RPackage
RPackage
Opinion Article
metrics
Revised
Introducing R as a smart version of calculators enables beginners to explore it on their own
[version 2; peer review: 3 approved]
Peer Reviewers
Lex Nederbragt;
Yasha Hasija;
Rayna M Harris
- Funders
- UCSF Bakar Computational Health Sciences Institute
- Gladstone Institutes
Software Tool Article
metrics
Revised
HGNChelper: identification and correction of invalid gene symbols for human and mouse
[version 2; peer review: 3 approved]
Peer Reviewers
Mikhail G. Dozmorov;
Susan Tweedie;
Marcin Cieślik
- Funder
- National Institutes of Health
Software Tool Article
metrics
Revised
pubassistant.ch: consolidating publication profiles of researchers
[version 3; peer review: 3 approved]
Peer Reviewers
Daniel W Hook;
Paul Albert and Curtis L. Cole;
Griffin M Weber
- Funder
- University Research Priority Program Evolution in Action at the University of Zurich
Software Tool Article
metrics
pTITAN2: Permutation of treatment labels and Threshold Indicator Taxa ANalysis
[version 1; peer review: 1 approved, 1 not approved]
Peer Reviewers
Cajo J. F. ter Braak;
Jonathan A Walter
- Funder
- U.S. Environmental Protection Agency
Software Tool Article
metrics
AWAITING PEER REVIEW
PressPurt: network sensitivity to press perturbations under interaction uncertainty
[version 1; peer review: awaiting peer review]
Peer Reviewers
Invited
- Funder
- National Science Foundation
Research Article
metrics
Quantification of the effects of chimerism on read mapping, differential expression and annotation following short-read de novo assembly.
[version 1; peer review: 2 approved with reservations]
Peer Reviewers
Ben J. Mans;
Kun Lu Lu
- Funder
- Fundacão para a Ciência e a Tecnologia (FCT)
Software Tool Article
metrics
ProSGPV: an R package for variable selection with second-generation p-values
[version 1; peer review: 1 approved, 1 approved with reservations]
Peer Reviewers
Georg Heinze;
Enrico Ripamonti
Software Tool Article
metrics
skater: an R package for SNP-based kinship analysis, testing, and evaluation
[version 1; peer review: 2 approved, 1 approved with reservations]
Peer Reviewers
Wei-Min Chen;
Magnus Dehli Vigeland;
Amy L. Williams
- Funder
- National Institute of Justice
Method Article
metrics
Revised
Space-log: a novel approach to inferring gene-gene net-works using SPACE model with log penalty
[version 2; peer review: 2 approved, 1 approved with reservations]
Peer Reviewers
Yuying Xie and Yuning Hao;
Chi Song;
Jessie Jeng
- Funder
- National Institutes of Health
Software Tool Article
metrics
Revised
RNfuzzyApp: an R shiny RNA-seq data analysis app for visualisation, differential expression analysis, time-series clustering and enrichment analysis
[version 2; peer review: 3 approved]
Peer Reviewers
Oliver Hahn;
Rhonda Bacher;
Anita Grigoriadis
- Funder
- Agence Nationale de la Recherche
Software Tool Article
metrics
Revised
rmcorrShiny: A web and standalone application for repeated measures correlation
[version 2; peer review: 2 approved]
Peer Reviewers
Ronan McGarrigle;
Emmeke Aarts and Sebastian Mildiner Moraga
Software Tool Article
metrics
Revised
FDRestimation: Flexible False Discovery Rate Computation in R
[version 2; peer review: 2 approved]
Peer Reviewers
Ted Westling and Yujian Wu;
David Colquhoun
Software Tool Article
metrics
SureTypeSCR: R package for rapid quality control and genotyping of SNP arrays from single cells
[version 1; peer review: 1 approved, 2 approved with reservations]
Peer Reviewers
Joris Robert Vermeesch;
Jason Torres;
Kun Lu Lu
- Funders
- Danmarks Grundforskningsfond
- European Research Council
- Novo Nordisk Fonden
Method Article
metrics
Revised
CODECHECK: an Open Science initiative for the independent execution of computations underlying research articles during peer review to improve reproducibility
[version 2; peer review: 2 approved]
Peer Reviewers
Nicolas P. Rougier;
Sarah Gibson
- Funders
- German Research Foundation
- Mozilla Foundation
- Sustainable Software Institute
Software Tool Article
metrics
Revised
iCAT: diagnostic assessment tool of immunological history using high-throughput T-cell receptor sequencing
[version 2; peer review: 2 approved]
Peer Reviewers
Shuo-Wang Qiao and Ying Yao;
Se-Ran Jun
- Funder
- Federal Bureau of Investigations
Software Tool Article
metrics
Revised
o2geosocial: Reconstructing who-infected-whom from routinely collected surveillance data
[version 2; peer review: 1 approved, 2 approved with reservations]
Peer Reviewers
Paige B. Miller;
Eben Kenah;
Gerry Tonkin Hill
- Funders
- Wellcome Trust Senior Research Fellowship in Basic Biomedical Science
- Medical Research Council
- Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society
Software Tool Article
metrics
Exploiting the DepMap cancer dependency data using the depmap R package
[version 1; peer review: 2 approved with reservations]
Peer Reviewers
Katharina Imkeller;
Ashir Borah and James M. McFarland
- Funder
- Université Catholique de Louvain
Software Tool Article
metrics
Revised
HPAStainR: a Bioconductor and Shiny app to query protein expression patterns in the Human Protein Atlas
[version 2; peer review: 3 approved]
Peer Reviewers
Mazdak Salavati;
Laurent Gatto;
Yasin Kaymaz
- Funders
- National Heart, Lung, and Blood Institute
- National Institutes of Health
Software Tool Article
metrics
Revised
Umpire 2.0: Simulating realistic, mixed-type, clinical data for machine learning
[version 2; peer review: 1 approved, 1 approved with reservations]
Peer Reviewers
Julia Wrobel;
Justin Mower and Andrew Zimolzak
- Funders
- National Center for Advancing Translational Sciences
- National Cancer Institute
Software Tool Article
metrics
Revised
TreeSummarizedExperiment: a S4 class for data with hierarchical structure
[version 2; peer review: 3 approved]
Peer Reviewers
Leo Lahti;
Shila Ghazanfar;
Matthew Ritchie
- Funders
- University Research Priority Program Evolution in Action at the University of Zurich
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
- Chan Zuckerberg Initiative DAF