User: ApoorvaB

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ApoorvaB140
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140
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United States
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Joined:
3 years, 10 months ago
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Posts by ApoorvaB

<prev • 54 results • page 1 of 6 • next >
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Answer: C: Error displaying GTEX like boxplot in UCSC Genome Browser
... I emailed this issue to UCSC and I heard back from them almost immediately. It was a very silly error. I'm posting this here just in case someone has a similar error This was the line from my trackDb file Track scRNA-Seq superTrack on show shortLabel scRNA-Seq longLabel This track contains expr ...
written 10 days ago by ApoorvaB140
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Error displaying GTEX like boxplot in UCSC Genome Browser - "Error creating boxplot from sample data"
... Hi, I'm trying to create a GTEx-like barChart and boxplot in UCSC Genome Browser for my data. I followed the instructions on the UCSC help page. The trackhub loads without an error. I can see the barChart in the browser. However, if I click on the barChart, I'm not getting the boxplot. Instead I ge ...
boxplot gtex barcharts genomebrowser ucsc written 13 days ago by ApoorvaB140
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Answer: A: how to do TSNEPlot which differentiate the sample and cluster at the same time i
... I'm sorry I don't really understand your question. If you mean highlight one specific cluster in the tsne, you can use the cells.highlight argument. So first select the cells you want to highlight (lets say cluster 1) and then plot it. cells=names(onject@ident[object@ident==1]) plot=TSNEPlo ...
written 15 days ago by ApoorvaB140
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Answer: A: Converting narrowpeak files to make it compatible with UCSC trackhub
... Found this in a google groups thread. It worked. There is a way to circumvent this error from bedToBigBed. Instead of declaring your bigBed as a 6+4, you can make a bed4+6, and supply the narrowPeak.as AutoSql file like so: $ bedToBigBed -type=bed4+6 -as=narrowPeak.as narrowPeakFile chrom.siz ...
written 25 days ago by ApoorvaB140 • updated 25 days ago by genomax55k
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Converting narrowpeak files to make it compatible with UCSC trackhub
... Hi, I am trying to create a trackhub on UCSC genome browser. I have trackfiles in bigwig format and some narrowpeak files as well. Narrowpeak isn't in the list of accepted formats for trackhub. So I tried to convert it to bigbed file using the ucsc utility bedToBigBed. This is the command i gave ...
narrowpeakfile ucscutilites genomebrowser ucsc written 25 days ago by ApoorvaB140
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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 5 months ago by ApoorvaB140
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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 6 months ago by ApoorvaB140
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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 6 months ago by ApoorvaB140
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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 7 months ago by ApoorvaB140 • updated 3 months ago by dppb0570
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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 11 months ago by ApoorvaB140

Latest awards to ApoorvaB

Popular Question 23 days ago, created a question with more than 1,000 views. For MACS2 Peak Calling : Different number of peaks for each replicate
Scholar 25 days ago, created an answer that has been accepted. For A: Converting narrowpeak files to make it compatible with UCSC trackhub
Popular Question 4 months ago, created a question with more than 1,000 views. For MACS2 Peak Calling : Different number of peaks for each replicate
Popular Question 4 months ago, created a question with more than 1,000 views. For Removing batch effects from RPKM data
Popular Question 6 months ago, created a question with more than 1,000 views. For MACS2 Peak Calling : Different number of peaks for each replicate
Popular Question 6 months ago, created a question with more than 1,000 views. For Removing batch effects from RPKM data
Popular Question 10 months ago, created a question with more than 1,000 views. For MACS2 Peak Calling : Different number of peaks for each replicate
Popular Question 11 months ago, created a question with more than 1,000 views. For MACS2 Peak Calling : Different number of peaks for each replicate
Popular Question 16 months ago, created a question with more than 1,000 views. For MACS2 Peak Calling : Different number of peaks for each replicate
Popular Question 22 months ago, created a question with more than 1,000 views. For PCA plot of RPKM data from RNA-Seq dataset
Supporter 2.0 years ago, voted at least 25 times.
Popular Question 2.1 years ago, created a question with more than 1,000 views. For PCA plot of RPKM data from RNA-Seq dataset

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