Software

Here you will find some functions or programs developed in our daily work. Feel free to use them and any comment will be welcome.

 

R packages

DigeUtils: An R library for proteomic analysis based on 2D-DIGE technology: Mixed models, Generalized Linear Square normalization, differential protein expression analysis trough linear mixed models, SpotImage visualization, filtering, etc. (Under development)

Agi4x44.2c: An R library for proprocessing of Agilent 4×44 experiments. It allows for quality control, background correction and normalization on wide gene expression analysis experiments base on two color 4×44 agilent chips.

lmDMELinear Model on Designed Multivariate Experiments in R.

ANFIS: an R library for Adaptative-Network-Based Fuzzy Inference System

Multi-Reference Contrast Method: article and RCode_1.0. [eGO: easy Gene Ontology, a tool for ontology analysis of multifactorial experiments (under development)]

RDAVIDWebService: a versatile R interface to DAVID (Under revision at Bioconductor. Coming soon…).

R functions

  • Kmeans: plot.kmeans.R
  • Addtional functions for R/MAANOVA package:  additional functions for MicroArray ANalysis Of VAriance. [Read More]
  • Recursive Feature Extraction with SVM: this function implements the SVM-RFE algorithm described by Guyon et al [Gene Selection for Cancer Classification using Support Vector Machines (2002)] . [R CODE, Help]

 

Other

DIGE-DeCyder XML Parser: extract raw and normalized data, experimental design and expression matrix of a 2D-DIGE experiment analyzed by Decyder. The results are saved in csv files. [Executable, Help]