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1-20 of 86 ARTICLES
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Featured Article
https://doi.org/10.12688/f1000research.24345.2
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Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz
[version 2; peer review: 3 approved]
Justin Wagner, Jayaram Kancherla, Domenick Braccia, James Matsumara, Victor Felix, Jonathan Crabtree, Anup Mahurkar, Héctor Corrada Bravo
Peer Reviewers Ekaterina Smirnova; Edoardo Pasolli; Levi Waldron
  • Funder
  • National Institutes of Health
LATEST VERSION PUBLISHED 21 Jun 2021
https://doi.org/10.12688/f1000research.168810.1
Software Tool Article metrics AWAITING PEER REVIEW
CBN2Path: an R/Bioconductor package for the analysis of cancer progression pathways using Conjunctive Bayesian Networks
[version 1; peer review: awaiting peer review]
William Choi-Kim, Sayed-Rzgar Hosseini
Peer Reviewers Invited
  • Funder
  • STPRZG
PUBLISHED 29 Aug 2025
https://doi.org/10.12688/f1000research.165543.1
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An updated Bioconductor workflow for correlation profiling subcellular proteomics
[version 1; peer review: 2 approved]
Charlotte Hutchings, Thomas Krueger, Oliver M Crook, Laurent Gatto, Kathryn S Lilley, Lisa M Breckels
Peer Reviewers Yu-Ping Poh and Jeremy G Wideman; Vanya Bhushan
  • Funders
  • Research Foundation Flanders (FWO)
  • BBSRC CASE award with AstraZeneca
  • Medical Research Council
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 21 Jul 2025
https://doi.org/10.12688/f1000research.155204.2
Software Tool Article metrics
Revised
A streamlined workflow for long-read DNA methylation analysis with NanoMethViz and Bioconductor
[version 2; peer review: 2 approved]
Shian Su, Lucinda Xiao, James Lancaster, Tamara Cameron, Kelsey Breslin, Peter F. Hickey, Marnie E. Blewitt, Quentin Gouil, Matthew E. Ritchie
Peer Reviewers Keegan Korthauer; Tim Triche Jr
  • Funders
  • National Health and Medical Research Council
  • Medical Research Future Fund
LATEST VERSION PUBLISHED 24 Feb 2025
https://doi.org/10.12688/f1000research.153949.1
Method Article metrics
A Bioconductor/R Workflow for the Detection and Visualization of Differential Chromatin Loops
[version 1; peer review: 3 approved, 1 approved with reservations]
JP Flores, Eric Davis, Nicole Kramer, Michael I Love, Douglas H Phanstiel
Peer Reviewers Benjamin Soibam; Vanessa Vermeirssen; Raúl de Haro Blázquez; Frank Johannes and Luca Schlegel
  • Funders
  • National Science Foundation Graduate Research Fellowship Program
  • National Institutes of Health
  • Wellcome Trust
  • Chan Zuckerberg Initiative
  • Howard Hughes Medical Institute Gilliam Fellows Program
PUBLISHED 11 Nov 2024
https://doi.org/10.12688/f1000research.155449.1
Software Tool Article metrics
AnVILWorkflow: A runnable workflow package for Cloud-implemented bioinformatics analysis pipelines
[version 1; peer review: 2 approved]
Sehyun Oh, Kai Gravel-Pucillo, Marcel Ramos, Michael C. Schatz, Sean Davis, Vincent Carey, Martin Morgan, Levi Waldron
Peer Reviewers Fabricio Almeida-Silva; Zachary S.L Foster
  • Funder
  • National Human Genome Research Institute
PUBLISHED 21 Oct 2024
https://doi.org/10.12688/f1000research.139116.2
Software Tool Article metrics
Revised
A Bioconductor workflow for processing, evaluating, and interpreting expression proteomics data
[version 2; peer review: 4 approved, 1 approved with reservations]
Charlotte Hutchings, Charlotte S. Dawson, Thomas Krueger, Kathryn S. Lilley, Lisa M. Breckels
Peer Reviewers Diogo Borges Lima; Marie Locard-Paulet; Amit Kumar Yadav; Giai Gianetto Quentin; Julian Bender
  • Funders
  • Herchel Smith Research Studentship
  • Gordon and Betty Moore Foundation
  • Horizon 2020
  • AstraZeneca
  • Wellcome Trust
  • Biotechnology and Biological Sciences Research Council
LATEST VERSION PUBLISHED 25 Sep 2024
https://doi.org/10.12688/f1000research.149494.1
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sSNAPPY: an R/Bioconductor package for single-sample directional pathway perturbation analysis
[version 1; peer review: 2 approved with reservations]
Wenjun Liu, Ville-Petteri Mäkinen, Wayne D Tilley, Stephen M Pederson
Peer Reviewers Dario Strbenac; Panagiotis Moulos
  • Funders
  • National Health and Medical Research Council
  • National Breast Cancer Foundation
PUBLISHED 13 Jun 2024
https://doi.org/10.12688/f1000research.74416.2
Software Tool Article metrics
Revised
BASiCS workflow: a step-by-step analysis of expression variability using single cell RNA sequencing data
[version 2; peer review: 1 approved, 2 approved with reservations]
Alan O'Callaghan, Nils Eling, John C. Marioni, Catalina A. Vallejos
Peer Reviewers Oliver M. Crook; Andrew McDavid; Michel S Naslavsky
  • Funders
  • Cancer Research UK
  • University of Edinburgh
  • European Molecular Biology Laboratory
LATEST VERSION PUBLISHED 07 May 2024
https://doi.org/10.12688/f1000research.134078.2
Method Article metrics
Revised
Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data
[version 2; peer review: 2 approved, 1 approved with reservations]
Jinming Cheng, Gordon K. Smyth, Yunshun Chen
Peer Reviewers Michael D Morgan; Koen Van den berge; Anna Alemany, Xuan Quy Nguyen and Noëlle Dommann
  • Funders
  • National Health and Medical Research Council
  • Chan Zuckerberg Initiative
  • Medical Research Future Fund
LATEST VERSION PUBLISHED 10 Nov 2023
https://doi.org/10.12688/f1000research.128354.1
Method Article metrics
BOREALIS: an R/Bioconductor package to detect outlier methylation from bisulfite sequencing data
[version 1; peer review: 2 approved with reservations]
Gavin R. Oliver, W. Garrett Jenkinson, Rory J. Olson, Laura E. Schultz-Rogers, Eric W. Klee
Peer Reviewers Philipp Jurmeister and Maximilian Leitheiser; Vicente Yepez
  • Funder
  • Center for Individualized Medicine, Mayo Clinic
PUBLISHED 20 Dec 2022
https://doi.org/10.12688/f1000research.51749.2
Method Article metrics
Revised
satuRn: Scalable analysis of differential transcript usage for bulk and single-cell RNA-sequencing applications
[version 2; peer review: 2 approved]
Jeroen Gilis, Kristoffer Vitting-Seerup, Koen Van den Berge, Lieven Clement
Peer Reviewers Marek Cmero; Alejandro Reyes
  • Funders
  • Belgian American Educational Foundation
  • Fonds Wetenschappelijk Onderzoek
LATEST VERSION PUBLISHED 08 Aug 2022
https://doi.org/10.12688/f1000research.26073.2
Method Article metrics
Revised
An R-based reproducible and user-friendly preprocessing pipeline for CyTOF data
[version 2; peer review: 2 approved]
Helena L. Crowell, Stéphane Chevrier, Andrea Jacobs, Sujana Sivapatham, Tumor Profiler Consortium, Bernd Bodenmiller, Mark D. Robinson
Peer Reviewers Marie Trussart; Felix Hartmann and Sean C. Bendall
  • Funders
  • Universitätsspital Basel
  • Universitätsspital Zürich
  • Roche
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
  • Universität Zürich
LATEST VERSION PUBLISHED 08 Aug 2022
https://doi.org/10.12688/f1000research.52173.4
Software Tool Article metrics
Revised
target: an R package to predict combined function of transcription factors
[version 4; peer review: 1 approved, 1 approved with reservations]
Mahmoud Ahmed, Deok Ryong Kim
Peer Reviewers Shulan Tian and Yan Huihuang; Mireia Ramos-Rodríguez
  • Funder
  • National Research Foundation of Korea
LATEST VERSION PUBLISHED 03 Aug 2022
https://doi.org/10.12688/f1000research.73600.2
Software Tool Article metrics
Revised
Doublet identification in single-cell sequencing data using scDblFinder
[version 2; peer review: 2 approved]
Pierre-Luc Germain, Aaron Lun, Carlos Garcia Meixide, Will Macnair, Mark D. Robinson
Peer Reviewers Zev J. Gartner and Chris McGinnis; Dennis Kostka and Hannah Schriever
  • Funder
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
LATEST VERSION PUBLISHED 16 May 2022
https://doi.org/10.12688/f1000research.27868.3
Method Article metrics
Revised
WIND (Workflow for pIRNAs aNd beyonD): a strategy for in-depth analysis of small RNA-seq data
[version 3; peer review: 2 approved]
Konstantinos Geles, Domenico Palumbo, Assunta Sellitto, Giorgio Giurato, Eleonora Cianflone, Fabiola Marino, Daniele Torella, Valeria Mirici Cappa, Giovanni Nassa, Roberta Tarallo, Alessandro Weisz, Francesca Rizzo
Peer Reviewers Juan Pablo Tosar; Wen Yao
  • Funders
  • Italian Association for Cancer Research
  • Ministero dell’Istruzione, dell’Università e della Ricerca
  • Horizon 2020
  • Regione Campania
LATEST VERSION PUBLISHED 12 Jul 2021
https://doi.org/10.12688/f1000research.52811.1
Software Tool Article metrics
Exploiting the DepMap cancer dependency data using the depmap R package
[version 1; peer review: 2 approved with reservations]
Theo Killian, Laurent Gatto
Peer Reviewers Katharina Imkeller; Ashir Borah and James M. McFarland
  • Funder
  • Université Catholique de Louvain
PUBLISHED 25 May 2021
https://doi.org/10.12688/f1000research.26771.2
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]
Tim O. Nieuwenhuis, Marc K. Halushka
Peer Reviewers Mazdak Salavati; Laurent Gatto; Yasin Kaymaz
  • Funders
  • National Heart, Lung, and Blood Institute
  • National Institutes of Health
LATEST VERSION PUBLISHED 22 Mar 2021
https://doi.org/10.12688/f1000research.26669.2
Software Tool Article metrics
Revised
TreeSummarizedExperiment: a S4 class for data with hierarchical structure
[version 2; peer review: 3 approved]
Ruizhu Huang, Charlotte Soneson, Felix G.M. Ernst, Kevin C. Rue-Albrecht, Guangchuang Yu, Stephanie C. Hicks, Mark D. Robinson
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
LATEST VERSION PUBLISHED 02 Mar 2021
https://doi.org/10.12688/f1000research.51143.1
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]
Jacques Serizay, Julie Ahringer
Peer Reviewers Ilya Ioshikhes; Sabarinathan Radhakrishnan; Eugene Korotkov; Boris Lenhard
  • Funders
  • Wellcome Trust Senior Research Fellowship
  • Medical Research Council DTP studentship
PUBLISHED 24 Feb 2021
1-20 of 86 ARTICLES
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