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Standard gene mapping software packages can be used, although it is often faster to use custom code such as QTL Reaper or the web-based eQTL mapping system GeneNetwork. GeneNetwork hosts many large eQTL mapping data sets and provide access to fast algorithms to map single loci and epistatic interactions. As is true in all QTL mapping studies ...
A quantitative trait locus (QTL) is a locus (section of DNA) that correlates with variation of a quantitative trait in the phenotype of a population of organisms. [1] QTLs are mapped by identifying which molecular markers (such as SNPs or AFLPs) correlate with an observed trait.
In genetics, association mapping, also known as "linkage disequilibrium mapping", is a method of mapping quantitative trait loci (QTLs) that takes advantage of historic linkage disequilibrium to link phenotypes (observable characteristics) to genotypes (the genetic constitution of organisms), uncovering genetic associations.
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.
It uses an online stochastic optimization approach to maximize the likelihood of the transcript abundances under the observed data. The software itself is capable of making use of many threads to produce accurate quantification estimates quickly. It is part of the Sailfish suite of software, and is the successor to the Sailfish tool.
Flexible and fast read mapping program (twice as fast as BWA), achieves a mapping sensitivity comparable to Stampy. Internally uses a memory efficient index structure (hash table) to store positions of all 13-mers present in the reference genome. Mapping regions where pairwise alignments are required are dynamically determined for each read.
Generic Mapping Tools (GMT) are an open-source collection of computer software tools for processing and displaying xy and xyz datasets, including rasterization, filtering and other image processing operations, and various kinds of map projections. The software stores 2-D grids as COARDS-compliant netCDF files and comes with a comprehensive ...
The term eQTL was first published around the 1990s-2000s*, but no specific person coined it** Gene expression technically refers to any product of a gene, but because quantifying RNA levels is vastly easier that quantifying proteins (on a high-throughput, genome-wide scale), scientists generally use "expression" to mean "RNA", not protein.