Bioinformatics

Bioinformatics

Methods and Tools

track_changes Track Tracking Be alerted when new articles are added in this gateway (manage your tracking alerts via your account) Stop tracking this gateway
Home Gateways Bioinformatics
61-80 of 81 ARTICLES
Previous Next
 in 
https://doi.org/10.12688/f1000research.76004.1
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]
Stephen D. Turner, V.P. Nagraj, Matthew Scholz, Shakeel Jessa, Carlos Acevedo, Jianye Ge, August E. Woerner, Bruce Budowle
Peer Reviewers Wei-Min Chen; Magnus Dehli Vigeland; Amy L. Williams
  • Funder
  • National Institute of Justice
PUBLISHED 07 Jan 2022
https://doi.org/10.12688/f1000research.73641.1
Software Tool Article metrics
PlotXpress, a webtool for normalization and visualization of reporter expression data
[version 1; peer review: 3 approved]
Elias Brandorff, Marc Galland, Joachim Goedhart
Peer Reviewers Lorena Pantano Rubino; Guillaume Jacquemet; Vincent J. Lynch
PUBLISHED 08 Nov 2021
https://doi.org/10.12688/f1000research.54159.1
Opinion Article metrics
Perspectives on automated composition of workflows in the life sciences
[version 1; peer review: 2 approved]
Anna-Lena Lamprecht, Magnus Palmblad, Jon Ison, Veit Schwämmle, Mohammad Sadnan Al Manir, Ilkay Altintas, Christopher J. O. Baker, Ammar Ben Hadj Amor, Salvador Capella-Gutierrez, Paulos Charonyktakis, Michael R. Crusoe, Yolanda Gil, Carole Goble, Timothy J. Griffin, Paul Groth, Hans Ienasescu, Pratik Jagtap, Matúš Kalaš, Vedran Kasalica, Alireza Khanteymoori, Tobias Kuhn, Hailiang Mei, Hervé Ménager, Steffen Möller, Robin A. Richardson, Vincent Robert, Stian Soiland-Reyes, Robert Stevens, Szoke Szaniszlo, Suzan Verberne, Aswin Verhoeven, Katherine Wolstencroft
Peer Reviewers Pinar Alper; Rafael Ferreira da Silva
  • Funder
  • European Commission Horizon 2020 Framework Programme
PUBLISHED 07 Sep 2021
https://doi.org/10.12688/f1000research.51755.2
Review metrics
Revised
Calcium imaging analysis – how far have we come?
[version 2; peer review: 3 approved]
Miranda Robbins, Charles N. Christensen, Clemens F. Kaminski, Marta Zlatic
Peer Reviewers Christopher Rowlands and Isabell Whiteley; William Zeiger; Anubhuti Goel
LATEST VERSION PUBLISHED 26 Aug 2021
https://doi.org/10.12688/f1000research.27214.2
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]
Ahmad Rajeh, Kyle Wolf, Courtney Schiebout, Nabeel Sait, Tim Kosfeld, Richard J. DiPaolo, Tae-Hyuk Ahn
Peer Reviewers Shuo-Wang Qiao and Ying Yao; Se-Ran Jun
  • Funder
  • Federal Bureau of Investigations
LATEST VERSION PUBLISHED 29 Jun 2021
https://doi.org/10.12688/f1000research.52460.1
Software Tool Article metrics
scNetViz: from single cells to networks using Cytoscape
[version 1; peer review: 2 approved]
Krishna Choudhary, Elaine C. Meng, J. Javier Diaz-Mejia, Gary D. Bader, Alexander R. Pico, John H. Morris
Peer Reviewers Luca Pinello; Kenji Kamimoto
  • Funders
  • National Resource for Network Biology
  • Chan Zuckerberg Initiative
PUBLISHED 07 Jun 2021
https://doi.org/10.12688/f1000research.50857.2
Brief Report metrics
Revised
Interactive SARS-CoV-2 mutation timemaps
[version 2; peer review: 3 approved]
René L. Warren, Inanc Birol
Peer Reviewers Ingo Ebersberger and Ruben Iruegas; Takahiko Koyama; Jale Moradi
  • Funders
  • National Institute for Health Research
  • Genome Canada
LATEST VERSION PUBLISHED 03 Jun 2021
https://doi.org/10.12688/f1000research.52141.1
Software Tool Article metrics AWAITING PEER REVIEW
Restriction site-associated DNA from Python-implemented Digestion Simulations (RApyDS): a companion tool for RAD sequencing experimental design
[version 1; peer review: awaiting peer review]
Kristianne Arielle Gabriel, Maria Rejane Nepacina, Francis Tablizo, Carlo Lapid, Mark Lenczner Mendoza, Daniella Jean Pamulaklakin, Jobeth Domingo, Marc Jermaine Pontiveros, Hannah Mae Magno, Joshua Gregor Dizon, El King Morado, Jan Michael Yap
Peer Reviewers Invited
  • Funder
  • Philippine Council for Industry, Energy and Emerging Technology Research and Development of the Department of Science and Technology
PUBLISHED 07 May 2021
https://doi.org/10.12688/f1000research.52531.1
Opinion Article metrics
Developing open-source software for bioimage analysis: opportunities and challenges
[version 1; peer review: 2 approved]
Florian Levet, Anne E. Carpenter, Kevin W. Eliceiri, Anna Kreshuk, Peter Bankhead, Robert Haase
Peer Reviewers Loïc A. Royer; Nico Stuurman
  • Funders
  • Deutsche Forschungsgemeinschaft
  • Institut National de la Santé et de la Recherche Médicale
  • National Institutes of Health
  • Chan Zuckerberg Initiative
PUBLISHED 19 Apr 2021
https://doi.org/10.12688/f1000research.27062.2
Software Tool Article metrics
Revised
SAPHIR: a Shiny application to analyze tissue section images
[version 2; peer review: 2 approved]
Elodie Germani, Hugues Lelouard, Mathieu Fallet
Peer Reviewers Mahmoud Ahmed; Seth Winfree
  • Funders
  • Agence Nationale de la Recherche
  • Aix-Marseille University
  • Fondation pour la Recherche Médicale
  • Centre National de la Recherche Scientifique and Institut National de la Santé et de la Recherche Médicale
LATEST VERSION PUBLISHED 08 Apr 2021
https://doi.org/10.12688/f1000research.25447.2
Software Tool Article metrics
Revised
DEVILS: a tool for the visualization of large datasets with a high dynamic range
[version 2; peer review: 2 approved]
Romain Guiet, Olivier Burri, Nicolas Chiaruttini, Olivier Hagens, Arne Seitz
Peer Reviewers Sebastien Tosi; Mehedi Masud
  • Funder
  • Norges Forskningsråd
LATEST VERSION PUBLISHED 22 Mar 2021
https://doi.org/10.12688/f1000research.51916.1
Software Tool Article metrics
CytoBrowser: a browser-based collaborative annotation platform for whole slide images
[version 1; peer review: 1 approved with reservations, 1 not approved]
Christopher Rydell, Joakim Lindblad
Peer Reviewers Simon Nørrelykke; Peter Bankhead
  • Funder
  • Sweden’s Innovation Agency, VINNOVA
PUBLISHED 22 Mar 2021
https://doi.org/10.12688/f1000research.50798.1
Software Tool Article metrics
Interactive biomedical segmentation tool powered by deep learning and ImJoy
[version 1; peer review: 1 approved, 1 approved with reservations]
Wei Ouyang, Trang Le, Hao Xu, Emma Lundberg
Peer Reviewers Jean-Yves Tinevez and Dmitry Ershov; Jan Funke
  • Funders
  • Knut and Alice Wallenberg Foundation
  • Swedish Research Council
  • LST Platform at KTH Royal Institute of Technology
PUBLISHED 24 Feb 2021
https://doi.org/10.12688/f1000research.26872.2
Software Tool Article metrics
Revised
Fiji plugins for qualitative image annotations: routine analysis and application to image classification
[version 2; peer review: 2 approved, 1 approved with reservations]
Laurent S. V. Thomas, Franz Schaefer, Jochen Gehrig
Peer Reviewers Jan Eglinger; Christian Tischer and Aliaksandr Halavatyi; Elisabet Teixido
  • Funder
  • Horizon 2020
LATEST VERSION PUBLISHED 12 Feb 2021
https://doi.org/10.12688/f1000research.25713.2
Software Tool Article metrics
Revised
VIRdb 2.0: Interactive analysis of comorbidity conditions associated with vitiligo pathogenesis using co-expression network-based approach
[version 2; peer review: 1 approved, 2 approved with reservations]
Priyansh Srivastava, Mehak Talwar, Aishwarya Yadav, Alakto Choudhary, Sabyasachi Mohanty, Samuel Bharti, Priyanka Narad, Abhishek Sengupta
Peer Reviewers Dinesh Gupta; Mitesh Dwivedi and Rasheedunnisa Begum; Animesh A Sinha
LATEST VERSION PUBLISHED 01 Feb 2021
https://doi.org/10.12688/f1000research.21782.4
Research Article metrics
Update
Benchmarking of long-read assemblers for prokaryote whole genome sequencing
[version 4; peer review: 4 approved]
Ryan R. Wick, Kathryn E. Holt
Peer Reviewers Aleksey V. Zimin and Steven Salzberg; Robert Vaser and Mile Šikić; Mikhail Kolmogorov; Olin Silander
  • Funders
  • Department of Education, Employment and Workplace Relations, Australian Government
  • Sylvia and Charles Viertel Charitable Foundation
  • Gates Foundation
LATEST VERSION PUBLISHED 01 Feb 2021
https://doi.org/10.12688/f1000research.21142.2
Software Tool Article metrics
Revised
Falco: high-speed FastQC emulation for quality control of sequencing data
[version 2; peer review: 2 approved]
Guilherme de Sena Brandine, Andrew D. Smith
Peer Reviewers R Henrik Nilsson; Weihong Qi
LATEST VERSION PUBLISHED 27 Jan 2021
https://doi.org/10.12688/f1000research.26429.2
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]
Shraddha Pai, Philipp Weber, Ruth Isserlin, Hussam Kaka, Shirley Hui, Muhammad Ahmad Shah, Luca Giudice, Rosalba Giugno, Anne Krogh Nøhr, Jan Baumbach, Gary D. Bader
Peer Reviewers Kim-Anh Lê Cao; Anais Baudot, Judith Lambert and Laurent Tichit
  • Funders
  • Villum Fonden
  • Horizon 2020
  • National Institutes of Health
LATEST VERSION PUBLISHED 22 Jan 2021
https://doi.org/10.12688/f1000research.24187.2
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]
Charlotte Soneson, Federico Marini, Florian Geier, Michael I. Love, Michael B. Stadler
Peer Reviewers Jean Fan; Lucy D'Agostino McGowan; Matthew Ritchie
  • Funders
  • National Institutes of Health
  • German Federal Ministry of Education and Research
LATEST VERSION PUBLISHED 16 Sep 2020
https://doi.org/10.12688/f1000research.18490.3
Research Article metrics
Revised
Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data
[version 3; peer review: 2 approved, 1 approved with reservations]
J. Javier Diaz-Mejia, Elaine C. Meng, Alexander R. Pico, Sonya A. MacParland, Troy Ketela, Trevor J. Pugh, Gary D. Bader, John H. Morris
Peer Reviewers Saskia Freytag; Jimmy Tsz Hang Lee and Tallulah Andrews; Lindsay Cowell
  • Funders
  • National Resource for Network Biology
  • Chan Zuckerberg Initiative
LATEST VERSION PUBLISHED 14 Oct 2019
61-80 of 81 ARTICLES
Previous Next
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
ISCB News and Announcements open_in_new
Our Links
Sign In
If you've forgotten your password, please enter your email address below and we'll send you instructions on how to reset your password.

The email address should be the one you originally registered with F1000.
Email address not valid, please try again

You registered with F1000 via Google, so we cannot reset your password.

To sign in, please click here.

If you still need help with your Google account password, please click here.

You registered with F1000 via Facebook, so we cannot reset your password.

To sign in, please click here.

If you still need help with your Facebook account password, please click here.

Code not correct, please try again
Email us for further assistance.
Server error, please try again.