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useful_tools_for_functional_and_pathway_analysis [2019/10/25 07:09]
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useful_tools_for_functional_and_pathway_analysis [2019/10/31 18:40] (current)
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-=====   ​=====+===== Useful tools for functional and pathway analysis ​=====
  
   * [[http://​www.humanmine.org/​%20|Humanmine ]] : given a list of genes as input (Entrez/​Ensembl/​Symbol or a mix), it returns interaction networks, pathways, Gene Ontology categories, relevant literature, protein domains, chromosome distributions and much more on a single page. There are also nice summaries that pop-up by hovering the mouse over a gene name.   * [[http://​www.humanmine.org/​%20|Humanmine ]] : given a list of genes as input (Entrez/​Ensembl/​Symbol or a mix), it returns interaction networks, pathways, Gene Ontology categories, relevant literature, protein domains, chromosome distributions and much more on a single page. There are also nice summaries that pop-up by hovering the mouse over a gene name.
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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.
  
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