User: O.rka

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O.rka70
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Posts by O.rka

<prev • 87 results • page 1 of 9 • next >
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Comment: C: Where can I download ALL pfam flat-file annotations?
... I essentially want to get the name and description given a pfam identifier. For example, `'PF01565': {'NAME': 'FAD_binding_4', 'DESCRIPTION': 'FAD binding domain'}` ...
written 4 days ago by O.rka70
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Comment: C: Where can I download ALL pfam flat-file annotations?
... I only found one file with annotations ^^^. Do you know if there is another file on the ftp site? ...
written 4 days ago by O.rka70
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Where can I download ALL pfam flat-file annotations?
... I tried downloading the following: ftp://ftp.ebi.ac.uk/pub/databases/Pfam/mappings/pdb_pfam_mapping.txt but it's missing a huge number of PFAM ids. For example, `PF13276` isn't in there. Is there another place where I can get these flatfiles? ...
domain pfam annotations flat-files written 4 days ago by O.rka70
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Comment: C: In GSEA, how can one "correlate" gene expression with categorical phenotype data
... I will keep that in mind for the future. Thanks for the help even though this was out of scope. These links are really useful. ...
written 5 days ago by O.rka70
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Does MetaCyc or BioCyc have an equivalent of KEGG orthologs that could be blasted against locally?
... I've been using [HUMAnN2](http://huttenhower.sph.harvard.edu/humann2) to go from human-removed microbiome shotgun metagenomic reads to HUMAnN2 attribute vectors with coverage and abundance values. The resulting attributes have identifiers that have the following structure: `HISDEG-PWY: L-histidine ...
metacyc orthologs biocyc humann2 metagenomics written 5 days ago by O.rka70
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Comment: C: In GSEA, how can one "correlate" gene expression with categorical phenotype data
... Hey Kevein, thanks this is making a lot of sense once I plotted data. I don't know why but it always seemed incorrect to look at correlations in this way but you're right and I definitely get it now. Also, your linear model at the end is interesting. I'm pretty new to linear models used in this ...
written 5 days ago by O.rka70
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In GSEA, how can one "correlate" gene expression with categorical phenotype data?
... > The magnitude of the increment depends on the correlation of the gene > with the phenotype. The enrichment score is the maximum deviation from > zero encountered in the random walk; it corresponds to a weighted > Kolmogorov–Smirnov-like statistic (ref. 7 and Fig. 1B). > http://www. ...
pearson genes correlation gsea expression written 6 days ago by O.rka70 • updated 6 days ago by Kevin Blighe32k
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Run GSEA with custom gene sets?
... Is there a way to use custom gene sets using GSEA? I downloaded GSEApy and would love to use it within Python but if this is not possible then I can definitely use the commandline version. For example, what if I had the following data: # Gene list gene_list = [ "gene_A", "gene_B" ...
gene enrichment differential-abundance custom gsea written 6 days ago by O.rka70 • updated 6 days ago by h.mon21k
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Comment: C: How to use Biopython for fetching metadata of NCBI/GenBank/RefSeq assembly ident
... Wow, this answer is incredible! Thank you so much. This actually makes a lot of sense on why my previous version wasn't working. Did you write this or did you find it in the docs somewhere? ...
written 27 days ago by O.rka70
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Comment: C: How to use Biopython for fetching metadata of NCBI/GenBank/RefSeq assembly ident
... handle = Entrez.efetch(db="assembly", id="GCF_000005845.2") record = Entrez.read(handle) record # ['5845', '2'] ...
written 27 days ago by O.rka70

Latest awards to O.rka

Popular Question 4 weeks ago, created a question with more than 1,000 views. For Differential Gene Expression (EdgeR?) : What are the steps in computing this?
Scholar 5 weeks ago, created an answer that has been accepted. For A: Can you assemble with merged paired end reads and unmatched reads as "single end
Popular Question 3 months ago, created a question with more than 1,000 views. For Differential Gene Expression (EdgeR?) : What are the steps in computing this?
Popular Question 3 months ago, created a question with more than 1,000 views. For Most up-to-date Gene Ontology [GO] analysis?
Great Question 6 months ago, created a question with more than 5,000 views. For How to tell bloodtype from SNPs data?
Popular Question 7 months ago, created a question with more than 1,000 views. For Differential Gene Expression (EdgeR?) : What are the steps in computing this?
Popular Question 11 months ago, created a question with more than 1,000 views. For Differential Gene Expression (EdgeR?) : What are the steps in computing this?
Supporter 20 months ago, voted at least 25 times.
Popular Question 21 months ago, created a question with more than 1,000 views. For How to tell bloodtype from SNPs data?
Student 2.3 years ago, asked a question with at least 3 up-votes. For Most up-to-date Gene Ontology [GO] analysis?

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