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# Useful info (AprendeBioinformáticaEnCasa: session 7)  #
# By: Juan Carlos Oliveros (BioinfoGP, CNB-CSIC)        #
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# FIESTA viewer: to filter RNA-seq tables and view the results in
# real time:

https://bioinfogp.cnb.csic.es/tools/FIESTA/index.php

# Generic URL for yeast genes to be used with FIESTA viewer:

http://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?g=##ACCESSION##

# Venny: tool to compare up to 4 gene lists (of other elements)
# with Venn diagrams:

https://bioinfogp.cnb.csic.es/tools/venny/

# Gene Ontology main page: controlled vocabulary of biological terms
# and a popular tool to perform functional enrichment analysis

http://geneontology.org/

# Enrichr (and modEnrichr): useful tool to perform quick functional
# enrichment analysis using several databases of annotations
# (available for a small number of model organisms)

https://amp.pharm.mssm.edu/modEnrichr/

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# GSEA (Broad Institute) tips  #
#   (Preranked analysis)       #
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-Use your own compendium of functional groups in gmt format

(MyGMT is a tool to convert  biomart tables containing GO terms into gmt
files to be used with GSEA tool)

https://bioinfogp.cnb.csic.es/tools/mygmt/

-Adjust "Basic fields": "Max size: exclude larger sets" and
"Min size: exclude smaller sets" to use more or less functional groups
as defined in the gmt file.

-To reproduce a given analysis, copy the "seed for permutation" value at
the results and copy it in "Advanced fields"


      Juan Carlos Oliveros    2020    BioinfoGP CNB-CSIC