RPackage
RPackage
Method Article
metrics
A Bioconductor workflow for the Bayesian analysis of spatial proteomics
[version 1; peer review: 1 approved, 2 approved with reservations]
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
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]
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
Software Tool Article
metrics
Revised
Radtools: R utilities for convenient extraction of medical image metadata
[version 3; peer review: 2 approved]
Peer Reviewers
Andrey Fedorov;
Volker Schmid
- Funder
- Cancer Center, University of Colorado
Software Tool Article
metrics
Revised
scClustViz – Single-cell RNAseq cluster assessment and visualization
[version 2; peer review: 2 approved]
Peer Reviewers
Martin Hemberg and Tallulah Andrews;
Michael Steinbaugh
- Funder
- Canada First Research Excellence Fund
Software Tool Article
metrics
shiny-pred: a server for the prediction of protein disordered regions
[version 1; peer review: 1 approved with reservations, 1 not approved]
Peer Reviewers
Jinbo Xu;
Appadurai Rajeswari and Anand Srivastava
Software Tool Article
metrics
Revised
The Mega2R package: R tools for accessing and processing genetic data in common formats
[version 2; peer review: 3 approved]
Peer Reviewers
Dajiang J. Lui;
Alejandro Q. Nato, Jr.;
Derek Gordon
- Funders
- The University of Pittsburgh
- National Institutes of Health
Method Article
metrics
Relative Abundance of Transcripts (RATs): Identifying differential isoform abundance from RNA-seq
[version 1; peer review: 1 approved, 2 approved with reservations]
Peer Reviewers
Sophie Shaw;
James P. B. Lloyd;
Michael I. Love
- Funders
- Wellcome Trust
- Biotechnology and Biological Sciences Research Council
Software Tool Article
metrics
Epidemic curves made easy using the R package incidence
[version 1; peer review: 1 approved, 2 approved with reservations]
Peer Reviewers
Benjamin M. Bolker;
Quirine ten Bosch;
Bertrand Sudre
- Funders
- Global Challenges Research Fund (GCRF)
- United Kingdom Department of Health and Social Care
- National Institute for Health Research - Health Protection Research Unit for Modelling Methodology
Software Tool Article
metrics
Revised
gganatogram: An R package for modular visualisation of anatograms and tissues based on ggplot2
[version 2; peer review: 2 approved]
Peer Reviewers
Helder I. Nakaya;
Saskia Freytag
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; peer review: 1 approved, 2 approved with reservations]
Peer Reviewers
Tristan Cordier;
Holly M. Bik;
Niklaus J. Grünwald and Zach Foster
- Funders
- University of California President’s Research Catalyst Awards
- National Science Foundation
Software Tool Article
metrics
Revised
epicontacts: Handling, visualisation and analysis of epidemiological contacts
[version 2; peer review: 2 approved, 1 approved with reservations]
Peer Reviewers
Melissa A. Rolfes;
Peter Adebayo Adewuyi;
Josie Athens
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