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1 -20 of 46 ARTICLES
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Featured Article
https://doi.org/10.12688/f1000research.11622.2
Method Article metrics
Revised
CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets [version 2; referees: 2 approved]
Malgorzata Nowicka, Carsten Krieg, Lukas M. Weber, Felix J. Hartmann, Silvia Guglietta, Burkhard Becher, Mitchell P. Levesque, Mark D. Robinson
Referees Invited
  • Funder
  • Swiss Institute of Bioinformatics
PUBLISHED 14 Nov 2017
https://doi.org/10.12688/f1000research.16613.1
Research Article metrics
False signals induced by single-cell imputation [version 1; referees: 4 approved with reservations]
Tallulah S. Andrews, Martin Hemberg
Referees Simone Tiberi; Jean Fan; Charlotte Soneson; Stephanie Hicks
  • Funder
  • Wellcome Trust
PUBLISHED 02 Nov 2018
https://doi.org/10.12688/f1000research.16516.1
Method Article metrics
Orchestrating a community-developed computational workshop and accompanying training materials [version 1; referees: 2 approved]
Sean Davis, Marcel Ramos, Lori Shepherd, Nitesh Turaga, Ludwig Geistlinger, Martin T. Morgan, Benjamin Haibe-Kains, Levi Waldron
Referees Ewy Mathe; Kevin Blighe
  • Funders
  • National Cancer Institute
  • Horizon 2020
  • National Human Genome Research Institute
PUBLISHED 17 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.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.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.15666.2
Research Article metrics
Revised
A systematic performance evaluation of clustering methods for single-cell RNA-seq data [version 2; referees: 2 approved]
Angelo Duò, Mark D. Robinson, Charlotte Soneson
Referees Jean Fan; Saskia Freytag
  • Funders
  • Swiss National Science Foundation
  • Chan Zuckerberg Initiative
PUBLISHED 10 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.9973.2
Software Tool Article metrics
Revised
BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests [version 2; referees: 2 approved, 1 approved with reservations]
Andrea Komljenovic, Julien Roux, Julien Wollbrett, Marc Robinson-Rechavi, Frederic B. Bastian
Referees Virag Sharma; Daniel S. Himmelstein; Leonardo Collado-Torres
  • Funder
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
PUBLISHED 07 Aug 2018
https://doi.org/10.12688/f1000research.14541.1
Software Tool Article metrics
drawProteins: a Bioconductor/R package for reproducible and programmatic generation of protein schematics [version 1; referees: 2 approved]
Paul Brennan
Referees Matej Lexa; Malachi Griffith
  • Funder
  • Bloodwise
PUBLISHED 18 Jul 2018
https://doi.org/10.12688/f1000research.15433.1
Software Tool Article metrics
Epiviz Web Components: reusable and extensible component library to visualize functional genomic datasets [version 1; referees: 1 approved, 2 approved with reservations]
Jayaram Kancherla, Alexander Zhang, Brian Gottfried, Hector Corrada Bravo
Referees Bianca H. Habermann; Ian Holmes; Zhaohui Steve Qin
  • Funder
  • National Institutes of Health
PUBLISHED 17 Jul 2018
https://doi.org/10.12688/f1000research.8967.2
Research Article metrics
Revised
An end to end workflow for differential gene expression using Affymetrix microarrays [version 2; referees: 2 approved]
Bernd Klaus, Stefanie Reisenauer
Referees James W. MacDonald; Andrea Rau
PUBLISHED 03 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.14966.1
Software Tool Article metrics
iSEE: Interactive SummarizedExperiment Explorer [version 1; referees: 3 approved]
Kevin Rue-Albrecht, Federico Marini, Charlotte Soneson, Aaron T.L. Lun
Referees James W. MacDonald; Lorena Pantano; Alejandro Reyes
  • Funders
  • Bundesministerium für Bildung und Forschung
  • Cancer Research UK
PUBLISHED 14 Jun 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; referees: 1 approved, 1 approved with reservations]
Tiago Chedraoui Silva, Antonio Colaprico, Catharina Olsen, Tathiane M Malta, Gianluca Bontempi, Michele Ceccarelli F1000Prime Faculty Member
, Benjamin P Berman, Houtan Noushmehr
Referees 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.14399.1
Software Tool Article metrics
Authoring Bioconductor workflows with BiocWorkflowTools [version 1; referees: 2 approved with reservations]
Mike L. Smith, Andrzej K. Oleś, Wolfgang Huber F1000Research Advisory Board member
Referees Justin Kitzes; Laurent Gatto
  • Funders
  • Bundesministerium für Bildung und Forschung
  • Horizon 2020
  • German Network for Bioinformatics Infrastructure
PUBLISHED 06 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; referees: 1 approved, 1 approved with reservations]
Dongmin Jung, Xijin Ge
Referees Cathy H. Wu and Karen E. Ross; Helen V. Cook
  • Funder
  • National Science Foundation
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; referees: 2 approved]
Enrico Ferrero
Referees Aaron T. L. Lun; Vincent J. Carey
PUBLISHED 23 Feb 2018
https://doi.org/10.12688/f1000research.13535.1
Method Article metrics
StateHub-StatePaintR: rapid and reproducible chromatin state evaluation for custom genome annotation [version 1; referees: 3 approved with reservations]
Simon G. Coetzee, Zachary Ramjan, Huy Q. Dinh, Benjamin P. Berman, Dennis J. Hazelett
Referees Maxwell W. Libbrecht; Yongjin Park; Guillaume J. Filion
  • Funder
  • National Institutes of Health
PUBLISHED 22 Feb 2018
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; referees: 3 approved with reservations]
Lauren Kemperman, Matthew N. McCall
Referees Levi Waldron; Simina M. Boca; Elana Judith Fertig
  • Funder
  • National Institutes of Health
PUBLISHED 23 Nov 2017
1 -20 of 46 ARTICLES
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