User: rgamini

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rgamini0
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Posts by rgamini

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graphite KEGG pathway list vs KEGG pathway list
...   Hi, Wondering why is the pathway list of KEGG truncated in graphite package. I see that KEGG database has 293 pathways (human), however in graphite the list contains only 242 pathways (to check in R; names(kegg)) Why is the discrepancy ? Or, why are some pathways not included ? Can anyone hel ...
graphite written 4.3 years ago by rgamini0 • updated 4.3 years ago by gabriele.sales100
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Answer: A: Question on graphite/SPIA; extracting DE gene list
... Works!!  Thanks much, Adi.  Ramya       ...
written 4.3 years ago by rgamini0
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Question on graphite/SPIA; extracting DE gene list
... Hi, I am doing the SPIA analysis via **graphite package** for I could do the SPIA not just on KEGG pathway but on others such as reactome, nci etc. So, one could use in graphite prepareSPIA(db,"user_defined_string") (where, db can be KEGG, reactome, nci etc) res <-runSPIA(de=my_DE, all=my_ALL, ...
spia graphite runspia written 4.3 years ago by rgamini0 • updated 5 months ago by Bioconductor Community ♦♦ 0

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