User: aheinzel

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aheinzel110
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Austria
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Posts by aheinzel

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Affymetric HuGene-2_0-st NetAffx transcript annot - [WARNING: THIS FIELD TRUNCATED]
... Hi everybody, while parsing Affymetrix's NetAffx transcript annotation file ([HuGene-2_0-st-v1.na35.hg19.transcript.csv][1]) for HuGene-2-0-st chips I discovered that some of the *gene_assignment* and *mrna_assignment* fields in the file are incomplete and that these fields contain the string *[WAR ...
netaffx annotation hugene-2_0-st written 2.9 years ago by aheinzel110
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Answer: A: Predict miRNA targets using multiple prediction algorithms
... miRWalk2.0 should be able to do both by either starting from a set of mRNAs or miRNAs and provides the option to use multiple prediction algorithms. ...
written 4.3 years ago by aheinzel110
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Answer: A: Convert gene name to uniprot ID
... your entries remind me of gene symbols. a couple of options are available, just to name a few: David gene id conversion tool (choose official_gene_symbol during upload) Ensembl biomart (use filters -> id list limit choose hgnc symbols to restrict the result to your genes of interest; select s ...
written 4.7 years ago by aheinzel110
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Answer: A: For One Hugo Id Several Ensemble Id - In 1Kg
... this most likely happens when alternate sequence assemblies exist. The ensembl id ENSG00000243649 identifies CFB on the primary assembly while ENSG00000204359 identifies CFB on some alternate assembly. Have a close look at the location information provided (Chromosome 6: 31,895,475-31,919,861 vs. Ch ...
written 5.2 years ago by aheinzel110
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Answer: A: Convert Kegg Kgml To Graph
... have a look at the bioconductor package KEGGgraph. In a recent post I listed some of the KEGGgraph functions relevant to get a graph from KGML. ...
written 5.2 years ago by aheinzel110
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Comment: C: Why Perl Or Sed Command Not Working
... looks like your input file comes from windows and you are on *NIX machine. try running it through dos2unix first e.g. cat IN | dos2unix | perl ... ...
written 5.2 years ago by aheinzel110
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Answer: A: Get Species Information From The Uniprot Ids
... you can get this information from uniprot directly. off the top of my head, I can think of the following three options: using UniProts REST like interface using UniProt batch retrieval service using UniProt's SPARQL endpoint (unfortunately it appears to be currently unavailable) @REST: the follo ...
written 5.2 years ago by aheinzel110
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Answer: A: How To Get The Topology Of A Kegg Pathway?
... try using the R package KEGGgraph to get a graph object from KGML files (check the methods parseKGML, KEGGpathway2Graph and getKEGGedgeData). Subsequently, you could use (as already suggested before) igraph for further analysis. ...
written 5.2 years ago by aheinzel110
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Answer: A: Gene Id Conversion Tool
... Not sure what your background is, however, we recently started to develop an id mapper / converter for experimentalists who prefer organizing their data in Excel. Therefore, the client directly integrates into MS Excel. Currently, we provide the possibility to map from various IDs to ensembl and b ...
written 5.3 years ago by aheinzel110

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Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Convert Kegg Kgml To Graph

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