User: mk

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mk190
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Posts by mk

<prev • 46 results • page 1 of 5 • next >
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Published data sets using 10x Feature Barcoding?
... How can I search for published data sets that use [Feature Barcoding][1]? Background and caveats: 1. The actual Cell Ranger output needs to be included with the publication: eg. features.tsv.gz, genes.tsv.gz, matrix.mtx.gz 2. Feature Barcoding allows CellRanger to export droplet-based single-ce ...
10x single-cell feature barcoding 10x genomics written 23 days ago by mk190
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Comment: C: what is the deal with bioconda?
... confirmed, thanks @genomax ...
written 27 days ago by mk190
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what is the deal with bioconda?
... Is there any kind of conflict-checking for this channel? I've never had a problem installing conda packages until I tried: conda create --name seur01 -y conda activate seur01 conda install -c bioconda r-seurat Collecting package metadata (current_repodata.json): done ...
bioconda conda written 28 days ago by mk190 • updated 28 days ago by genomax92k
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Comment: C: content negotiation for the ontobee sparql endpoint
... Whoops, thanks for the link @genomax, somehow I missed that (my above reply concerned obo-discuss) This question is now mirrored on [ontobee-discuss][1], once a solution is tested I will post here [1]: https://groups.google.com/g/ontobee-discuss/c/CxX6kSonc_s ...
written 8 weeks ago by mk190 • updated 8 weeks ago by _r_am30k
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Comment: C: content negotiation for the ontobee sparql endpoint
... I can't post without a mod accepting my join-request, which is currently pending :I edit: see comment by @genomax and reply ...
written 8 weeks ago by mk190
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Comment: C: content negotiation for the ontobee sparql endpoint
... [Ontobee][1] is the default ontology for the [Open Biomedical Ontology Foundry][2] . If there is a 'more standard' access point for the OBO I would be happy to try that instead! [1]: http://www.ontobee.org/faqs [2]: http://www.obofoundry.org/ ...
written 8 weeks ago by mk190
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content negotiation for the ontobee sparql endpoint
... I'm using both the ```format``` query parameter (SPARQL standard) and the HTTP ```Accept``` header (HTTP content negotiation) to specify my desired results format (```application/sparql-results+xml```) and it only returns the full web page with an embedded html table of results. Is there any docume ...
ontobee obofoundry sparql written 8 weeks ago by mk190
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Comment: C: what is the uniprot RDF entity for "uniprot accession"?
... thanks for the thorough answer ...
written 9 weeks ago by mk190
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what is the uniprot RDF entity for "uniprot accession"?
... All proteins on UniProt have a unique accession number. Ex "O15169" is the accession for human Axin 1. Other RDF stores referring to proteins on UniProt use this accession (eg [Pathway Commons reference][2]) [This document][1] describes the RDF schema for UniProt. Where is the UniProt accession ...
rdf uniprot written 9 weeks ago by mk190 • updated 9 weeks ago by me730
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error when trying to perform a federated query in Pathway Commons SPARQL endpoint
... The following query works at [Pathway Commons SPARQL endpoint][1] and returns all proteins that form complexes controlling Wnt signaling pathways: PREFIX rdf: PREFIX owl: PREFIX rdfs: PREFIX xsd: PREFIX bp: PREFIX up: SELECT ?pathway ?protein ?eref WHERE { ...
rdf biopax pathway commons sparql uniprot written 9 weeks ago by mk190 • updated 9 weeks ago by me730

Latest awards to mk

Great Question 8 weeks ago, created a question with more than 5,000 views. For Mapping Ensembl Gene IDs with dot suffix
Supporter 8 weeks ago, voted at least 25 times.
Good Question 10 weeks ago, asked a question that was upvoted at least 5 times. For Mapping Ensembl Gene IDs with dot suffix
Scholar 10 weeks ago, created an answer that has been accepted. For A: Creation of cellDataSet in Monocle 2 wants undocumented AnnotatedDataFrame: assa
Popular Question 4 months ago, created a question with more than 1,000 views. For Linking patient survival to gene-set analysis
Appreciated 18 months ago, created a post with more than 5 votes. For Mapping Ensembl Gene IDs with dot suffix
Popular Question 18 months ago, created a question with more than 1,000 views. For Linking patient survival to gene-set analysis
Popular Question 22 months ago, created a question with more than 1,000 views. For GDC API query to map HT-seq FPKM UUID to a Case UUID
Popular Question 23 months ago, created a question with more than 1,000 views. For GDC API query to map HT-seq FPKM UUID to a Case UUID
Popular Question 2.0 years ago, created a question with more than 1,000 views. For GDC API query to map HT-seq FPKM UUID to a Case UUID
Student 2.0 years ago, asked a question with at least 3 up-votes. For Mapping Ensembl Gene IDs with dot suffix
Scholar 2.9 years ago, created an answer that has been accepted. For A: Creation of cellDataSet in Monocle 2 wants undocumented AnnotatedDataFrame: assa

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