rSWeeP: A R/Bioconductor package deal with SWeeP sequences representation
Danrley R. Fernandes, Mariane Gonçalves-KulikiD, Diogo J. S. Machado, Jeroniza Nunes MarchaukoskiiD, Fábio O. PedrosaiD, Camilla Reginatto De PierriiD, Roberto Tadeu RaittziD
Abstract
The rSWeeP package is an R implementation of the SWeeP model, designed to handle Big Data. rSweeP meets to the growing demand for efficient methods of heuristic representation in the field of Bioinformatics, on platforms accessible to the entire scientific community. We explored the implementation of rSWeeP using a dataset containing 31,386 viral proteomes, performing phylogenetic and principal component analysis. As a case study we analyze the viral strains closest to the SARS-CoV, responsible for the current pandemic of COVID-19, confirming that rSWeeP can accurately classify organisms taxonomically. rSWeeP package is freely available at https://bioconductor.org/packages/release/bioc/html/rSWeeP.html.
02 /Specification & Classification
Click any tag to browse matching papers- Citations
- 1
- Organism
- Assay
- Research Focus
- Approach
Reproducibility ledger
Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.
Sign in to file a reproducibility report.
Related papers
- idCOV: a pipeline for quick clade identification of SARS-CoV-2 isolates
Xun Zhu, Ti-Cheng Chang, … Gang Wu·bioRxiv·Oct 8, 2020
- wastewaterSPAdes: SARS-CoV-2 strain deconvolution using SPAdes toolkit
Anton Korobeynikov·bioRxiv·Dec 8, 2022
- ViReaDB: A user-friendly database for compactly storing viral sequence data and rapidly computing consensus genome sequences
Niema Moshiri·bioRxiv·Oct 21, 2022
- MultiStageSearch: a multi-step proteogenomic workflow for taxonomic identification of viral proteome samples adressing database bias
Julian Pipart, Tanja Holstein, … Thilo Muth·bioRxiv·May 15, 2024
- An Analysis of SARS-CoV-2 Using ViReport
Miranda Song, Niema Moshiri·bioRxiv·Jun 20, 2020
- Deep learning based on stacked sparse autoencoder applied to viral genome classification of SARS-CoV-2 virus
Maria G. F. Coutinho, Gabriel Bezerra Motta Câmara, … Marcelo A. C. Fernandes·bioRxiv·Oct 14, 2021