Query relating pathway enrichment analysis for DEGs using KEGG or any other database.
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omarrafiqued ▴ 50
@omarrafiqued-21833
Last seen 12 weeks ago
India

KEGG is a database resource (http://www.genome.jp/kegg/) that contains all information of genomes, their relationships to biological systems and their interactions with the environment. We use KEGG pathway database to identify the main functional and metabolic pathways in deferentially expressed genes. This is known as Pathway enrichment analysis for DEG. We can do this in R programming using different packages but most of the packages need an internet connection to work. I wont be having access to internet for 3 months, so, is there any R package which can do the Pathway enrichment analysis for DEG with no access to internet. (I wont mind if it uses anything other than KEGG)

Grateful.

KEGG R offline Pathway Enrichment • 724 views
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@gordon-smyth
Last seen 36 minutes ago
WEHI, Melbourne, Australia

See my answer to your later question: https://support.bioconductor.org/p/128353/

KEGG analysis requires an internet connection because KEGG licensing restrictions prevent anyone from storing and distributing the KEGG pathways. Other databasese such as GO or MSigDb etc can be stored as R packages or R objects and do not require an ongoing internet connection.

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