Each draw is a number of fragments that the function probabilistically assigns to transcripts in the transcriptome to determine the assignment uncertainty and to estimate the variance-covariance matrix for assigned fragment counts. Example: 'NumFragSamples',90 Data Types: double NumThreads— Number of...
The true signal S was simulated from a negative binomial distribution based on the mean and variance estimated from the 5000 promoters. 10 % or 30 % of the promoters were selected to be differen- tially methylated with enrichment fold change either 2 or 3. We simulated experiments with either...
DispersionMethod—Method to model variance in fragment counts "pooled"(default) |"per-condition"|"blind"|"poisson" DoIsoformSwitch—Flag to perform isoform switching tests true(default) |false EffectiveLengthCorrection—Flag to normalize fragment counts ...
DESeq, DESeq2, and EdgeR are based on negative binomial regression to model read counts from an RNA-Seq experiment, and thus it is natural for these methods to incorporate covariates. To estimate the variance in a negative binomial distribution, EdgeR relates the variance to the mean through ...
For variance-preserving diffusion process,29, ; for variance-exploding process,30,44αt = 1. Following recently proposed variational diffusion models,28,45 where signal-to-noise ratio is defined as4 The Markov representation of the diffusion process can be equivalently written with transition ...
where \(\widetilde{x}\) is the whitened trajectory of XYZ coordinates and \({C}_{00}\) is the covariance matrix for the XYZ coordinates. Whitening decorrelates the inputs and adjusts their variance to be unity. After whitening, we use one out of every ten simulation frames for each ...
The significance is assessed using either an empirical test, based on TF activities from permuted sample labels, or an analytical procedure, which provides a p value based on t statistic and estimated variance (see STAR Methods; Figures S2D and S2E). For classification mode, diffTF additionally...
Each draw is a number of fragments that the function probabilistically assigns to transcripts in the transcriptome to determine the assignment uncertainty and to estimate the variance-covariance matrix for assigned fragment counts. Example: 'NumFragSamples',90 Data Types: double NumThreads— Number of...
It is generally defined as follows: 𝛼𝑡=1−𝛽𝑡αt=1−βt where 𝛽𝑡βt is the variance of the noise added at time step t, which is usually linear or cosine decay: 𝛽𝑡=schedule(𝑡)βt=schedule(t). Figure 1. The forward diffusion process and the backward process...