RPackage
RPackage
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
Software Tool Article
metrics
Peer Reviewers
Thodoris Kypraios;
Huitong Qiu
- Funder
- Seventh Framework Programme
Software Tool Article
metrics
Revised
epiflows: an R package for risk assessment of travel-related spread of disease
[version 3; peer review: 2 approved]
Peer Reviewers
Noam Ross;
Jon Zelner
- Funders
- National Institute for Health Research
- UK Medical Research Council
- Imperial College Junior Research Fellowship
Research Article
metrics
Revised
Predicting transcription factor binding using ensemble random forest models
[version 2; peer review: 2 approved]
Peer Reviewers
Jan Grau;
Gary D Stormo
- Funder
- Cluster of Excellence on Multimodal Computing and Interaction (DFG)
Software Tool Article
metrics
Revised
seqCAT: a Bioconductor R-package for variant analysis of high throughput sequencing data
[version 2; peer review: 1 approved, 1 not approved]
Peer Reviewers
Matej Lexa;
Jean Fan
- Funder
- European Community 7th Framework Program
Software Tool Article
metrics
ChIPdig: a comprehensive user-friendly tool for mining multi-sample ChIP-seq data
[version 1; peer review: 3 approved with reservations]
Peer Reviewers
Tao Liu;
Hinrich Gronemeyer and Marco Antonio Mendoza-Parra;
Thomas Carroll
- Funder
- National Institutes of Health
Method Article
metrics
Revised
Enhancing gene set enrichment using networks
[version 2; peer review: 2 approved, 2 approved with reservations]
Peer Reviewers
Kimberly Glass;
Monther Alhamdoosh;
Jill P. Mesirov and Alexander Wenzel;
Rita Casadio
Software Tool Article
metrics
Detection and mitigation of spurious antisense expression with RoSA
[version 1; peer review: 2 approved with reservations]
Peer Reviewers
Ian Sudbery;
John Casement and Andreas Werner
- Funder
- Biotechnology and Biological Sciences Research Council
Software Tool Article
metrics
BiocPkgTools: Toolkit for mining the Bioconductor package ecosystem
[version 1; peer review: 2 approved, 1 approved with reservations]
Peer Reviewers
Simina M. Boca;
Mike Smith;
Henrik Bengtsson
- Funders
- EU H2020 Personalizing Health and Care Program
- Intramural Research Program, National Institutes of Health
- National Cancer Institute
- National Human Genome Research Institute
Software Tool Article
metrics
A new method for detecting abrupt shifts in time series
[version 1; peer review: 2 approved with reservations]
Peer Reviewers
Valerie N. Livina;
Sonia Kéfi
- Funder
- Natural Environment Research Council