User: hfang.shanghai

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Posts by hfang.shanghai

<prev • 11 results • page 1 of 2 • next >
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Answer: A: Assigning Pathway Type to MSigDB gene sets
... Maybe irrelevant but you may look at 'http://supfam.org/dnet/dGSEA.html' in an R package 'dnet'. ...
written 4.3 years ago by hfang.shanghai140
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Comment: C: Available pipelines for functional annotaiton (COG, KEGG, GO) of genomes
... Sorry for that. Now all sequences you are providing must be included in the database SUPERFAMILY. Another way to do so is first get domain assignments from the SUPERFAMILY or similar databases. Then, use the dcGO open-source R package called dcGOR, if you are familiar with the R software environmen ...
written 4.4 years ago by hfang.shanghai140
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Comment: C: Semantic similarity of non-GO ontologies
... Hi Khader, Below are the long answers for your questions. Hope they are useful. 1. HPO has three namespaces (sub-ontologies). This situation is very similar to GO and its sub-ontologies (Biological Process, Molecular Function, Cellular Component). For this reason, you have to calculate semantic ...
written 4.4 years ago by hfang.shanghai140
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Answer: A: Semantic similarity of non-GO ontologies
... This is what dnet package can do. See http://supfam.org/dnet/dDAGtermSim.html. However, in this example you need to replace with human phenotype ontology. More information about how to load different ontologies can be found in http://supfam.org/dnet/docs.html.  If you provide details about your ann ...
written 4.4 years ago by hfang.shanghai140
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Answer: A: How to visualize the similarity between transcriptome expression in different co
... Maybe unrelated to your question but you could get better sample relations using the package 'supraHex'. See demo: http://supfam.org/supraHex/demo-Fang.html ...
written 4.4 years ago by hfang.shanghai140
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Answer: A: R code for clinico-genomic survival prediction
... Maybe this R package 'dnet' can give your idea. See http://supfam.org/dnet/demo-TCGA.html and its paper http://genomemedicine.com/content/6/8/64#B15 ...
written 4.4 years ago by hfang.shanghai140
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Answer: A: Available pipelines for functional annotaiton (COG, KEGG, GO) of genomes
... If you want to use structional information (protein domains), you can try dcGO Predictor (http://supfam.org/SUPERFAMILY/cgi-bin/dcpredictormain.cgi). There are dozens of ontologies for your further consideration, which might increase your research scope. ...
written 4.4 years ago by hfang.shanghai140
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Tool: dcGOR: an R package for analysing ontologies and protein domain annotations
... An R package for analysing ontologies and protein domain annotations has been published in PLoS Computational Biology (http://dx.doi.org/10.1371/journal.pcbi.1003929). The package is distributed as part of CRAN (http://cran.r-project.org/package=dcGOR), and also at GitHub for version control. The ...
R domains tool go enrichment analysis written 4.4 years ago by hfang.shanghai140
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Answer: A: How To Get Dag Level Of A Gene Ontology Term Using Bioconductor
... It has been supported in the 'dnet' package: http://supfam.org/dnet/visDAG.html ...
written 4.5 years ago by hfang.shanghai140
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Answer: A: A Tree Viewer Software For The Gene Ontology Terms?
... http://supfam.org/dnet/visDAG.html ...
written 4.5 years ago by hfang.shanghai140

Latest awards to hfang.shanghai

Scholar 4.2 years ago, created an answer that has been accepted. For A: Semantic similarity of non-GO ontologies
Appreciated 4.4 years ago, created a post with more than 5 votes. For dcGOR: an R package for analysing ontologies and protein domain annotations

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