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| useful_tools_for_functional_and_pathway_analysis [2019/10/31 16:40] – admin | useful_tools_for_functional_and_pathway_analysis [2020/04/22 18:09] – [Useful tools for functional and pathway analysis] isha |
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| * There are some [[https://www.biostars.org/p/274514/|R tools]] for pathway analysis including [[https://yulab-smu.github.io/clusterProfiler-book/|ClusterProfiler]]. | * There are some [[https://www.biostars.org/p/274514/|R tools]] for pathway analysis including [[https://yulab-smu.github.io/clusterProfiler-book/|ClusterProfiler]]. |
| * Mouse Genome Informatics ([[http://www.informatics.jax.org/|MGI]]) has a nice hierarchal Gene Ontology [[http://www.informatics.jax.org/vocab/gene_ontology|Browser]] similar to Reactome. | * Mouse Genome Informatics ([[http://www.informatics.jax.org/|MGI]]) has a nice hierarchal Gene Ontology [[http://www.informatics.jax.org/vocab/gene_ontology|Browser]] similar to Reactome. |
| * Isha's list of [[https://docs.google.com/presentation/d/1c4HAcImyyU1as5qEwzmH8QIAxD25N4Z5__sUZE3n6kk/edit#slide=id.g6f90f06c9f_0_0|functional enrichment]] analysis tools in R. | * Functional Enrichment Analysis [[https://yulab-smu.github.io/clusterProfiler-book/chapter1.html|overview]]. Isha's list of [[https://docs.google.com/presentation/d/1c4HAcImyyU1as5qEwzmH8QIAxD25N4Z5__sUZE3n6kk/edit#slide=id.g6f90f06c9f_0_0|functional enrichment]] analysis tools in R. |
| | * [[http://gepia.cancer-pku.cn/|GEPIA]] and [[http://gepia2.cancer-pku.cn/#index|GEPIA2]] are web based resources for interactive gene expression profiling and analysis. The data sources used are TCGA and GTEx. |
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