Search results
Results from the WOW.Com Content Network
A Manhattan plot is a type of plot, usually used to display data with a large number of data-points, many of non-zero amplitude, and with a distribution of higher-magnitude values. The plot is commonly used in genome-wide association studies (GWAS) to display significant SNPs .
After odds ratios and P-values have been calculated for all SNPs, a common approach is to create a Manhattan plot. In the context of GWA studies, this plot shows the negative logarithm of the P-value as a function of genomic location. Thus the SNPs with the most significant association stand out on the plot, usually as stacks of points because ...
The Manhattan plot is named as such as the statistically significant genes appear to show up as "skyscrapers" on the plot, and when there are many genes that are associated with the trait, the plot resembles the Manhattan skyline. Although the Manhattan plot image is for a GWAS study, TWAS results are shown the same way.
This is a list of free and open-source software for geological data handling and interpretation. The list is split into broad categories, depending on the intended use of the software and its scope of functionality. Notice that 'free and open-source' requires that the source code is available and users are given a free software license.
Universal platform for the management, storage and analysis of all types of biological data, including tree and network inference of sequence data: W [21] Dendroscope: An interactive viewer for large phylogenetic trees and networks: All [22] DensiTree A viewer capable of viewing multiple overlaid trees. All [23] FigTree
Sequence similarity plots (SimPlots [44]), detection of intragenic and intergenic recombination events, bootscan analysis [45] and sequence similarity networks: SimPlot using different nucleotide/protein distance models; Phi, χ2 and NSS recombination tests; Sequence similarity network analysis: S. Samson, E. Lord, V. Makarenkov sowhat [46]
GWAS Central is a core component of the GEN2PHEN project and intends to provide an operational model, plus an open-source software package, so others can create similar databases across the world. These will be hosted by institutes, consortia, and even individual laboratories; providing those groups a toolkit for publicising and publishing ...
An effect size is also calculated at this significance level, indicating the difference in methylation when comparing two qualitative groups, or different quantitative values depending on your phenotype. CpG sites significantly associated with the phenotype and/or treatment/environmental stimulus are typically represented in a manhattan plot. [12]