Bioconductor
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
Method Article
metrics
Revised
Fast effect size shrinkage software for beta-binomial models of allelic imbalance
[version 2; peer review: 1 approved, 2 approved with reservations]
Peer Reviewers
Matthew Stephens;
Jarad Niemi and Ignacio Alvarez-Castro;
Ernest Turro
- Funder
- National Institutes of Health
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
Method Article
metrics
A guide to creating design matrices for gene expression experiments
[version 1; peer review: 2 approved]
Peer Reviewers
Federico Marini;
Jenny Drnevich
- Funders
- National Health and Medical Research Council
- Chan Zuckerberg Initiative
Research Article
metrics
Revised
A systematic performance evaluation of clustering methods for single-cell RNA-seq data
[version 3; peer review: 2 approved]
Peer Reviewers
Jean Fan;
Saskia Freytag
- Funders
- Swiss National Science Foundation
- Chan Zuckerberg Initiative
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
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
Method Article
metrics
Revised
StateHub-StatePaintR: rapid and reproducible chromatin state evaluation for custom genome annotation
[version 2; peer review: 3 approved with reservations]
Peer Reviewers
Maxwell W. Libbrecht;
Yongjin Park;
Guillaume J. Filion
- Funder
- National Institutes of Health
Software Tool Article
metrics
Revised
microbiomeDASim: Simulating longitudinal differential abundance for microbiome data
[version 2; peer review: 2 approved]
Peer Reviewers
Leo Lahti;
Kris Sankaran
Method Article
metrics
Fluent genomics with plyranges and tximeta
[version 1; peer review: 1 approved, 2 approved with reservations]
Peer Reviewers
Mark Dunning;
PuXue Qiao, Ruqian Lyu and Davis J. McCarthy;
Mickaël Mendez and Michael M. Hoffman
- Funders
- Department of Industry, Innovation, Science, Research and Tertiary Education, Australian Government
- CSL Behring
- National Institutes of Health
Method Article
metrics
Revised
CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets
[version 4; peer review: 2 approved]
Peer Reviewers
Aaron T. L. Lun and John C. Marioni;
Greg Finak and Raphael Gottardo
- Funders
- Swiss National Science Foundation
- Swiss Institute of Bioinformatics
- University of Zurich
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
Revised
Using singscore to predict mutation status in acute myeloid leukemia from transcriptomic signatures
[version 3; peer review: 2 approved]
Peer Reviewers
Marina Lizio;
Luiza Handschuh
- Funder
- National Health and Medical Research Council
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
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
A step-by-step guide to analyzing CAGE data using R/Bioconductor
[version 1; peer review: 3 approved]
Peer Reviewers
Aaron T. L. Lun;
Kenta Nakai and Luis Augusto Eijy Nagai;
Nevena Cvetesic
- Funders
- Danmarks Frie Forskningsfond
- Kræftens Bekæmpelse
- Danish Innovation Fund
- Lundbeckfonden
- Novo Nordisk Fonden
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
Revised
TFutils: Data structures for transcription factor bioinformatics
[version 2; peer review: 2 approved, 1 not approved]
Peer Reviewers
Lihua Julie Zhu, Haibo Liu and Rui Li;
Giovanna Ambrosini, Philipp Bucher and Rui Li;
Kevin Ernst and Matthew T. Weirauch
- Funders
- National Institute of Allergy and Infectious Diseases
- National Heart, Lung, and Blood Institute
- National Cancer Institute
Software Tool Article
metrics
Optimized functional annotation of ChIP-seq data
[version 1; peer review: 3 approved with reservations]
Peer Reviewers
Vincent J. Carey;
Ruslan I. Sadreyev;
Michael Lawrence
- Funders
- American Heart Association
- National Institutes of Health
- Army Research Office