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Welcome to eQTNMiner wiki

eQTNMiner is a computational package to carry out high-resolution mapping of quantitative trait loci (QTL) for high-dimensional genomic features like gene expression, epigenetic modifications, etc... and much more.

eQTNMiner is distributed under the GPL licence.

Why this name ?

Historically, the program was developed to perform genome-wide mapping of causal expression single nucleotide polymorphisms (SNP). This explains the prefix "eQTN" which means expression quantitative trait nucleotide (which has a narrower meaning comparing to eQTL which can encompass either different polymorphisms or different levels of mapping resolutions). The second part of the name, namely "Miner", is a standard term in the high-dimensional statistical learning community, making an explicit reference to the fact that inference is like working into a mine and trying to extract the valuable parts of the soil.

Programs

Short Description Language Category
Eqmr-db Create the main database C Data Management
Eqmr-dbget Query the main database C Data Management
Eqmr-dbmv Move a database to another location C Data Management
Eqmr-expca PCA on the expression dataset C Data Analysis
Eqmr-fcfdr Summary of cis-regression results C Data Analysis
Eqmr-fcr Cis phenotype x genotype mapping C Data Analysis
Eqmr-fcrdat Get the cis-regression raw data C Data Management
Eqmr-fcrout Get the cis-regression results C Data Management
Eqmr-fcrth Perform cis-regression (multi-thread) C Data Analysis
Eqmr-fdb Create a phenotypic feature database C Data Management
Eqmr-fenet Feature elastic-net regression C Data Analysis
Eqmr-fenetth Feature elastic-net regression (multi-thread) C Data Analysis
Eqmr-fexp Extract the feature phenotype matrix C Data Management
Eqmr-flm Feature standard linear regression C Data Analysis
Eqmr-flmth Feature standard linear regression (multi-thread) C Data Analysis
Eqmr-ftr Trans phenotype x genotype mapping C Data Analysis
Eqmr-ftrth Trans phenotype x genotype mapping (multi-thread) C Data Analysis
Eqmr-gmrge Join genotype datasets C Data Management
Eqmr-hmax ML estimate of a hierarchical model's parameters v1 C Hierarchical Model
Eqmr-hmax3 ML estimate of a hierarchical model's parameters v2 C Hierarchical Model
Eqmr-hmaxth ML estimate of a hierarchical model's parameters v1 (multi-thread) C Hierarchical Model
Eqmr-hmaxth3 ML estimate of a hierarchical model's parameters v2 (multi-thread) C Hierarchical Model
Eqmr-hmci Compute 95% CI of the hierarchical model's parameters v1 C Hierarchical Model
Eqmr-hmci3 Compute 95% CI of the hierarchical model's parameters v2 C Hierarchical Model
Eqmr-hmcith Compute 95% CI of the hierarchical model's parameters v1 (multi-thread) C Hierarchical Model
Eqmr-hmcith3 Compute 95% CI of the hierarchical model's parameters v2 (multi-thread) C Hierarchical Model
Eqmr-hmdb3 Create the hierarchical database C Data Management
Eqmr-prbannot Output the probe annotation file C Data Management
HapMapUtil Handle genotype data in the HapMap format C Data Management


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