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61-80 of 86 ARTICLES
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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; peer review: 2 approved]
Enrico Ferrero
Peer Reviewers Aaron T. L. Lun; Vincent J. Carey
LATEST VERSION PUBLISHED 23 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; peer review: 3 approved with reservations]
Lauren Kemperman, Matthew N. McCall
Peer Reviewers Levi Waldron; Simina M. Boca; Elana J. Fertig
  • Funder
  • National Institutes of Health
PUBLISHED 23 Nov 2017
https://doi.org/10.12688/f1000research.12544.1
Software Tool Article metrics
Easy and efficient ensemble gene set testing with EGSEA
[version 1; peer review: 1 approved, 3 approved with reservations]
Monther Alhamdoosh, Charity W. Law, Luyi Tian, Julie M. Sheridan, Milica Ng, Matthew E. Ritchie
Peer Reviewers Robert Castelo; Jenny Drnevich; Weijun Luo; Pekka Kohonen and Roland Grafström
  • Funders
  • NHMRC IRIISS
  • NHMRC
  • Victorian State Government Operational Infrastructure Support
PUBLISHED 14 Nov 2017
https://doi.org/10.12688/f1000research.12223.1
Method Article metrics
recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor
[version 1; peer review: 1 approved, 2 approved with reservations]
Leonardo Collado-Torres, Abhinav Nellore, Andrew E. Jaffe
Peer Reviewers Davide Risso; Alejandro Reyes; Nick Schurch
  • Funder
  • National Institutes of Health
PUBLISHED 24 Aug 2017
https://doi.org/10.12688/f1000research.12122.1
Method Article metrics
Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inference
[version 1; peer review: 1 approved, 2 approved with reservations]
Fanny Perraudeau, Davide Risso, Kelly Street, Elizabeth Purdom, Sandrine Dudoit
Peer Reviewers Stephanie C. Hicks; Andrew McDavid; Michael I. Love
  • Funders
  • National Institutes of Health
  • National Human Genome Research Institute
PUBLISHED 21 Jul 2017
https://doi.org/10.12688/f1000research.9259.2
Software Tool Article metrics
Revised
GeneBreak: detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes
[version 2; peer review: 2 approved]
Evert van den Broek, Stef van Lieshout, Christian Rausch, Bauke Ylstra, Mark A. van de Wiel, Gerrit A. Meijer, Remond J.A. Fijneman, Sanne Abeln
Peer Reviewers Tobias Marschall; Angel Rubio
LATEST VERSION PUBLISHED 06 Jul 2017
https://doi.org/10.12688/f1000research.8839.3
Method Article metrics
Revised
A cross-package Bioconductor workflow for analysing methylation array data
[version 3; peer review: 4 approved]
Jovana Maksimovic, Belinda Phipson, Alicia Oshlack
Peer Reviewers Timothy J Peters; Peter F.  Hickey; Michael I. Love; Davide Risso
LATEST VERSION PUBLISHED 05 Apr 2017
https://doi.org/10.12688/f1000research.8923.2
Software Tool Article metrics
Revised
TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages
[version 2; peer review: 1 approved, 2 approved with reservations]
Tiago C. Silva, Antonio Colaprico, Catharina Olsen, Fulvio D'Angelo, Gianluca Bontempi, Michele Ceccarelli, Houtan Noushmehr
Peer Reviewers Kyle Ellrott; Elena Papaleo; Charlotte Soneson
LATEST VERSION PUBLISHED 28 Dec 2016
https://doi.org/10.12688/f1000research.8900.2
Method Article metrics
Revised
DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics
[version 2; peer review: 2 approved]
Malgorzata Nowicka, Mark D. Robinson
Peer Reviewers Alejandro Reyes; Robert Castelo
LATEST VERSION PUBLISHED 06 Dec 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.7035.2
Research Article metrics
Revised
RNA-Seq workflow: gene-level exploratory analysis and differential expression
[version 2; peer review: 2 approved]
Michael I. Love, Simon Anders, Vladislav Kim, Wolfgang Huber
Peer Reviewers Davide Risso; Zhijin Wu
LATEST VERSION PUBLISHED 17 Nov 2016
https://doi.org/10.12688/f1000research.8986.2
Research Article metrics
Revised
Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses
[version 2; peer review: 3 approved]
Ben J. Callahan, Kris Sankaran, Julia A. Fukuyama, Paul J. McMurdie, Susan P. Holmes
Peer Reviewers Leo Lahti; Zachary Charlop-Powers; Nandita R. Garud
LATEST VERSION PUBLISHED 02 Nov 2016
https://doi.org/10.12688/f1000research.9501.2
Software Tool Article metrics
Revised
A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor
[version 2; peer review: 3 approved, 2 approved with reservations]
Aaron T.L. Lun, Davis J. McCarthy, John C. Marioni
Peer Reviewers Diana H.P. Low; Hongkai Ji; Andrew McDavid; David duVerle; Antonio Rausell
LATEST VERSION PUBLISHED 31 Oct 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.8987.2
Software Tool Article metrics
Revised
From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline
[version 2; peer review: 5 approved]
Yunshun Chen, Aaron T. L. Lun, Gordon K. Smyth
Peer Reviewers Conrad J. Burden; Nick Schurch; Devon P. Ryan; Tsung Fei Khang; Steve Lianoglou
LATEST VERSION PUBLISHED 02 Aug 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.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.6758.2
Editorial metrics NOT PEER REVIEWED
Revised
The Bioconductor channel in F1000Research
[version 2; peer review: not peer reviewed]
Wolfgang Huber, Vincent J. Carey, Sean Davis, Kasper Daniel Hansen, Martin Morgan
LATEST VERSION PUBLISHED 20 Apr 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
61-80 of 86 ARTICLES
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