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41-60 of 86 ARTICLES
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https://doi.org/10.12688/f1000research.18636.1
Method Article metrics
A Bioconductor workflow for the Bayesian analysis of spatial proteomics
[version 1; peer review: 1 approved, 2 approved with reservations]
Oliver M. Crook, Lisa M. Breckels, Kathryn S. Lilley, Paul D.W. Kirk, Laurent Gatto
Peer Reviewers Pierre M. Jean Beltran; Susan Holmes; Angus Lamond and Alejandro Brenes Murillo
  • Funders
  • Medical Research Council
  • Wellcome Trust
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 11 Apr 2019
https://doi.org/10.12688/f1000research.17548.2
Software Tool Article metrics
Revised
Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python
[version 2; peer review: 2 approved]
Klara Kaleb, Alex Warwick Vesztrocy, Adrian M. Altenhoff, Christophe Dessimoz
Peer Reviewers Bastian Greshake Tzovaras and Ngoc-Vinh Tran; Laurent Gatto
  • Funders
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
  • University College London
  • Swiss State Secretariat for Education
  • Biotechnology and Biological Sciences Research Council
LATEST VERSION PUBLISHED 29 Mar 2019
https://doi.org/10.12688/f1000research.16613.2
Research Article metrics
Revised
False signals induced by single-cell imputation
[version 2; peer review: 4 approved]
Tallulah S. Andrews, Martin Hemberg
Peer Reviewers Simone Tiberi; Jean Fan; Charlotte Soneson; Stephanie C Hicks
  • Funders
  • Chan Zuckerberg Initiative
  • Wellcome Trust
LATEST VERSION PUBLISHED 05 Mar 2019
https://doi.org/10.12688/f1000research.17518.1
Software Tool Article metrics
restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor
[version 1; peer review: 2 approved]
Shweta Gopaulakrishnan, Samuela Pollack, BJ Stubbs, Hervé Pagès, John Readey, Sean Davis, Levi Waldron, Martin Morgan, Vincent Carey
Peer Reviewers Dennis J. Hazelett; Sheila Reynolds
  • Funders
  • National Institutes of Health
  • Chan Zuckerberg Initiative
PUBLISHED 07 Jan 2019
https://doi.org/10.12688/f1000research.9005.3
Software Tool Article metrics
Revised
RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR
[version 3; peer review: 3 approved]
Charity W. Law, Monther Alhamdoosh, Shian Su, Xueyi Dong, Luyi Tian, Gordon K. Smyth, Matthew E. Ritchie
Peer Reviewers James W. MacDonald; Maria A. Doyle; Jovana Maksimovic
  • Funders
  • Australian Government NHMRC IRIISS
  • State Government Operational Infrastructure Support
  • National Health and Medical Research Council
LATEST VERSION PUBLISHED 28 Dec 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.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.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.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.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; peer review: 2 approved, 1 approved with reservations]
Andrea Komljenovic, Julien Roux, Julien Wollbrett, Marc Robinson-Rechavi, Frederic B. Bastian
Peer Reviewers Virag Sharma; Daniel S. Himmelstein; Leonardo Collado-Torres
  • Funder
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
LATEST VERSION 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; peer review: 2 approved]
Paul Brennan
Peer Reviewers 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; peer review: 1 approved, 2 approved with reservations]
Jayaram Kancherla, Alexander Zhang, Brian Gottfried, Hector Corrada Bravo
Peer Reviewers 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; peer review: 2 approved]
Bernd Klaus, Stefanie Reisenauer
Peer Reviewers James W. MacDonald; Andrea Rau
LATEST VERSION 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; peer review: 2 approved]
Lisa M. Breckels, Claire M. Mulvey, Kathryn S. Lilley, Laurent Gatto
Peer Reviewers Leonard J. Foster; Daniel J. Stekhoven
  • Funders
  • Wellcome Trust
  • Biotechnology and Biological Sciences Research Council
LATEST VERSION 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; peer review: 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
Peer Reviewers Charlotte Soneson; Davide Risso
LATEST VERSION PUBLISHED 20 Jun 2018
https://doi.org/10.12688/f1000research.14966.1
Software Tool Article metrics
iSEE: Interactive SummarizedExperiment Explorer
[version 1; peer review: 3 approved]
Kevin Rue-Albrecht, Federico Marini, Charlotte Soneson, Aaron T.L. Lun
Peer Reviewers 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; 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.14399.1
Software Tool Article metrics
Authoring Bioconductor workflows with BiocWorkflowTools
[version 1; peer review: 2 approved with reservations]
Mike L. Smith, Andrzej K. Oleś, Wolfgang Huber
Peer Reviewers 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; 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.13930.1
Software Tool Article metrics
Seqfam: A python package for analysis of Next Generation Sequencing DNA data in families
[version 1; peer review: 1 approved with reservations, 1 not approved]
Matthew Frampton, Elena R. Schiff, Nikolas Pontikos, Anthony W. Segal, Adam P. Levine
Peer Reviewers Brent S. Pedersen; Alexandre Bureau and Ingo Ruczinski
  • Funder
  • Charles Wolfson Charitable Trust
PUBLISHED 06 Mar 2018
41-60 of 86 ARTICLES
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