Objectif: intégrer les données de type "compound" quantitative à la visualisation des cartes en utilisant le package PathView (see http://www.bioconductor.org/packages/release/bioc/manuals/pathview/man/pathview.pdf)
Compounds definition : metabolites, drugs, small molecules, etc.
Structure "Compound Data" as input: data matrices in tab- or comma-delimited format (txt or csv). The format maybe the same as Gene Data in format (and you may also need to specify sample columns and experiment design), except rows are compounds
Example Compound Data 1:
Example Compound Data 2: compound_ID / control 1, control 2, exp.1, exp.2
Like the gene concept, here the compound concept is also generic, including multiple types of metabolites, drugs, small molecules. Users must specify the Compound ID Type option such as below:
ChEMBL compound
KEGG COMPOUND accession
KEGG DRUG accession
DrugBank accession
Example of GUI (from pathview.org) to be adapted according to Galaxy wrapper possibilities
A décider: Faire une extension à cet outil (qui n'est que gene/protein differentielle) ou créer un nvel outil (qui sera gene/protein diff + compound diff) ?
Output à améliorer en rendant les display interactifs ; i.e. Nodes in native KEGG view graphs are hyperlinked.
Objectif: intégrer les données de type "compound" quantitative à la visualisation des cartes en utilisant le package PathView (see http://www.bioconductor.org/packages/release/bioc/manuals/pathview/man/pathview.pdf) Compounds definition : metabolites, drugs, small molecules, etc. Structure "Compound Data" as input: data matrices in tab- or comma-delimited format (txt or csv). The format maybe the same as Gene Data in format (and you may also need to specify sample columns and experiment design), except rows are compounds Example Compound Data 1:
Example Compound Data 2: compound_ID / control 1, control 2, exp.1, exp.2
Like the gene concept, here the compound concept is also generic, including multiple types of metabolites, drugs, small molecules. Users must specify the Compound ID Type option such as below: ChEMBL compound KEGG COMPOUND accession KEGG DRUG accession DrugBank accession Example of GUI (from pathview.org) to be adapted according to Galaxy wrapper possibilities
A décider: Faire une extension à cet outil (qui n'est que gene/protein differentielle) ou créer un nvel outil (qui sera gene/protein diff + compound diff) ? Output à améliorer en rendant les display interactifs ; i.e. Nodes in native KEGG view graphs are hyperlinked.