6 papers · ranked by Valyu relevance
Christopher Noune, Caroline Hauxwell
A pipeline developed to establish sequence identity and estimate abundance of non-model organisms (such as viral quasispecies) using customized ultra-deep sequence ‘meta-barcodes’ has been modified to improve performance by re-development in the Python programming language. Redundant packages were removed and new…
Joshua M. Mitchell, Yuanye Chi, Maheshwor Thapa, Zhiqiang Pang + 2 more
To standardize metabolomics data analysis and facilitate future computational developments, it is essential is have a set of well-defined templates for common data structures. Here we describe a collection of data structures involved in metabolomics data processing and illustrate how they are utilized in a…
Nathan J. LeRoy, Oleksandr Khoroshevskyi, Aaron O’Brien, Rafał Stepień + 2 more
As biological data increases, we need additional infrastructure to share it and promote interoperability. While major effort has been put into sharing data, relatively less emphasis is placed on sharing metadata. Yet, sharing metadata is also important, and in some ways has a wider scope than sharing data itself. Here…
Weiyuntian Dai, Yonglin Yi, Anqi Lin, Chaozheng Zhou + 4 more
Meta-analysis is a common statistical method used to summarize multiple studies that cover the same topic. It can provide less biased results and explain heterogeneity between studies. Although there exists a variety of meta-analysis softwares, they are rarely both convenient to use and capable of comprehensive…
Fabien Campagne, William ER Digan, Manuele Simi
Data analysis tools have become essential to the study of biology. Tools available today were constructed with layers of technology developed over decades. Here, we explain how some of the principles used to develop this technology are sub-optimal for the construction of data analysis tools for biologists. In contrast…
Eftychia Eva Kontou, Axel Walter, Oliver Alka, Julianus Pfeuffer + 5 more
Metabolomics experiments generate highly complex datasets, which are time and work-intensive, sometimes even error-prone if inspected manually. Therefore, new methods for automated, fast, reproducible, and accurate data processing and dereplication are required. Here, we present UmetaFlow, a computational workflow for…