Main Page
From Eqtnminer
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 |
