User: ApoorvaB

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ApoorvaB230
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3 weeks, 5 days ago
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Posts by ApoorvaB

<prev • 61 results • page 1 of 7 • next >
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Answer: A: Label Clusters in Seurat
... Another option is to use [Garnett][1] by the Trapnell lab, the same people who gave us monocle. It uses machine learning to train classifiers for a certain cell type and apply those classifiers to a single cell dataset [1]: https://cole-trapnell-lab.github.io/garnett/ ...
written 5 weeks ago by ApoorvaB230
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Answer: A: Remove duplicate genes with lower significance in microarray data analysis
... Order your dataframe by geneid and pvalue and remove duplicated values tT = tT[order(tT$SYMBOL,tT$p.val),] new_tT = tT[ !duplicated(tT$SYMBOL), ] ...
written 7 weeks ago by ApoorvaB230
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Answer: A: Why does Rsubread featureCounts with Ensemble GRCm38.96.GTF picks ensembl_exon_i
... Probably because your gtf file doesnt have a "gene_id". Try featureCounts(data.bam, isPairedEnd = T, isGTFAnnotationFile=T,annot.ext="Mus_musculus.GRCm38.96.gtf", GTF.attrType = "ensembl_gene_id") ...
written 3 months ago by ApoorvaB230
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Answer: A: how to make input data R packge limma
... Hi, If I understand correctly, this is what you need file = read.csv("groupdata.csv") group = factor(file$x, levels=c("Human Lung Tumor","Human Lung Control")) ...
written 3 months ago by ApoorvaB230
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Answer: A: Saving 3D plot from rgl as a pdf
... Thank you. That was very helpful. I did manage to make a gif file. But what i really wanted was a 3D plot in the right orientation for a paper. So i needed a pdf. I used the plot3D package and got the results i was hoping for. For anyone trying to do the same, you can use the links [here][1] and [ ...
written 5 months ago by ApoorvaB230
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Saving 3D plot from rgl as a pdf
... Hi everyone, I made a 3D plot using RGL using the plot3d function. The data is from Diffusion map coordinates of a single cell RNASeq dataset. I tried using rgl.postscript() function to save the plot as a pdf. But there are way too many points and after rendering for nearly an hour, my R studio cra ...
rgl 3dplot written 5 months ago by ApoorvaB230
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Count empty rows in Rhandsontable
... Hi, I'm building a shiny app that uses the rhandson package. I want to make one column editable but also make sure none of the cells can be left empty. I used the following code table= reactive({ a= levels(object$column) b=vector(mode="character",length(a)) df=data.frame(a,b,strin ...
rhandsontable shiny written 11 months ago by ApoorvaB230
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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 12 months ago by ApoorvaB230
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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 12 months ago by ApoorvaB230
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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 12 months ago by ApoorvaB230

Latest awards to ApoorvaB

Popular Question 10 weeks 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 MACS2 Peak Calling : Different number of peaks for each replicate
Popular Question 5 months ago, created a question with more than 1,000 views. For MACS2 Peak Calling : Different number of peaks for each replicate
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 7 months ago, created a question with more than 1,000 views. For Removing batch effects from RPKM data
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Converting narrowpeak files to make it compatible with UCSC trackhub
Popular Question 9 months ago, created a question with more than 1,000 views. For MACS2 Peak Calling : Different number of peaks for each replicate
Popular Question 9 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
Great Question 11 months ago, created a question with more than 5,000 views. For PCA plot of RPKM data from RNA-Seq dataset
Popular Question 12 months ago, created a question with more than 1,000 views. For MACS2 Peak Calling : Different number of peaks for each replicate
Popular Question 12 months ago, created a question with more than 1,000 views. For MACS2 Peak Calling : Different number of peaks for each replicate
Scholar 12 months ago, created an answer that has been accepted. For A: Converting narrowpeak files to make it compatible with UCSC trackhub
Popular Question 17 months ago, created a question with more than 1,000 views. For MACS2 Peak Calling : Different number of peaks for each replicate
Popular Question 17 months ago, created a question with more than 1,000 views. For Removing batch effects from RPKM data
Popular Question 19 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 Removing batch effects from RPKM data
Popular Question 22 months ago, created a question with more than 1,000 views. For MACS2 Peak Calling : Different number of peaks for each replicate
Popular Question 23 months ago, created a question with more than 1,000 views. For MACS2 Peak Calling : Different number of peaks for each replicate
Popular Question 2.3 years ago, created a question with more than 1,000 views. For MACS2 Peak Calling : Different number of peaks for each replicate
Popular Question 2.9 years ago, created a question with more than 1,000 views. For PCA plot of RPKM data from RNA-Seq dataset
Supporter 3.0 years ago, voted at least 25 times.
Popular Question 3.1 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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