The ABCs of Reproducibility: Effecting Attitudes, Behaviors and Change to Realize Reproducibility

Free, Tristan

doi:10.2144/btn-2020-0082

Cited by 3 publications

(1 citation statement)

References 8 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The advent of readily available, low-cost high throughput DNA sequencing has promoted the rampant growth of microbiome and metagenome studies. These studies, while informative and insightful, are often fraught by well-meaning but ultimately incorrect data assumptions and statistical test applications (Martin, 2019;Free, 2020). The selection of statistical tests requires knowledge of underlying data characteristics such as sample distribution, sample size and equivariance (Figure 1), which can be easily misinterpreted especially for complex studies with a lot of groups and relatively small sample sizes per group (Makin and De Xivry, 2019;Konietschke, Schwab and Pauly, 2021).…”

Section: Introductionmentioning

confidence: 99%

statSuma: automated selection and performance of statistical comparisons for microbiome studies

Leigh

Murphy

Walsh

2021

Preprint

View full text Add to dashboard Cite

There is a reproducibility crisis in scientific studies. Some of these crises arise from incorrect application of statistical tests to data that follow inappropriate distributions, have inconsistent equivariance, or have very small sample sizes. As determining which test is most appropriate for all data in a multicategorical study (such as comparing taxa between sites in microbiome studies), we present statsSuma, an interactive Python notebook (which can be run from any desktop computer using the Google Colaboratory web service) and does not require a user to have any programming experience. This software assesses underlying data structures in a given dataset to advise what pairwise or listwise statistical procedure would be best suited for all data. As some users may be interested in further mining specific trends, statSuma performs 5 different two-tailed pairwise tests (Student's t-test, Welch's t-test, Mann-Whitney U-test, Brunner-Munzel test, and a pairwise Kruskal-Wallis H-test) and advises the best test for each comparison. This software also advises whether ANOVA or a multicategorical Kruskal-Wallis H-test is most appropriate for a given dataset and performs both procedures. A data distribution-vs-Gaussian distribution plot is produced for each taxon at each site and a variance plot between all combinations of 2 taxa at each site are produced so Gaussian tests and variance tests can be visually confirmed alongside associated statistical determinants.

show abstract

Section: Introductionmentioning

confidence: 99%

statSuma: automated selection and performance of statistical comparisons for microbiome studies

Leigh

Murphy

Walsh

2021

Preprint

View full text Add to dashboard Cite

show abstract

Quality control of purified proteins to improve data quality and reproducibility: results from a large-scale survey

et al. 2021

View full text Add to dashboard Cite

Path2Green: introducing 12 green extraction principles and a novel metric for assessing sustainability in biomass valorization

de Souza Mesquita,

Contieri,

e Silva

et al. 2024

Green Chem.

View full text Add to dashboard Cite

show abstract

The ABCs of Reproducibility: Effecting Attitudes, Behaviors and Change to Realize Reproducibility

Abstract: With the abundance of information and increased availability of tools to assist in reproducibility, Tristan Free investigates why progress so slow.

Cited by 3 publications

References 8 publications

statSuma: automated selection and performance of statistical comparisons for microbiome studies

statSuma: automated selection and performance of statistical comparisons for microbiome studies

Quality control of purified proteins to improve data quality and reproducibility: results from a large-scale survey

Path2Green: introducing 12 green extraction principles and a novel metric for assessing sustainability in biomass valorization

Contact Info

Product

Resources

About