5 years strong: The best of the Bioconductor Gateway
| 4 August, 2021 | Tom Sinden |
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It has been over five years since the launch of the Bioconductor Gateway on F1000Research and what an incredible five years it has been. The Gateway, which hosts task-oriented workflows, package-based vignettes, and more, continues to go from strength to strength.
As we reflect on this fifth-year anniversary of Bioconductor’s dedicated publishing hub for open bioinformatics research, we invite you to look back on just some of the Gateway’s most impactful research to date.
Most views and downloads
Bioconductor workflow for microbiome data analysis: from raw reads to community analyses
Ben J. Callahan, Kris Sankaran, Julia A. Fukuyama, Paul J. McMurdie, Susan P. Holmes
This Research Article gives a complete workflow for microbiome data analysis showcasing good statistical practice based on existing software packages available through Bioconductor. With clear explanations and step-by-step instructions, the workflow has become a useful resource for microbiome researchers looking to process their data. As a result, it has accumulated over 81,000 views and over 11,300 downloads since its publication.
A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor
Aaron T.L. Lun, Davis J. McCarthy, John C. Marioni
This Software Tool Article is another workflow broken down step-by-step, this time for low-level analysis of single-cell RNA-seq data. With analyses demonstrated on various publicly available datasets, the authors provide a range of scenarios for users to work from. This software tool is a valuable guide for the community and has amassed over 67,000 views and 10,700 downloads
Top on Twitter
Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences
Charlotte Soneson, Michael I. Love, Mark D. Robinson
Published in December 2015, this Method Article was one of the first to feature in the Bioconductor Gateway. It has been shared on Twitter by over 160 users. Importantly, it shows that gene-level abundance estimates and statistical inference, rather than transcript-level analyses, are superior in terms of performance and interpretation. With over 60,000 views and 10,000 downloads, it is perhaps no surprise that this article has accumulated over 1,500 citations on Dimensions since it was published.
Advisors’ picks
Tensor decomposition: A versatile method for heterogeneous biological data fusion
Koki Tsuyuzaki
“It’s great that F1000Research host the slides from different Bioconductor meetings, and these slides from Dr Koki Tsuyuzaki from RIKEN present a nice introduction to their recent Bioconductor packages scTensor & DelayedTensor.”
– Aedin Culhane, Co-chair – Bioconductor Community Advisory Board
These slides were presented at BiocAsia2020 and published in the Gateway in October 2020. They accompanied a presentation that introduced tensor decomposition as a potential unified framework to solve the problems of how best to represent heterogeneous datasets. Additionally, this presentation introduced virtual conference attendees to the DelayedTensor package: an out-of-core and sparse implementation of tensor format to tackle extremely large-scaled tensor data.
A cross-package Bioconductor workflow for analysing methylation array data
Jovana Maksimovic, Belinda Phipson, Alicia Oshlack
“The methylation workflow by Maksimovic et al. highlights how easy it is to analyze data from popular array-based technologies in Bioconductor. The authors use minfi, limma, DMRcate, missMethyl (which has a super cool logo!) together with various annotation and other supporting packages to demonstrate a complete beginning to end workflow for Infinium methylation arrays. I like this work because it reminds us that Bioconductor tools serve many applications beyond gene expression analysis.”
– Matt Ritchie, Co-chair – Bioconductor Community Advisory Board
This paper provides a workflow for Bioconductor users utilizing multiple packages for the analysis of methylation array data. As a result, this method article has been viewed over 18,000 times on both the F1000Research platform and PubMed Central. Additionally, the article was highlighted by the Bioconductor Community Advisory Board as a paper of value on the Gateway when it was published in June 2016.
In short, the Bioconductor Gateway has been a tremendous success since it launched on F1000Research in 2016. We look forward to the future articles and other bioinformatics materials that will be published in this hub in the coming years. You can find the Gateway’s full scope in this accompanying Bioconductor editorial. Could your research be published next?
Call for papers—BioC2021
Following on from previous years, we invite BioC2021 conference attendees to submit articles on Bioconductor workflows or packages to the Bioconductor Gateway. Likewise, we welcome posters and slides from this year’s conference to be hosted on the Gateway. Do not miss this unique opportunity to get credit for your work and increase its visibility and impact. Find out more about how to submit to the Gateway today.
The deadline to submit your article or poster is September 30th, 2021.
If you are interested in contributing or have any other questions, please email us at research@f1000.com. Similarly, you can also contact the Gateway Advisors directly.
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