RPackage track_changes Track Tracking Be alerted when new articles are added in this gateway (manage your tracking alerts via your account) Stop tracking this gateway

1 -20 of 58 ARTICLES
Previous Next
 in 
Featured Article
https://doi.org/10.12688/f1000research.11997.1
Software Tool Article metrics
valr: Reproducible genome interval analysis in R [version 1; referees: 2 approved]
Kent A. Riemondy, Ryan M. Sheridan, Austin Gillen, Yinni Yu, Christopher G. Bennett, Jay R. Hesselberth
Referees Invited
  • Funders
  • U.S. National Library of Medicine
  • Colorado Office of Economic Development and International Trade
  • National Institutes of Health
  • BioFrontiers Institute, University of Colorado Boulder
  • University of Colorado
PUBLISHED 29 Jun 2017
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; referees: 2 approved]
Jesper L.V. Maag
Referees Helder I. Nakaya; Saskia Freytag
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; referees: 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
Referees 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; referees: 1 approved, 1 approved with reservations]
VP Nagraj, Nistara Randhawa, Finlay Campbell, Thomas Crellen, Bertrand Sudre, Thibaut Jombart
Referees Melissa A. Rolfes; Peter Adebayo Adewuyi
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; referees: 2 approved, 1 approved with reservations]
Yunshun Chen, Bhupinder Pal, Jane E. Visvader, Gordon K. Smyth
Referees Simon Andrews; James W. MacDonald; Peter F.  Hickey
  • Funders
  • Victorian State Government
  • National Health and Medical Research Council
PUBLISHED 08 Oct 2018
https://doi.org/10.12688/f1000research.16200.1
Research Article metrics
Predicting transcription factor binding using ensemble random forest models [version 1; referees: 1 approved with reservations]
Fatemeh Behjati Ardakani, Florian Schmidt, Marcel H. Schulz
Referee Jan Grau
  • Funder
  • Cluster of Excellence on Multimodal Computing and Interaction (DFG)
PUBLISHED 04 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; referees: 3 approved]
Michael I. Love, Charlotte Soneson, Rob Patro
Referees 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
PUBLISHED 01 Oct 2018
https://doi.org/10.12688/f1000research.16198.1
Software Tool Article metrics
scClustViz – Single-cell RNAseq cluster assessment and visualization [version 1; referees: 2 approved with reservations]
Brendan T. Innes, Gary D. Bader F1000Research Advisory Board member
F1000Prime Section Head
Referees Martin Hemberg and Tallulah Andrews; Michael Steinbaugh
  • Funder
  • Canada First Research Excellence Fund
PUBLISHED 21 Sep 2018
https://doi.org/10.12688/f1000research.16216.1
Software Tool Article metrics
Feature selection with the R package MXM [version 1; referees: awaiting peer review]
Michail Tsagris, Ioannis Tsamardinos
Referee Thodoris Kypraios
  • Funder
  • Seventh Framework Programme
PUBLISHED 20 Sep 2018
https://doi.org/10.12688/f1000research.16083.1
Software Tool Article metrics AWAITING PEER REVIEW
seqCAT: a Bioconductor R-package for variant analysis of high throughput sequencing data [version 1; referees: awaiting peer review]
Erik Fasterius, Cristina Al-Khalili Szigyarto
Referees Invited
  • Funder
  • European Community 7th Framework Program
PUBLISHED 14 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; referees: 4 approved]
Zachary S.L. Foster, Scott Chamberlain, Niklaus J. Grünwald
Referees Ethan P. White and Kristina Riemer; Titus Brown and Taylor Reiter; Damiano Oldoni and Peter Desmet; Holly M. Bik
  • Funders
  • Agricultural Research Service
  • rOpenSci
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; referees: 1 not approved]
Nima S. Hejazi, Rachael V. Phillips, Alan E. Hubbard, Mark J. van der Laan
Referee Peter F.  Hickey
  • Funders
  • National Institute of Environmental Health Sciences
  • U.S. National Library of Medicine
PUBLISHED 07 Sep 2018
https://doi.org/10.12688/f1000research.15949.1
Software Tool Article metrics
The Mega2R package: R tools for accessing and processing genetic data in common formats [version 1; referees: 3 approved]
Robert V. Baron, Justin R. Stickel, Daniel E. Weeks
Referees Dajiang J. Lui; Alejandro Q. Nato, Jr.; Derek Gordon
  • Funders
  • National Institutes of Health
  • The University of Pittsburgh
PUBLISHED 29 Aug 2018
https://doi.org/10.12688/f1000research.15858.1
Software Tool Article metrics
Visualizing balances of compositional data: A new alternative to balance dendrograms [version 1; referees: 2 approved]
Thomas P. Quinn
Referees Vera Pawlowsky-Glahn and Juan José Egozcue; Marc Noguera-Julian
PUBLISHED 14 Aug 2018
https://doi.org/10.12688/f1000research.13925.3
Software Tool Article metrics
Revised
BED: a Biological Entity Dictionary based on a graph data model [version 3; referees: 2 approved]
Patrice Godard, Jonathan van Eyll
Referees Denise Slenter and Martina M. Summer-Kutmon; T. Ian Simpson
  • Funder
  • UCB Pharma
PUBLISHED 19 Jul 2018
https://doi.org/10.12688/f1000research.13511.3
Method Article metrics
Revised
netSmooth: Network-smoothing based imputation for single cell RNA-seq [version 3; referees: 2 approved]
Jonathan Ronen, Altuna Akalin
Referees Fernando J. Calero-Nieto and Fiona Kathryn Hamey; Siddharth Dey F1000Prime Faculty Member
  • Funder
  • Helmholtz-Gemeinschaft
PUBLISHED 10 Jul 2018
https://doi.org/10.12688/f1000research.10411.2
Software Tool Article metrics
Revised
A Bioconductor workflow for processing and analysing spatial proteomics data [version 2; referees: 2 approved]
Lisa M. Breckels, Claire M. Mulvey, Kathryn S. Lilley, Laurent Gatto
Referees Leonard J. Foster; Daniel J. Stekhoven
  • Funders
  • Wellcome Trust
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 03 Jul 2018
https://doi.org/10.12688/f1000research.12093.2
Software Tool Article metrics
Revised
bcbioRNASeq: R package for bcbio RNA-seq analysis [version 2; referees: 1 approved, 1 approved with reservations]
Michael J. Steinbaugh, Lorena Pantano, Rory D. Kirchner, Victor Barrera, Brad A. Chapman, Mary E. Piper, Meeta Mistry, Radhika S. Khetani, Kayleigh D. Rutherford, Oliver Hofmann, John N. Hutchinson, Shannan Ho Sui
Referees Charlotte Soneson; Davide Risso
PUBLISHED 20 Jun 2018
https://doi.org/10.12688/f1000research.14361.1
Software Tool Article metrics
freesurfer: Connecting the Freesurfer software with R [version 1; referees: 2 approved]
John Muschelli, Elizabeth Sweeney, Ciprian M. Crainiceanu
Referees Seth 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; referees: 1 approved, 1 approved with reservations]
Eric T. Leung, Roshan Noronha, Ali Mirza, Reva Shenwai, Asterios Mpatziakas
Referees 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; referees: 2 approved]
Travis L. Jensen, Michael Frasketi, Kevin Conway, Leigh Villarroel, Heather Hill, Konstantinos Krampis, Johannes B. Goll
Referees Anup Mahurkar; Ben Busby
  • Funders
  • Emmes Corporation
  • National Institutes of Health
PUBLISHED 13 Apr 2018
1 -20 of 58 ARTICLES
Previous Next
The F1000Research website uses cookies. By continuing to browse the site, you are agreeing to our use of cookies. Find out more »
Sign In
If you've forgotten your password, please enter your email address below and we'll send you instructions on how to reset your password.

The email address should be the one you originally registered with F1000.
Email address not valid, please try again

You registered with F1000 via Google, so we cannot reset your password.

To sign in, please click here.

If you still need help with your Google account password, please click here.

You registered with F1000 via Facebook, so we cannot reset your password.

To sign in, please click here.

If you still need help with your Facebook account password, please click here.

Code not correct, please try again
Email for further assistance.
Server error, please try again.