In the analysis of spatially resolved transcriptomics data, detecting spatially variable genes (SVGs) is crucial. Numerous computational methods exist, but varying SVG definitions and methodologies lead to incomparable results. We review 34 state-of-the-
Despite the widespread use of the Research Domain Criteria (RDoC) framework in psychiatry and neuroscience, recent studies suggest that the RDoC is insufficiently specific or excessively broad relative to the underlying brain circuitry it seeks to elucid
resulting in diverse meanings for the detected SVGs and making understanding difficult. Consequently, the inconsistent definitions of SVGs may lead to ambiguous usage of computational methods. Although 19 methods were reviewed previously21, the review did not categorize...
cm(varlist [, noconstant ]) may be used only with distribution(tnormal). Here frontier will fit a conditional mean model in which the mean of the truncated-normal distribution is modeled as a linear function of the set of covariates specified in varlist. Specifying noconstant suppresses the...
To account for this, authors have added covariates to detection probability that aim to capture potential sources of this variation (e.g., one might include the length of the list of all species recorded during a visit, aka “list length,” as a proxy for sample effort; Isaac et al., ...
The spatiotemporal correlation is covered by the hidden dynamic geostatistical model (HDGM) of Calculli et al. (2015). Mean non-stationarity in space and in time is covered by interacting the covariates with seasons, regional zoning, and local conditions. Similarly the lockdown/restart impact ...
However, the MNL model can also be found used without an underlying utility theory, and the units of analysis do not necessarily have to be individuals or other decision-making entities. In what follows, however, we will refer to individuals for the sake of simplicity, and the set of ...
We concluded that the observed differ- ences were most likely caused by optimal foraging of in- dividuals in relation to habitat differences on a local scale, leading to a complex pattern of interactions with environmental covariates, combined with avoidance of predation [5]. Such a flexible ...
is generated. For the time points associated with confidence bands that include0, we cannot reject the null hypothesis that the nonlinear functions are the same for this time point. The data frame that is used to generate this figure can be found in the second element of the output list. ...
When MI and bootstrapping were combined at the range of 0% (full model) to 90% of variable selection, bootstrap corrected c-index values of 0.70 to 0.71 and slope values of 0.64 to 0.86 were found. Conclusion We recommend to account for both imputation and sampling variation in sets of...