordon K. Smyth
Peer Reviewers Simon Andrews; James W. MacDonald; Peter F.  Hickey
  • Funders
  • Victorian State Government
  • National Health and Medical Research Council
LATEST VERSION PUBLISHED 08 Oct 2018
https://doi.org/10.12688/f1000research.16231.1
Research Article metrics
Raising the status of software in research: A survey-based evaluation of the Software Sustainability Institute Fellowship Programme
[version 1; peer review: 3 approved with reservations]
Shoaib Sufi, Caroline Jay
Peer Reviewers Colin C. Venters; Dan Sholler; Lois Curfman McInnes
  • Funders
  • Economic and Social Research Council
  • Biotechnology and Biological Sciences Research Council
  • Engineering and Physical Sciences Research Council
PUBLISHED 03 Oct 2018
https://doi.org/10.12688/f1000research.15398.3
Method Article metrics
Revised
Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification
[version 3; peer review: 3 approved]
Michael I. Love, Charlotte Soneson, Rob Patro
Peer Reviewers Kristoffer Vitting-Seerup and Malte Thodberg; Alicia Oshlack and Marek Cmero; Nick Schurch
  • Funders
  • National Institute of Environmental Health Sciences
  • National Cancer Institute
  • National Human Genome Research Institute
  • National Science Foundation
LATEST VERSION PUBLISHED 01 Oct 2018
https://doi.org/10.12688/f1000research.16415.1
Method Article metrics
Large-scale protein function prediction using heterogeneous ensembles
[version 1; peer review: 2 approved]
Linhua Wang, Jeffrey Law, Shiv D. Kale, T. M. Murali, Gaurav Pandey
Peer Reviewers Guoxian Yu; Predrag Radivojac
  • Funders
  • International Business Machines Corporation
  • Intelligence Advanced Research Projects Activity
  • National Institutes of Health
PUBLISHED 28 Sep 2018
https://doi.org/10.12688/f1000research.16026.2
Software Tool Article metrics
Revised
DRETools: A tool-suite for differential RNA editing detection
[version 2; peer review: 1 approved, 1 approved with reservations, 1 not approved]
Tyler Weirick, Patrick Trainor, Eric Rouchka, Andrew DeFilippis, Shizuka Uchida
Peer Reviewers Ernesto Picardi; Yicheng Zhao; Graziano Pesole
  • Funders
  • Gheens Foundation
  • National Institutes of Health
  • V.V. Cooke Foundation
  • University of Louisville
LATEST VERSION PUBLISHED 19 Sep 2018
https://doi.org/10.12688/f1000research.15931.2
Software Tool Article metrics
Revised
FastQ Screen: A tool for multi-genome mapping and quality control
[version 2; peer review: 4 approved]
Steven W. Wingett, Simon Andrews
Peer Reviewers Russell Hamilton; Ian J. Donaldson; Stéphane Le Crom and Laurent Jourdren; Matthew D. Teasdale
  • Funders
  • Medical Research Council
  • Biotechnology and Biological Sciences Research Council
LATEST VERSION PUBLISHED 17 Sep 2018
https://doi.org/10.12688/f1000research.14013.2
Software Tool Article metrics
Revised
Taxa: An R package implementing data standards and methods for taxonomic data
[version 2; peer review: 4 approved]
Zachary S.L. Foster, Scott Chamberlain, Niklaus J. Grünwald
Peer Reviewers Ethan P. White and Kristina Riemer; C. Titus Brown and Taylor Reiter; Damiano Oldoni and Peter Desmet; Holly M. Bik
  • Funders
  • Agricultural Research Service
  • rOpenSci
LATEST VERSION PUBLISHED 11 Sep 2018
https://doi.org/10.12688/f1000research.16047.1
Software Tool Article metrics
methyvim: Targeted, robust, and model-free differential methylation analysis in R
[version 1; peer review: 1 approved with reservations, 2 not approved]
Nima S. Hejazi, Rachael V. Phillips, Alan E. Hubbard, Mark J. van der Laan
Peer Reviewers Peter F.  Hickey; Jimmy Breen and Nader Aryamanesh; Nandita Mitra and Ted Westling
  • Funders
  • National Institute of Environmental Health Sciences
  • U.S. National Library of Medicine
PUBLISHED 07 Sep 2018
https://doi.org/10.12688/f1000research.15704.1
Software Tool Article metrics
ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis
[version 1; peer review: 2 approved]
Adam R. Rivers, Kyle C. Weber, Terrence G. Gardner, Shuang Liu, Shalamar D. Armstrong
Peer Reviewers J. Gregory Caporaso; Johanna B. Holm
  • Funder
  • USDA Agricultural Research Service
PUBLISHED 06 Sep 2018
https://doi.org/10.12688/f1000research.8219.2
Data Note metrics
Revised
The ICR142 NGS validation series: a resource for orthogonal assessment of NGS analysis
[version 2; peer review: 2 approved]
Elise Ruark, Anthony Renwick, Matthew Clarke, Katie Snape, Emma Ramsay, Anna Elliott, Sandra Hanks, Ann Strydom, Sheila Seal, Nazneen Rahman
Peer Reviewers Richard Bagnall; Brad Chapman and Oliver Hofmann
  • Funder
  • Institute of Cancer Research
LATEST VERSION PUBLISHED 05 Sep 2018
https://doi.org/10.12688/f1000research.14819.2
Software Tool Article metrics
Revised
WordCommentsAnalyzer: A windows software tool for qualitative research
[version 2; peer review: 2 approved]
Ehsan Abdekhodaie, Javad Hatami, Hadi Bahrami Ehsan, Reza Kormi-Nouri
Peer Reviewers Ronggui Huang; Yazdan Mansourian
LATEST VERSION PUBLISHED 04 Sep 2018
https://doi.org/10.12688/f1000research.15708.1
Software Tool Article metrics
Providing gene-to-variant and variant-to-gene database identifier mappings to use with BridgeDb mapping services.
[version 1; peer review: 1 approved, 1 not approved]
Friederike Ehrhart, Jonathan Melius, Elisa Cirillo, Martina Kutmon, Egon L. Willighagen, Susan L. Coort, Leopold M.G. Curfs, Chris T. Evelo
Peer Reviewers Patrice Godard; Osman Ugur Sezerman
  • Funder
  • ELIXIR
PUBLISHED 03 Sep 2018
https://doi.org/10.12688/f1000research.16015.1
Opinion Article metrics
Long-term preservation of biomedical research data
[version 1; peer review: 4 approved, 1 approved with reservations]
Vivek Navale, Matthew McAuliffe
Peer Reviewers Jane Greenberg; George Alter; Chaitan Baru; David Giaretta; Ravi Madduri
PUBLISHED 29 Aug 2018
https://doi.org/10.12688/f1000research.15726.1
Opinion Article metrics
Silicon Valley new focus on brain computer interface: hype or hope for new applications?
[version 1; peer review: 2 approved, 1 approved with reservations]
Stefan Mitrasinovic, Alexander P.Y. Brown, Andreas T. Schaefer, Steven D. Chang, Geoff Appelboom
Peer Reviewers Jeffrey V. Rosenfeld and Yan Tat Wong; Ujwal Chaudhary; Theresa M. Vaughan
PUBLISHED 21 Aug 2018
https://doi.org/10.12688/f1000research.15936.1
Editorial metrics NOT PEER REVIEWED
The 2018 Bioinformatics Open Source Conference (GCCBOSC 2018)
[version 1; peer review: not peer reviewed]
Nomi L. Harris, Heather Wiencko, Brad Chapman, Peter J.A. Cock, Karsten Hokamp, Hilmar Lapp, Chris Fields, Bastian Greshake Tzovaras
PUBLISHED 17 Aug 2018
541-560 of 1,017 ARTICLES
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