Waldir Leoncio Netto

• Ghannoum, Salim; Fantini, Damiano; Zahoor, Muhammad; Reiterer, Veronika; Phuyal, Santosh & Leoncio Netto, Waldir [Show all 13 contributors for this article] (2023). A combined experimental-computational approach uncovers a role for the Golgi matrix protein Giantin in breast cancer progression. PLoS Computational Biology. ISSN 1553-734X. 19(4). doi: 10.1371/journal.pcbi.1010995. Full text in Research Archive
• Battauz, Michela & Leoncio Netto, Waldir (2023). A Likelihood Approach to Item Response Theory Equating of Multiple Forms. Applied Psychological Measurement. ISSN 0146-6216. 47(3), p. 200–220. doi: 10.1177/01466216231151702.
• Reis Costa, Denise & Leoncio Netto, Waldir (2022). Process Data Analysis in ILSAs. In Nilsen, Trude; Stancel-Piątak, Agnes & Gustafsson, Jan-Eric (Ed.), International Handbook of Comparative Large-Scale Studies in Education. Springer. ISSN 978-3-030-38298-8. p. 927–952. doi: 10.1007/978-3-030-88178-8_60.
• Leoncio Netto, Waldir; Wiberg, Marie & Battauz, Michela (2022). Evaluating Equating Transformations in IRT Observed-Score and Kernel Equating Methods. Applied Psychological Measurement. ISSN 0146-6216. doi: 10.1177/01466216221124087. Full text in Research Archive Show summary

  Test equating is a statistical procedure to ensure that scores from different test forms can be used interchangeably. There are several methodologies available to perform equating, some of which are based on the Classical Test Theory (CTT) framework and others are based on the Item Response Theory (IRT) framework. This article compares equating transformations originated from three different frameworks, namely IRT Observed-Score Equating (IRTOSE), Kernel Equating (KE), and IRT Kernel Equating (IRTKE). The comparisons were made under different data-generating scenarios, which include the development of a novel data-generation procedure that allows the simulation of test data without relying on IRT parameters while still providing control over some test score properties such as distribution skewness and item difficulty. Our results suggest that IRT methods tend to provide better results than KE even when the data are not generated from IRT processes. KE might be able to provide satisfactory results if a proper pre-smoothing solution can be found, while also being much faster than IRT methods. For daily applications, we recommend observing the sensibility of the results to the equating method, minding the importance of good model fit and meeting the assumptions of the framework.

• Ghannoum, Salim; Antos, Kamil; Netto, Waldir Leoncio; Gomes, Cecil; Köhn-Luque, Alvaro & Farhan, Hesso (2021). CellMAPtracer: A User-Friendly Tracking Tool for Long-Term Migratory and Proliferating Cells Associated with FUCCI Systems. Cells. ISSN 2073-4409. 10(2), p. 1–18. doi: 10.3390/cells10020469. Full text in Research Archive
• Ghannoum, Salim; Netto, Waldir Leoncio; Fantini, Damiano; Ragan-Kelley, Benjamin; Parizadeh, Seyedamirabbas & Jonasson, Emma [Show all 9 contributors for this article] (2021). DIscBIO: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics. International Journal of Molecular Sciences. ISSN 1661-6596. 22(3). doi: 10.3390/ijms22031399. Full text in Research Archive

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• Leoncio Netto, Waldir; Ruxton, Graeme & Fagerland, Morten Wang (2023). permChacko: Chacko Test for Order-Restriction with Permutation.
• Leoncio Netto, Waldir; Matta, Tyler; Rutkowski, Leslie; Rutkowski, David & Liaw, Yuan-Ling (2023). lsasim: Functions to Facilitate the Simulation of Large Scale Assessment Data.
• Leoncio Netto, Waldir & Holst, Rene (2022). TruncExpFam: Truncated Exponential Family. Show summary

  Handles truncated members from the exponential family of probability distributions. Contains functions such as rtruncnorm() and dtruncpois(), which are truncated versions of rnorm() and dpois() from the stats package that also offer richer output containing, for example, the distribution parameters. It also provides functions to retrieve the original distribution parameters from a truncated sample by maximum-likelihood estimation.

• Leoncio Netto, Waldir & Dietrich, Jan Philipp (2022). citation: Software Citation Tools. Show summary

  A collection of functions to extract citation information from 'R' packages and to deal with files in 'citation file format' (<https://citation-file-format.github.io/>), extending the functionality already provided by the citation() function in the 'utils' package.

• Leoncio Netto, Waldir (2022). matlab2r: Translation Layer from MATLAB to R. Show summary

  Allows users familiar with MATLAB to use MATLAB-named functions in R. Several basic MATLAB functions are written in this package to mimic the behavior of their original counterparts, with more to come as this package grows.

• Leoncio Netto, Waldir; Fagerland, Morten; Lydersen, Stian; Laake, Petter & Lingjærde, Ole Christian (2022). contingencytables: Statistical Analysis of Contingency Tables.
• Netto, Waldir Leoncio; Ghannoum, Salim; Fantini, Damiano & Sørensen, Øystein (2021). cellmigRation: Track Cells, Analyze Cell Trajectories and Compute Migration Statistics.
• Netto, Waldir Leoncio; Ghannoum, Salim; Köhn-Luque, Alvaro & Fantini, Damiano (2021). DIscBIO: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics. Show summary

  An open, multi-algorithmic pipeline for easy, fast and efficient analysis of cellular sub-populations and the molecular signatures that characterize them. The pipeline consists of four successive steps: data pre-processing, cellular clustering with pseudo-temporal ordering, defining differential expressed genes and biomarker identification. More details on Ghannoum et. al. (2021) <doi:10.3390/ijms22031399>. This package implements extensions of the work published by Ghannoum et. al. (2019) <doi:10.1101/700989>.

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