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A volcano plot is constructed by plotting the negative logarithm of the p value on the y axis (usually base 10). This results in data points with low p values (highly significant) appearing toward the top of the plot. The x axis is the logarithm of the fold change between the two conditions. The logarithm of the fold change is used so that ...
RNA-Seq (named as an abbreviation of RNA sequencing) is a technique that uses next-generation sequencing to reveal the presence and quantity of RNA molecules in a biological sample, providing a snapshot of gene expression in the sample, also known as transcriptome.
The three dimensional structure of biological macromolecules like proteins and nucleic acids play a critical role in determining their functional role. [2] This process of decoding function from the sequence is an experimentally and computationally challenging question addressed widely.
In bioinformatics, sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand its features, function, structure, or evolution. It can be performed on the entire genome, transcriptome or proteome of an organism, and can also involve only selected segments or regions ...
Name Description Knots [Note 1]Links References trRosettaRNA: trRosettaRNA is an algorithm for automated prediction of RNA 3D structure. It builds the RNA structure by Rosetta energy minimization, with deep learning restraints from a transformer network (RNAformer). trRosettaRNA has been validated in blind tests, including CASP15 and RNA-Puzzles, which suggests that the automated predictions ...
RNA-Seq [1] [2] [3] is a technique [4] that allows transcriptome studies (see also Transcriptomics technologies) based on next-generation sequencing technologies. This technique is largely dependent on bioinformatics tools developed to support the different steps of the process. Here are listed some of the principal tools commonly employed and ...
Heatmap of RNA-Seq data showing two dendrograms in the left and top margins. A dendrogram is a diagram representing a tree. This diagrammatic representation is frequently used in different contexts: in hierarchical clustering, it illustrates the arrangement of the clusters produced by the corresponding analyses. [4]
Trajectory inference as implemented in Slingshot for (a) a simulated two-dimensional dataset and (b) a single-cell RNA-seq dataset of the olfactory epithelium.. Trajectory inference or pseudotemporal ordering is a computational technique used in single-cell transcriptomics to determine the pattern of a dynamic process experienced by cells and then arrange cells based on their progression ...