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Question: Which resources for pathway analysis?
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gravatar for January Weiner
7.5 years ago by
January Weiner370 wrote:
Dear all, my tool of choice currently is SPIA, a package that seems to provide sophisticated analysis of pathways (including both, gene set enrichment analysis and pathway perturbation analysis). I wonder what other tools you could recommend? The task at hand is to identify differentially regulated pathways given information on differentially expressed genes, using a solid, but broad pathway database. There is, of course, a wide range of tools outside of R (e.g. PathVisio) which can be used for data mining and visualisation as well as running specific statistical analyses. I wonder what are you using in R. kind regards, j. -- -------- Dr. January Weiner 3 -------------------------------------- Max Planck Institute for Infection Biology Charit?platz 1 D-10117 Berlin, Germany Web?? : www.mpiib-berlin.mpg.de Tel? ?? : +49-30-28460514
ADD COMMENTlink modified 7.5 years ago by Gilbert Feng300 • written 7.5 years ago by January Weiner370
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gravatar for Gilbert Feng
7.5 years ago by
Gilbert Feng300
Gilbert Feng300 wrote:
Hi, January GeneAnswers integrates GO, DO, KEGG, and caBIO(NCI, Reactome and Biocarta) as well as gene interaction and entrez keywords search for gene set enrichment analysis. Finally, it can automatically generate a html report for one or multiple groups of gene set enrichment analysis with interactive networks. Best Gilbert On 2/28/11 9:43 AM, January Weiner wrote: > Dear all, > > my tool of choice currently is SPIA, a package that seems to provide > sophisticated analysis of pathways (including both, gene set > enrichment analysis and pathway perturbation analysis). I wonder what > other tools you could recommend? The task at hand is to identify > differentially regulated pathways given information on differentially > expressed genes, using a solid, but broad pathway database. > > There is, of course, a wide range of tools outside of R (e.g. > PathVisio) which can be used for data mining and visualisation as well > as running specific statistical analyses. I wonder what are you using > in R. > > kind regards, > > j. >
ADD COMMENTlink written 7.5 years ago by Gilbert Feng300
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