Bioinformatics

Bioinformatics

Methods and Tools

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 in 
https://doi.org/10.12688/f1000research.175540.1
Software Tool Article metrics AWAITING PEER REVIEW
Workflow graphical editor and translator to Nextflow
[version 1; peer review: awaiting peer review]
Ilya Kiselev, Anna Ryabova, Fedor Kolpakov
Peer Reviewers Invited
  • Funder
  • «Sirius» Federal Territory
PUBLISHED 29 Jan 2026
https://doi.org/10.12688/f1000research.173901.1
Method Article metrics AWAITING PEER REVIEW
From Quality Control to Visualization: scToolkit for Reproducible Single-Cell RNA-Seq
[version 1; peer review: awaiting peer review]
Christopher Krolla, Tonmoy Das, Ariane Metzger, Melanie Boerries, Sajib Chakraborty, Geoffroy Andrieux
Peer Reviewers Invited
  • Funders
  • Bundesministerium für Bildung und Forschung
  • Deutsche Forschungsgemeinschaft
PUBLISHED 28 Jan 2026
https://doi.org/10.12688/f1000research.170680.2
Review metrics
Revised
Integrating spatial omics with routine haematoxylin and eosin in formalin-fixed paraffin-embedded: a step-by-step clinical workflow
[version 2; peer review: 1 approved, 1 approved with reservations]
Nasar Alwahaibi
Peer Reviewers Marie-Liesse Asselin-Labat; Da-Wei Yang
  • Funder
  • None
LATEST VERSION PUBLISHED 19 Jan 2026
https://doi.org/10.12688/f1000research.176328.1
Software Tool Article metrics AWAITING PEER REVIEW
MorphoCloud: Democratizing Access to High-Performance Computing for Morphological Data Analysis
[version 1; peer review: awaiting peer review]
A. Murat Maga, Jean-Christophe Fillion-Robin
Peer Reviewers Invited
  • Funders
  • Directorate for Biological Sciences
  • National Institutes of Health
PUBLISHED 14 Jan 2026
https://doi.org/10.12688/f1000research.175162.1
Software Tool Article metrics AWAITING PEER REVIEW
Spotsweeper-py: spatially-aware quality control metrics for spatial omics data in the Python ecosystem
[version 1; peer review: awaiting peer review]
Xingyi Chen, Michael Totty, Stephanie Hicks
Peer Reviewers Invited
  • Funders
  • National Institute of Mental Health
  • National Institute of General Medical Sciences
PUBLISHED 09 Jan 2026
https://doi.org/10.12688/f1000research.173844.1
Research Article metrics
Insights into the Datasets, Tools, and Training Needs of the AnVIL Community: 2024
[version 1; peer review: 1 approved with reservations]
Kathryn J. Isaac, Katherine E. L. Cox, Kai Yin Ho, Elizabeth M. Humphries, Natalie Kucher, Jeffrey T. Leek, Stephen Mosher, Michael C. Schatz, Frederick J. Tan, Ava M. Hoffman
Peer Reviewers Hassan Rehan
  • Funder
  • National Institutes of Health, National Human Genome Research Institute
PUBLISHED 22 Dec 2025
https://doi.org/10.12688/f1000research.165281.1
Software Tool Article metrics
DataMap: A Browser-based App for Visualizing High-Dimensional Data
[version 1; peer review: 1 approved with reservations]
Xijin Ge
Peer Reviewers Guangchuang Yu
  • Funders
  • National Institute of General Medical Sciences
  • National Human Genome Research Institute
PUBLISHED 10 Nov 2025
https://doi.org/10.12688/f1000research.171468.1
Software Tool Article metrics
DTAShiny: An Interactive R Shiny Application for Diagnostic Test Accuracy Analysis and Visualization
[version 1; peer review: 3 approved with reservations]
Syed Faizaan Shah Quadri, Ahmad Mahmood, Joanne Lac
Peer Reviewers Christos Nakas; Budi Sunaryo; Pedro Castaneda
PUBLISHED 30 Oct 2025
https://doi.org/10.12688/f1000research.171282.1
Research Article metrics
’Spanscriptomics’: towards bioinformatics training materials in Spanish.
[version 1; peer review: 2 approved with reservations]
Jurgi Giraud, Stefana Dreptate, Wendi Bacon, The Galaxy Community
Peer Reviewers Carlos C. Goller; Wei Ruan
  • Funder
  • Company of Biologists
PUBLISHED 20 Oct 2025
https://doi.org/10.12688/f1000research.129581.2
Software Tool Article metrics
Revised
AmpSeqR: an R package for amplicon deep sequencing data analysis
[version 2; peer review: 3 approved]
Jiru Han, Jacob E. Munro, Melanie Bahlo
Peer Reviewers Eduardo Castro-Nallar; Cristian Koepfli and Gustavo Da Silva; Patrick Murigu Kamau Njage
  • Funders
  • Institute Infrastructure Support Scheme (IRIISS)
  • National Health and Medical Research Council
LATEST VERSION PUBLISHED 17 Oct 2025
https://doi.org/10.12688/f1000research.168245.1
Software Tool Article metrics AWAITING PEER REVIEW
Computational Modeling and Visualization of Ischemic Effects on an Advanced Purkinje Network
[version 1; peer review: awaiting peer review]
Laiba Khan, Maham khan, Nijat Rzayev, Mahmood Ahmad, Joanne Lac
Peer Reviewers Invited
PUBLISHED 18 Sep 2025
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.160063.2
Software Tool Article metrics
Revised
mimicINT: A workflow for microbe-host protein interaction inference
[version 2; peer review: 2 approved, 1 approved with reservations]
Sébastien A. Choteau, Kevin Maldonado, Aurélie Bergon, Marceau Cristianini, Mégane Boujeant, Lilian Drets, Christine Brun, Lionel Spinelli, Andreas Zanzoni
Peer Reviewers Ylva Ivarsson; Sobia Idrees; Leandro Simonetti
  • Funders
  • Excellence Initiative of Aix-Marseille University - A*MIDEX
  • Agence Nationale de la Recherche
  • Fondation pour la Recherche Médicale
  • European Union’s Horizon 2020 Research and Innovation Programme
LATEST VERSION PUBLISHED 28 Mar 2025
https://doi.org/10.12688/f1000research.162719.1
Software Tool Article metrics
The EpiFusion Analysis Framework for joint phylodynamic and epidemiological analysis of outbreak characteristics
[version 1; peer review: 2 approved, 1 approved with reservations]
Ciara Judge, Oliver Brady, Sarah Hill
Peer Reviewers Vijaykrishna Dhanasekaran and Ruopeng Xie; Claire Guinat; Leo A Featherstone
  • Funders
  • National Universities of Ireland Denis Phelan Scholarship
  • Medical Research Council
  • Wellcome Trust
  • Bloomsbury Colleges PhD Studentship
PUBLISHED 28 Mar 2025
https://doi.org/10.12688/f1000research.161076.1
Software Tool Article metrics
ShinyCellPlus: an improved ShinyCell application for the interactive visualization of single cell dat
[version 1; peer review: 2 approved with reservations]
Drew Moore, Bryan Granger, Stefano Berto
Peer Reviewers Valdemaras Petrošius; Pierre-Luc Germain
  • Funder
  • National Institute of General Medical Sciences
PUBLISHED 27 Mar 2025
https://doi.org/10.12688/f1000research.127142.3
Software Tool Article metrics
Revised
Med-ImageTools: An open-source Python package for robust data processing pipelines and curating medical imaging data
[version 3; peer review: 2 approved]
Sejin Kim, Michal Kazmierski, Kevin Qu, Jacob Peoples, Minoru Nakano, Vishwesh Ramanathan, Joseph Marsilla, Mattea Welch, Amber Simpson, Benjamin Haibe-Kains
Peer Reviewers Rachel Sparks; Johann Faouzi
  • Funders
  • Canadian Cancer Society
  • Canadian Institutes of Health Research
LATEST VERSION PUBLISHED 07 Feb 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.130618.2
Research Article metrics
Revised
In silico molecular docking and molecular dynamic simulation of agarwood compounds with molecular targets of Alzheimer’s disease 
[version 2; peer review: 3 approved, 1 not approved]
Phaniendra Alugoju, Vishwambar Vishnu Bhandare, Vishal S. Patil, Krishna Swamy V. K. D, Prem Kumar Borugadda, Tewin Tencomnao
Peer Reviewers Sailu Sarvagalla; Yassir Boulaamane and Iman Touati; Abdul Rajjak Shaikh; James Adams
  • Funder
  • Thailand Science Research and Innovation Fund Chulalongkorn University
LATEST VERSION PUBLISHED 16 Dec 2024
https://doi.org/10.12688/f1000research.73999.3
Research Article metrics
Revised
A computational biology approach for the identification of potential SARS-CoV-2 main protease inhibitors from natural essential oil compounds.
[version 3; peer review: 2 approved, 1 approved with reservations]
Rizone Al Hasib, Md. Chayan Ali, Md. Shahedur Rahman, Md. Mafizur Rahman, Fee Faysal Ahmed, Md. Abdullah Al Mashud, Md. Azizul Islam, Mohammad Abu Hena Mostofa Jamal
Peer Reviewers Thi Thanh Binh Nguyen; Rituraj Purohit; Behrooz sadeghi kalani
  • Funder
  • Ministry of Science and Technology, Government of the People’s Republic of Bangladesh
LATEST VERSION PUBLISHED 07 Oct 2024
https://doi.org/10.12688/f1000research.152290.2
Software Tool Article metrics
Revised
Metagenome quality metrics and taxonomical annotation visualization through the integration of MAGFlow and BIgMAG
[version 2; peer review: 2 approved, 1 approved with reservations]
Jeferyd Yepes-García, Laurent Falquet
Peer Reviewers Abraham Gihawi; Fotis Baltoumas; Juliette Hayer
  • Funders
  • Centenary Research Fund of the University of Fribourg
  • Fondation de Recherche en Biochimie, Epalinges, Switzerland
LATEST VERSION PUBLISHED 23 Sep 2024
1-20 of 81 ARTICLES
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  • 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
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    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
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    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
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    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
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    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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