Pack: HD chromatin analysis

Description:

This workflow uses the array express library to download data from the array express repository and creates two separate files. The gene expression and the phenotype files. The files are saved in the directory that the user has to specify in the input. NOTE: The library(ArrayExpress) is a prerequisite for this workflow

Description:

****IMPORTANT****:if libraries: library(ArrayExpress), library(hgu133a.db), library(limma) are not installed in the local R installation, then they need to be installed before running this workflow.

Original data come from Hodges et. al 2006 "Regional and cellular gene expression changes in human Huntington’s disease brain" This workflow loads the two necessary files (gene expression data & phenotype data), and creates the expression set object to be used by the R package limma, to test for DE. In this example we test for DE between HD and controls for each brain region. To test for DE between other variables, this information can be changed at the workflow "compute_DE_limma"

Description:

****IMPORTANT****:if libraries: library(ArrayExpress), library(hgu133b.db), library(limma) are not installed in the local R installation, then they need to be installed before running this workflow.

Original data come from Hodges et. al 2006 "Regional and cellular gene expression changes in human Huntington’s disease brain" This workflow loads the two necessary files (gene expression data & phenotype data), and creates the expression set object to be used by the R package limma, to test for DE. In this example we test for DE between HD and controls for each brain region. To test for DE between other variables, this information can be changed at the workflow "compute_DE_limma"

Description:

Finds the overlap between two datasets which contain genomic information (e.g. [gene id], chromosome name, gene start, gene end), plus some statistics. Returns rows of file_1 which overlap with the second file. A kolmogorov smirnov test is applied between the list that overlaps and the one that does not. NOTE: The library(GenomicRanges) is a prerequisite for this workflow

Description:

This workflow maps a gene list to the genome using the biomart service, and afterwards computes a promoter region for each gene. The user needs to define the promoter region to be computed. The direction that a gene is transcribed is being taken into account in the "compute_promoter_region_with_strand" component. The variable "strand" is responsible for that. NOTE: The library(biomaRt) is a prerequisite for this workflow

Description:

Sketch that demonstrates how the workflows of our chromatin analysis in HD are connected with each other, plus a short explanation for each one.