DSpace Repository

Vignette rKOMICS application example

Show simple item record

dc.contributor Universitat de Vic - Universitat Central de Catalunya. Facultat de Ciències i Tecnologia
dc.contributor Universitat de Vic - Universitat Central de Catalunya. Màster Universitari en Anàlisi de Dades Òmiques
dc.contributor.author Geerts, Manon
dc.contributor.author Van Den Broeck, Frederik
dc.date.accessioned 2021-12-22T08:26:29Z
dc.date.available 2021-12-22T08:26:29Z
dc.date.created 2021-07-21
dc.date.issued 2021-07-21
dc.identifier.uri http://hdl.handle.net/10854/6875
dc.description Curs 2020-2021 es
dc.description.abstract The core features of the rKOMICS package include data aggregation, analyses and visualization that allows to examine, summarize and extract meaningful information from minicircle sequence alignments as obtained by KOMICS or a custom bioinformatic pipeline, and from USEARCH cluster format (UC) files as generated by USEARCH or VSEARCH. In addition to storing data files, rKOMICS stores the analyses and visualization results into single list objects that can be called by the user at a later stage. rKOMICS incorporates multiple methods of visualizations using the ggplot2 R package to plot the foundation of graphs. By adding ggplot2 functions to the rKOMICS visualization functions, the user has direct control over the finishing touches of the graph’s appearances. Our package also utilizes sample specific metadata that allows multi-group data visualizations to facilitate exploratory analysis. The overall data set can be examined using barplots, heatmaps, PCA plots and box plots that are generated for each specified minimum percent identity. This makes it possible to visualize population structure and diversity based on minicircle sequence composition. To show the functionality of rKOMICS, we performed an example analysis using whole-genome se quencing data from a recently published study on the history of diversification of the Leishmania brazilien sis species complex in Peru. This species complex comprises two closely related species: the lowland and zoonotic L. braziliensis parasite circulating in a diverse range of wild mammals in Neotropical rainforests, and the highland anthroponotic L. peruviana parasite that is largely endemic to the Pacific slopes of the Peruvian Andes. A total of 67 Leishmania parasites from 47 localities in Peru were cultured and subjected to whole genome sequencing. es
dc.format application/pdf es
dc.format.extent 9 p. es
dc.language.iso eng es
dc.rights Tots els drets reservats es
dc.subject.other Genòmica es
dc.subject.other Clusterització es
dc.subject.other rKOMICS es
dc.subject.other Parasitisme es
dc.subject.other Protozoologia es
dc.subject.other Mitocondris es
dc.title Vignette rKOMICS application example es
dc.type info:eu-repo/semantics/masterThesis es
dc.rights.accessRights info:eu-repo/semantics/openAccess es

Files in this item

Show simple item record

Search RIUVic

Advanced Search