RPackage
RPackage
Software Tool Article
metrics
periodicDNA: an R/Bioconductor package to investigate k-mer periodicity in DNA
[version 1; peer review: 1 approved, 3 approved with reservations]
Peer Reviewers
Ilya Ioshikhes;
Sabarinathan Radhakrishnan;
Eugene Korotkov;
Boris Lenhard
- Funders
- Wellcome Trust Senior Research Fellowship
- Medical Research Council DTP studentship
Software Tool Article
metrics
Revised
netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks
[version 2; peer review: 2 approved]
Peer Reviewers
Kim-Anh Lê Cao;
Anais Baudot, Judith Lambert and Laurent Tichit
- Funders
- Villum Fonden
- Horizon 2020
- National Institutes of Health
Software Tool Article
metrics
rANOMALY: AmplicoN wOrkflow for Microbial community AnaLYsis
[version 1; peer review: 2 approved]
Peer Reviewers
Florent Murat;
Simon Roux
Method Article
metrics
A pipeline to analyse time-course gene expression data
[version 1; peer review: 2 approved with reservations]
Peer Reviewers
Michael I. Love;
Rodolphe Thiébaut
- Funders
- U.S. Department of Energy
- École Normale Supérieure
- Gordon and Betty Moore Foundation
- Alfred P. Sloan Foundation
Software Tool Article
metrics
Revised
iMutSig: a web application to identify the most similar mutational signature using shiny
[version 2; peer review: 2 approved]
Peer Reviewers
Adrian Baez-Ortega;
Vittorio Perduca
- Funders
- National Institute of Environmental Health Sciences
- National Cancer Institute
Software Tool Article
metrics
Revised
gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler
[version 2; peer review: 2 approved]
Peer Reviewers
Egon L. Willighagen;
Ewy Mathe
- Funders
- Eesti Teadusagentuur
- Seventh Framework Programme
- European Regional Development Fund
Software Tool Article
metrics
Revised
sPop: Age-structured discrete-time population dynamics model in C, Python, and R
[version 3; peer review: 2 approved]
Peer Reviewers
Juliane Liepe;
Matthew Silk
Software Tool Article
metrics
Revised
ExploreModelMatrix: Interactive exploration for improved understanding of design matrices and linear models in R
[version 2; peer review: 3 approved]
Peer Reviewers
Jean Fan;
Lucy D'Agostino McGowan;
Matthew Ritchie
- Funders
- National Institutes of Health
- German Federal Ministry of Education and Research
Method Article
metrics
Extraction of CPRD additional clinical data using R
[version 1; peer review: 2 approved with reservations]
Peer Reviewers
Zhi Yang;
Jessica Pinaire
- Funder
- National Institute for Health Research Oxford Health Biomedical Research Centre
Software Tool Article
metrics
CRI iAtlas: an interactive portal for immuno-oncology research
[version 1; peer review: 3 approved]
Peer Reviewers
Vincent Rouilly;
David L. Goode;
Nathan E. Reticker-Flynn
- Funders
- Susan G. Komen
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill
- Cancer Research Institute
Software Tool Article
metrics
Dictionary of disease ontologies (DODO): a graph database to facilitate access and interaction with disease and phenotype ontologies
[version 1; peer review: 1 approved, 1 approved with reservations]
Peer Reviewers
Nicole Vasilevsky;
Jeremy G. Frey and Samantha Kanza
- Funder
- UCB Pharma
Software Tool Article
metrics
Revised
clustifyr: an R package for automated single-cell RNA sequencing cluster classification
[version 2; peer review: 2 approved]
Peer Reviewers
Keegan Korthauer;
Kamil Slowikowski
- Funders
- University of Colorado School of Medicine
- National Institute of General Medical Sciences
Software Tool Article
metrics
Revised
scRepertoire: An R-based toolkit for single-cell immune receptor analysis
[version 2; peer review: 2 approved]
Peer Reviewers
Lorenzo Drufuca, Raoul Jean Pierre Bonnal and Massimiliano Pagani;
Tim Stuart and Raoul Jean Pierre Bonnal
- Funder
- National Cancer Institute
Software Tool Article
metrics
Revised
R package “QRISK3”: an unofficial research purposed implementation of ClinRisk’s QRISK3 algorithm into R
[version 3; peer review: 1 approved, 1 approved with reservations, 1 not approved]
Peer Reviewers
Mohieddin Jafari and Ali Amiryousefi;
Angela K. Birnbaum and Ashwin Karanam;
Fadratul Hafinaz Hassan
- Funder
- China Scholarship Council
Software Tool Article
metrics
Revised
Generalized EmbedSOM on quadtree-structured self-organizing maps
[version 2; peer review: 2 approved]
Peer Reviewers
Evan Newell and Hugh MacMilan;
Nikolay Oskolkov
- Funders
- Institute of Organic Chemistry and Biochemistry of the CAS
- Ministerstvo Školství, Mládeže a Tělovýchovy
- European Regional Development Fund
Software Tool Article
metrics
Revised
bwimage: A package to describe image patterns in natural structures
[version 3; peer review: 2 approved]
Peer Reviewers
Francesco Chianucci;
Roy Francis
- Funders
- Conselho Nacional de Desenvolvimento Científico e Tecnológico
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
Software Tool Article
metrics
vhcub: Virus-host codon usage co-adaptation analysis
[version 1; peer review: 2 approved]
Peer Reviewers
Raj Kumar Singh;
Oscar Leonardo Ramírez Suárez and Adriana Patricia Corredor-Figueroa
Software Tool Article
metrics
Revised
HDCytoData: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats
[version 2; peer review: 2 approved]
Peer Reviewers
Shila Ghazanfar;
Laurent Gatto
- Funder
- Universität Zürich
Software Tool Article
metrics
Peer Reviewers
James Denvir;
Krithika Bhuvaneshwar;
Ludwig Geistlinger
- Funders
- National Institute of General Medical Sciences
Software Tool Article
metrics
Creating and sharing reproducible research code the workflowr way
[version 1; peer review: 3 approved]
Peer Reviewers
Peter F. Hickey;
Przemysław Biecek;
Peter Baker
- Funder
- Gordon and Betty Moore Foundation