README.md

In FRPV/KEGGIdeaMex: Get enriched pathways from KEGG using a list of differentially expressed genes.

KEGGIdeaMex

Description

This pipeline was created in the CDSB-Mexico 2018 by request of Leticia Vega and Veronica Jimenez.

The pipeline takes as input a list of genes (NCBI gene Ids) differentially expressed and creates descriptive plots.

Input

List of genes

The pipeline takes as input plaint text files with the next structure:

6083    UP
26804   UP
2224    UP
8431    UP
30836   UP
6924    DOWN
6464    DOWN
3399    DOWN
148327  DOWN
6278    DOWN

The first colum is the NCBI gene id and the second column if the gene is UP (up-expressed) or DOWN (down-expressed).

Species KEGG id

Select from the KEGG database the three letter code for the species who belong the genes id. Check the complete KEGG species IDs in the next url: link.

Number of pathways to plot

Declare the number of pathways to plot.

Output example

The package generates the next class of plots:

Developers

• Irving García
• Lorena J. Gómez
• Bernardo M. Quiroga
• Fernando Pérez

FRPV/KEGGIdeaMex documentation built on May 22, 2019, 3:38 p.m.