1,720,965 research outputs found
Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data
Full text linkBackgroundThe correct identification of differentially abundant microbial taxa between experimental conditions is a methodological and computational challenge. Recent work has produced methods to deal with the high sparsity and compositionality characteristic of microbiome data, but independent benchmarks comparing these to alternatives developed for RNA-seq data analysis are lacking.ResultsWe compare methods developed for single-cell and bulk RNA-seq, and specifically for microbiome data, in terms of suitability of distributional assumptions, ability to control false discoveries, concordance, power, and correct identification of differentially abundant genera. We benchmark these methods using 100 manually curated datasets from 16S and whole metagenome shotgun sequencing.ConclusionsThe multivariate and compositional methods developed specifically for microbiome analysis did not outperform univariate methods developed for differential expression analysis of RNA-seq data. We recommend a careful exploratory data analysis prior to application of any inferential model and we present a framework to help scientists make an informed choice of analysis methods in a dataset-specific manner
benchdamic: benchmarking of differential abundance methods for microbiome data
Full text linkA Summary: Recently, an increasing number of methodological approaches have been proposed to tackle the complexity of metagenomics and microbiome data. In this scenario, reproducibility and replicability have become two critical issues, and the development of computational frameworks for the comparative evaluations of such methods is of utmost importance. Here, we present benchdamic, a Bioconductor package to benchmark methods for the identification of differentially abundant taxa
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Benchmarking of differential abundance methods and development of bioinformatics and statistical tools for metagenomics data analysis
Full text linkL'analisi di dati nell'ambito del microbioma e della metagenomica è stato il tema principale del mio dottorato. L'obiettivo primario di questa tesi si muove attorno all'osservazione dei limiti dei metodi per lo studio dell'abbondanza differenziale e culmina con la creazione di un framework analitico che permette la loro misurazione e comparazione. Come obiettivo secondario, inoltre, la tesi vuole enfatizzare la necessità di una solida analisi statistica esplorativa ed inferenziale nei dati di metabarcoding, tramite la presentazione di alcuni casi studio. Inizio presentando 2 studi strettamente collegati in cui i metodi per l'analisi di abbondanza differenziale sono i protagonisti. L'analisi di abbondanza differenziale è lo strumento principale per individuare differenze nelle composizioni delle comunità microbiche in gruppi di campioni di diversa provenienza. Rappresenta quindi il primo passo per la comprensione delle comunità microbiche, delle relazioni tra i loro membri e di questi con l'ambiente. Il primo studio riguarda un lavoro di confronto tra metodi. A partire da una collezione di dataset metagenomici, l'obiettivo era di valutare le performance di metodi per l'analisi dell'abbondanza differenziale, anche nati in altri ambiti di ricerca (e.g., RNA-Seq e single-cell RNA-Seq). Invece, con il secondo studio presento un software che ho sviluppato grazie ai risultati ottenuti dalla precedente ricerca. Attualmente, il pacchetto software, in linguaggio R, è disponibile su Bioconductor (i.e., una piattaforma open-source per l'analisi e la visualizzazione di dati biologici). Esso consente agli utenti di replicare sui propri dataset il confronto tra metodi per lo studio dell'abbondanza differenziale e la conseguente analisi delle performance. Infine, mostro alcune delle sfide che ho incontrato nell'analisi di questo tipo di dato attraverso 2 casi studio riguardanti il microbioma umano, la sua composizione e dinamica, sia in stato di salute che malattia. Nel primo studio, dei soggetti sani sono stati trattati con una mistura di probiotici per valutare variazioni del microbiota intestinale ed eventuali associazioni con alcuni aspetti psicologici. Un'attenta analisi esplorativa, l'impiego di tecniche di clustering e l'utilizzo di modelli di regressione lineare ad effetti misti hanno consentito di svelare un forte effetto soggetto-specifico e la presenza di diversi batteriotipi di partenza che mascheravano l'effetto complessivo del trattamento probiotico. Invece, nel secondo studio mostro come, a partire da campioni salivari, sono stati individuati dei biomarcatori associati all'esofagite eosinofila (i.e., una malattia cronica immuno-mediata a carico dell'esofago che causa disfagia, occlusioni e stenosi esofagee). Nonostante la bassa numerosità campionaria è stato possibile costruire un modello per discriminare tra casi e controlli con una buona accuratezza. Anche se ancora prematuro, questo risultato rappresenta un passo promettente verso la diagnosi non invasiva di questa malattia che per il momento viene fatta solo tramite biopsia esofagea.Microbiome and metagenomics data analysis has been the main theme of my PhD programme. As a main goal, the thesis moves from the observed limitations of the differential abundance analysis tools to a benchmark and a framework against which they could be measured and compared. Furthermore, as a secondary goal, the presentation of some case studies wants to emphasise the need for a sound exploratory and inferential statistical analysis in metabarcoding data. Firstly, I present two closely related studies in which differential abundance analysis methods play the main role. The differential abundance analysis is the principal approach to detect differences in microbial community compositions between different sample groups, and hence, for understanding microbial community structures and the relationships between microbial compositions and the environment. I start by introducing a benchmarking study in which differential abundance analysis methods, even from different domains (e.g., RNA-Seq and single-cell RNA-Seq), were used in a collection of microbiome datasets to evaluate their performance. Then, I continue with the presentation of software package that I developed from the results obtained in the previous research. The software package, in R language, is currently available on Bioconductor (i.e., an open-source software platform for analysing and visualising biological data). It allows users to replicate the benchmarking of differential abundance analysis methods and evalute their performances on their own datasets. Secondly, I highlight the microbiome data analysis challenges presenting two case studies about the human microbiome and its composition and dynamics in both disease and healthy states. In the first study, healthy volunteers were treated with a probiotic mixture and the changes in the gut microbiome were studied in conjunction with some psychological aspects. A careful data exploration, clustering, and mixed-effects regression models, unveiled subject-specific effects and the presence of different bacteriotypes which masked the probiotic effect. Instead, in the second study I show how to identify disease-related microbial biomarkers for eosinophilic oesophagitis (i.e., a chronic immune-mediated inflammatory disease of the oesophagus that causes dysphagia, food impaction of the oesophagus, and esophageal strictures) from saliva. Despite the low sample size it was possible to train a model to discriminate between case and control states with a decent accuracy. While still premature, this represents a promising step for the non-invasive diagnosis of eosinophilic oesophagitis which is now possible only through esophageal biopsy
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