Bioinformatics

Bioinformatics

Transcriptomics

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1-18 of 18 ARTICLES
 in 
https://doi.org/10.12688/f1000research.155223.2
Review metrics
Revised
Selecting differential splicing methods: Practical considerations for short-read RNA sequencing
[version 2; peer review: 2 approved, 3 approved with reservations]
Ben J. Draper, Mark J. Dunning, David C. James
Peer Reviewers Stefano Donega; Charlotte Capitanchik; Julia Olivieri; Zhaoqi Liu; Monica Salinas and Juan Valcarcel
  • Funders
  • Lonza Biologics plc
  • University of Sheffield
LATEST VERSION PUBLISHED 30 May 2025
https://doi.org/10.12688/f1000research.153698.1
Software Tool Article metrics
scRICA: An R package for multiple-sample single-cell RNA-seq data integrative comparative analysis
[version 1; peer review: 1 approved with reservations, 1 not approved]
Yan Li, Jason Shapiro, Qiaoshan Lin, Qing Gong, Michiko Ryu, Mengjie Chen
Peer Reviewers Pedro L Baldoni; Sebastiaan Valkiers
  • Funders
  • University of Chicago
  • National Institutes of Health
  • Institute for Translational Medicine
PUBLISHED 20 Jan 2025
https://doi.org/10.12688/f1000research.149237.1
Software Tool Article metrics
ZARP: A user-friendly and versatile RNA-seq analysis workflow
[version 1; peer review: 2 approved with reservations]
Maria Katsantoni, Foivos Gypas, Christina J Herrmann, Dominik Burri, Maciej Bąk, Paula Iborra, Krish Agarwal, Meriç Ataman, Máté Balajti, Noè Pozzan, Niels Schlusser, Youngbin Moon, Aleksei Mironov, Anastasiya Börsch, Mihaela Zavolan, Alexander Kanitz
Peer Reviewers Silvia Liu; Bo Li
  • Funders
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
  • National Center of Competence in Research RNA & Disease
PUBLISHED 24 May 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.126215.2
Method Article metrics
Revised
Bayesian Multi-View Clustering given complex inter-view structure
[version 2; peer review: 2 approved]
Benjamin D. Shapiro, Alexis Battle
Peer Reviewers Sara Mostafavi; Max Moldovan
  • Funders
  • Microsoft
  • National Institute of General Medical Sciences
LATEST VERSION PUBLISHED 29 Feb 2024
https://doi.org/10.12688/f1000research.131861.2
Research Article metrics
Revised
Single-cell transcriptional uncertainty landscape of cell differentiation
[version 2; peer review: 2 approved]
Nan Papili Gao, Olivier Gandrillon, András Páldi, Ulysse Herbach, Rudiyanto Gunawan
Peer Reviewers Alessandro Giuliani; Geneviève Dupont
  • Funders
  • Swiss National Science Foundation
  • Agence Nationale de la Recherche
LATEST VERSION PUBLISHED 20 Jul 2023
https://doi.org/10.12688/f1000research.122949.2
Software Tool Article metrics
Revised
DEVEA: an interactive shiny application for Differential Expression analysis, data Visualization and Enrichment Analysis of transcriptomics data
[version 2; peer review: 2 approved]
Miriam Riquelme-Perez, Fernando Perez-Sanz, Jean-François Deleuze, Carole Escartin, Eric Bonnet, Solène Brohard
Peer Reviewers Hélène Hirbec; Wenbin Guo
  • Funder
  • PhD fellowship from the CEA (Amont-Aval).
LATEST VERSION PUBLISHED 24 Mar 2023
https://doi.org/10.12688/f1000research.110492.2
Research Article metrics
Revised
From head to rootlet: comparative transcriptomic analysis of a rhizocephalan barnacle Peltogaster reticulata (Crustacea: Rhizocephala)
[version 2; peer review: 2 approved]
Maksim Nesterenko, Aleksei Miroliubov
Peer Reviewers Andreas Hejnol and Ferenc Kagan; Viatcheslav Ivanenko
  • Funder
  • Russian Science Foundation
LATEST VERSION PUBLISHED 09 Jan 2023
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.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.111175.2
Software Tool Article metrics
Revised
DSMZCellDive: Diving into high-throughput cell line data
[version 2; peer review: 2 approved]
Julia Koblitz, Wilhelm G. Dirks, Sonja Eberth, Stefan Nagel, Laura Steenpass, Claudia Pommerenke
Peer Reviewers Beate Rinner; Arihiro Kohara
  • Funder
  • Leibniz SAW project DiASPora
LATEST VERSION PUBLISHED 20 Jul 2022
https://doi.org/10.12688/f1000research.75321.1
Method Article metrics
Improving prediction of core transcription factors for cell reprogramming and transdifferentiation
[version 1; peer review: 2 not approved]
Mikhail Raevskiy, Anna Kondrashina, Yulia Medvedeva
Peer Reviewers Valentiva Boeva and Samuel Gunz; Erdem B. Dashinimaev
  • Funder
  • Ministry of Science and Higher Education of the Russian Federation
PUBLISHED 13 Jan 2022
https://doi.org/10.12688/f1000research.74836.1
Method Article metrics
Slinker: Visualising novel splicing events in RNA-Seq data
[version 1; peer review: 3 approved]
Breon Schmidt, Marek Cmero, Paul Ekert, Nadia Davidson, Alicia Oshlack
Peer Reviewers George Wiggins; Stephen Montgomery; Amy Huei-Yi Lee
  • Funder
  • NHMRC
PUBLISHED 07 Dec 2021
https://doi.org/10.12688/f1000research.28142.2
Software Tool Article metrics
Revised
MIREyA: a computational approach to detect miRNA-directed gene activation
[version 2; peer review: 1 approved, 2 approved with reservations]
Anna Elizarova, Mumin Ozturk, Reto Guler, Yulia A. Medvedeva
Peer Reviewers Michiel Jan Laurens De Hoon; Xiangfu Zhong; Chaogang Shao
  • Funders
  • European and Developing Countries Clinical Trials Partnership
  • Russian Foundation for Basic Research
  • South Africa National Research Foundation
LATEST VERSION PUBLISHED 26 Aug 2021
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.25148.2
Research Article metrics
Revised
First draft genome assembly of the desert locust, Schistocerca gregaria
[version 2; peer review: 3 approved]
Heleen Verlinden, Lieven Sterck, Jia Li, Zhen Li, Anna Yssel, Yannick Gansemans, Rik Verdonck, Michiel Holtof, Hojun Song, Spencer T. Behmer, Gregory A. Sword, Tom Matheson, Swidbert R. Ott, Dieter Deforce, Filip Van Nieuwerburgh, Yves Van de Peer, Jozef Vanden Broeck
Peer Reviewers Uwe Homberg; Surya Saha; Joshua B. Benoit
  • Funders
  • U.S. Department of Agriculture
  • University of Pretoria
  • KU Leuven
  • Fonds Wetenschappelijk Onderzoek
  • Universiteit Gent
  • Biotechnology and Biological Sciences Research Council
  • National Science Foundation
LATEST VERSION PUBLISHED 21 May 2021
https://doi.org/10.12688/f1000research.40668.1
Software Tool Article metrics
RP-REP Ribosomal Profiling Reports: an open-source cloud-enabled framework for reproducible ribosomal profiling data processing, analysis, and result reporting
[version 1; peer review: 2 approved]
Travis L. Jensen, William F. Hooper, Sami R. Cherikh, Johannes B. Goll
Peer Reviewers Molly Hannigan and Christopher Nicchitta; Jordan A. Berg
  • Funders
  • The Emmes Company
  • National Institutes of Allergy and Infectious Disease
PUBLISHED 24 Feb 2021
https://doi.org/10.12688/f1000research.24163.2
Method Article metrics
Revised
Spatial mapping of single cells in the Drosophila embryo from transcriptomic data based on topological consistency
[version 2; peer review: 2 approved]
Maryam Zand, Jianhua Ruan
Peer Reviewers Tianci Song and Rui Kuang; Adi Tarca
  • Funders
  • National Institutes of Health
  • National Science Foundation
LATEST VERSION PUBLISHED 09 Feb 2021
1-18 of 18 ARTICLES
Gateway Areas
  • Methods and Tools
    The Methods and Tools Gateway Area will allow researchers to publish outputs concerning both the application and research into the use of various computational methods to analyse quantities of biological data for a range of different results, including predictions and discoveries. Read more keyboard_arrow_right
  • Genetics and Genomics
    The Genetics & Genomics Gateway Area will enable researchers to publish content related to the analysis, storage and accessibility of DNA, RNA and protein sequences. This analysis can be conducted in a variety of ways, including comparison of sequences and relationships, identification of functions, and recognition of patterns across the samples. Read more keyboard_arrow_right
  • Transcriptomics
    By curating all outputs related to the analysis of the RNA transcripts produced by a genotype, the Transcriptomics Gateway Area will allow readers to easily access content pertinent to this research. Read more keyboard_arrow_right
  • Proteomics
    The Proteomics Gateway Area has been established to allow authors to access and publish research content related to the large-scale study of entire sets of proteins as proteomes. Read more keyboard_arrow_right
  • Metagenomics
    This Gateway Area will allow members of the bioinformatics community to collate all research related to the collection of genomes from an environmental sample. Read more keyboard_arrow_right
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