RPackage
RPackage
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]
Peer Reviewers
Simon Andrews;
James W. MacDonald;
Peter F. Hickey
- Funders
- Victorian State Government
- National Health and Medical Research Council
Method Article
metrics
Revised
Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification
[version 3; peer review: 3 approved]
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
Software Tool Article
metrics
Revised
Taxa: An R package implementing data standards and methods for taxonomic data
[version 2; peer review: 4 approved]
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
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]
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
Software Tool Article
metrics
Visualizing balances of compositional data: A new alternative to balance dendrograms
[version 1; peer review: 2 approved]
Peer Reviewers
Vera Pawlowsky-Glahn and Juan José Egozcue;
Marc Noguera-Julian
Software Tool Article
metrics
Revised
BED: a Biological Entity Dictionary based on a graph data model
[version 3; peer review: 2 approved]
Peer Reviewers
Denise Slenter and Martina M. Summer-Kutmon;
T. Ian Simpson
- Funder
- UCB Pharma
Method Article
metrics
Revised
netSmooth: Network-smoothing based imputation for single cell RNA-seq
[version 3; peer review: 2 approved]
Peer Reviewers
Fernando J. Calero-Nieto and Fiona Kathryn Hamey;
Siddharth Dey
- Funder
- Helmholtz-Gemeinschaft
Software Tool Article
metrics
Revised
A Bioconductor workflow for processing and analysing spatial proteomics data
[version 2; peer review: 2 approved]
Peer Reviewers
Leonard J. Foster;
Daniel J. Stekhoven
- Funders
- Wellcome Trust
- Biotechnology and Biological Sciences Research Council
Software Tool Article
metrics
Revised
bcbioRNASeq: R package for bcbio RNA-seq analysis
[version 2; peer review: 1 approved, 1 approved with reservations]
Peer Reviewers
Charlotte Soneson;
Davide Risso
Software Tool Article
metrics
freesurfer: Connecting the Freesurfer software with R
[version 1; peer review: 2 approved]
Peer Reviewers
Seth T. Lirette;
Pierre Lafaye de Micheaux
- Funder
- National Institutes of Health
Software Tool Article
metrics
ShinyDiversity - Understanding Alpha and Beta Diversity through Interactive Visualizations
[version 1; peer review: 1 approved, 1 approved with reservations]
Peer Reviewers
Jianguo Xia;
Richard E. Isaacson
- Funder
- U.S. National Library of Medicine
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; peer review: 2 approved]
Peer Reviewers
Anup Mahurkar;
Ben Busby
- Funders
- Emmes Corporation
- National Institutes of Health
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]
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
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]
Peer Reviewers
Cathy H. Wu and Karen E. Ross;
Helen V. Cook
- Funder
- National Science Foundation
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]
Peer Reviewers
Aaron T. L. Lun;
Vincent J. Carey
Software Tool Article
metrics
Revised
GAC: Gene Associations with Clinical, a web based application
[version 4; peer review: 2 approved, 1 approved with reservations]
Peer Reviewers
Shengjie Yang;
Matthew N. McCall;
Cedric Simillion
- Funders
- Winship Cancer Institute of Emory University
- National Cancer Institute
Software Tool Article
metrics
archiDART v3.0: A new data analysis pipeline allowing the topological analysis of plant root systems
[version 1; peer review: 2 approved, 1 approved with reservations]
Peer Reviewers
Magdalena M. Julkowska;
Alexander Bucksch;
Nathan D. Miller
- Funder
- Leuphana University
Software Tool Article
metrics
Revised
exprso: an R-package for the rapid implementation of machine learning algorithms
[version 2; peer review: 2 approved]
Peer Reviewers
Dariusz Plewczynski and Julian Zubek;
Henry Löffler-Wirth
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]
Peer Reviewers
Levi Waldron;
Simina M. Boca;
Elana J. Fertig
- Funder
- National Institutes of Health
Software Tool Article
metrics
lakemorpho: Calculating lake morphometry metrics in R
[version 1; peer review: 2 approved]
Peer Reviewers
Samantha K. Oliver;
Luke A. Winslow