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Final analyses on the matched dataset were performed using a logistic regression with a random effect on the paired observations except for the length of stay analyzed with a Cox random effect model.
Maximum likelihood analyses of the single protein alignments, as well as the concatenated dataset were performed using the program RAxML on the Bioportal at University of Oslo (www.bioportal.uio.no), using the PROTMIXWAG amino acid substitution model.
Analyses of incongruence length differences (ILD; [ 29]) among partitions of the dataset were performed using PAUP* 4.0 [ 30].
Bayesian phylogenetic analyses of the amino acid dataset were performed using softwares MrBayes version 3.1.1 [ 82] and PhyloBayes version 2.1 [ 65].
FDR calculation and GO enrichment analyses of the array dataset were performed using R statistics software for selection of significant DE miRNAs and genes.
The alignment and phasing of the entire dataset were performed using MUSCLE [ 29] and PHASE [ 30], respectively, and the haplotypes were unambiguously reconstructed.
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The calculation of most of these descriptors for each compound of the dataset was performed using online E-Dragon software (version 1.0).
Preprocessing of the original and the reconstructed fMRI dataset are performed using SPM12.3 We performed motion correction that is used to suppress motion-related artifacts.
A molecular alignment of the selected scaffolds with molecules of active dataset was performed using the vROCS (release 3.1.2) [43] and visualized in VIDA (4.1.1) [44] available from OpenEye Scientific Software, Inc. [45].
The association between variables in the 93 patients dataset was performed using the chi square test.
Normalization of the miRNA dataset was performed using the 11 most rank-preserving miRNAs across all 40 samples (Figure S1).
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