User: AB

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AB90
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90
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3 weeks, 5 days ago
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3 years, 7 months ago
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Posts by AB

<prev • 49 results • page 1 of 5 • next >
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Answer: A: KEGGREST: how to retrieve compound list by pathway ID
... This should work ``` keggGet("pathway_id")[[1]]$COMPOUND ``` As for using the KEGG API in R, I'm not aware of it. You should be able to pull all the data you need using KEGGREST ...
written 11 weeks ago by AB90
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Answer: A: How to extract PRDM9 binding motifs in bed format?
... Not entirely sure if this will help but maybe you can try using the HOMER software's scanMotifGenomeWide.pl ...
written 12 weeks ago by AB90
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Answer: A: Protein-protein Docking Software?
... I would suggest Hex or Haddock. But there are others. Maybe this list will help http://www.geneinfinity.org/sp/sp_structdocking.html ...
written 12 weeks ago by AB90
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Classify cells using seurat
... Hi, I am working on single cell data and I have a general question. Monocle has a function 'classifyCells' to assign celltype using known marker genes. Here is the bit from the documentation ``` cth <- newCellTypeHierarchy() MYF5_id <- row.names(subset(fData(cds), gene_short_name == "MYF5") ...
monocle scrna seurat written 3 months ago by AB90 • updated 2 days ago by dppb0550
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Answer: C: converting vcf to text file
... This post here has a very similar question https://www.biostars.org/p/100779/ However, i just read in my VCF file into R using the vcfR package, converted it into a dataframe and manually changed the genotype information. Also, as mentioned in one of the comments in that post, vcf-to-tab can be ...
written 8 months ago by AB90
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Comment: C: converting vcf to text file
... So this is the format of the snp.txt file as required by Matrix EQTL R package. The description only says the file should have the genotype information for the markers across all the samples id Sam_01 Sam_02 Sam_03 Sam_04 Sam_05 Sam_06 Sam_07 Sam_08 Sam_09 Sam_10 Sam_11 Sam_12 Sam_13 Sam_14 Sam ...
written 8 months ago by AB90 • updated 8 months ago by Pierre Lindenbaum108k
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converting vcf to text file
... Hi, I want to run Matrix EQTL on my data. I have the genotype information as an imputed VCF file and matrix EQTL requires a Snp.txt file. How can convert the vcf to a text file ?? Thanks, Apoorva ...
vcf matrix eqtl eqtl written 8 months ago by AB90
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Comment: C: UCSC Fasta files by chromosome for rn6
... Thank you very much Apoorva ...
written 8 months ago by AB90
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UCSC Fasta files by chromosome for rn6
... Hi, Ive noticed UCSC downloads page has fasta files by chromosome for hg19 and mm9. But that isn't available for rn6. Is there some place from where i can download fasta files by chromosome for rn6 genome assembly ? Apoorva ...
fasta rn6 ucsc written 8 months ago by AB90 • updated 8 months ago by genecats.ucsc500
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Database of mouse ligand receptors
... Hi All, I was wondering if there is a website or a database where you can download a list of mouse genes that are ligand receptors in a tab-delimited format. Thanks AB ...
mm9 database ligand-receptor written 8 months ago by AB90 • updated 8 months ago by jared.andrews07730

Latest awards to AB

Popular Question 7 weeks ago, created a question with more than 1,000 views. For MACS2 Peak Calling : Different number of peaks for each replicate
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Removing batch effects from RPKM data
Popular Question 3 months ago, created a question with more than 1,000 views. For MACS2 Peak Calling : Different number of peaks for each replicate
Popular Question 3 months ago, created a question with more than 1,000 views. For Removing batch effects from RPKM data
Popular Question 7 months ago, created a question with more than 1,000 views. For MACS2 Peak Calling : Different number of peaks for each replicate
Popular Question 8 months ago, created a question with more than 1,000 views. For MACS2 Peak Calling : Different number of peaks for each replicate
Popular Question 13 months ago, created a question with more than 1,000 views. For MACS2 Peak Calling : Different number of peaks for each replicate
Popular Question 19 months ago, created a question with more than 1,000 views. For PCA plot of RPKM data from RNA-Seq dataset
Supporter 21 months ago, voted at least 25 times.
Popular Question 22 months ago, created a question with more than 1,000 views. For PCA plot of RPKM data from RNA-Seq dataset

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