User: Apoorva

gravatar for Apoorva
Apoorva250
Reputation:
250
Status:
Trusted
Location:
United States
Last seen:
1 month, 1 week ago
Joined:
5 years, 9 months ago
Email:
a************@gmail.com

Posts by Apoorva

<prev • 62 results • page 1 of 7 • next >
0
votes
1
answer
123
views
1
answer
Identifying appearance or disappearance of cell populations between WT and Mut single cell RNA-Seq data
... Hi everyone, I've done single cell RNA-seq data analysis using Seurat. Now if I have 2 samples, a wild type and a mutant and I want to find out if any new cell populations appear or any cell population disappears in the mutant, how do i test for it ? I looked at this [tutorial][1] and it explains ...
single cell rna-seq seurat written 7 weeks ago by Apoorva250 • updated 7 weeks ago by igor11k
0
votes
2
answers
2.8k
views
2
answers
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 11 months ago by Apoorva250
2
votes
2
answers
839
views
2
answers
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$SYMBOL), ] ...
written 12 months ago by Apoorva250
0
votes
2
answers
535
views
2
answers
Answer: A: Why does Rsubread featureCounts with Ensemble GRCm38.96.GTF picks ensembl_exon_i
... Probably because your gtf file doesnt have a "gene_id". Try featureCounts(data.bam, isPairedEnd = T, isGTFAnnotationFile=T,annot.ext="Mus_musculus.GRCm38.96.gtf", GTF.attrType = "ensembl_gene_id") ...
written 14 months ago by Apoorva250
1
vote
1
answer
460
views
1
answers
Answer: A: how to make input data R packge limma
... Hi, If I understand correctly, this is what you need file = read.csv("groupdata.csv") group = factor(file$x, levels=c("Human Lung Tumor","Human Lung Control")) ...
written 14 months ago by Apoorva250
1
vote
3
answers
2.8k
views
3
answers
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 15 months ago by Apoorva250
3
votes
3
answers
2.8k
views
3
answers
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 16 months ago by Apoorva250
0
votes
0
answers
702
views
0
answers
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 21 months ago by Apoorva250
0
votes
1
answer
568
views
1
answers
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 23 months ago by Apoorva250
0
votes
1
answer
568
views
1
answer
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 23 months ago by Apoorva250

Latest awards to Apoorva

Great Question 6 weeks ago, created a question with more than 5,000 views. For PCA plot of RPKM data from RNA-Seq dataset
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 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 Determine Condition using LogFC values
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 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 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 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 14 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 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
Teacher 17 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 20 months ago, created a question with more than 1,000 views. For MACS2 Peak Calling : Different number of peaks for each replicate
Popular Question 20 months ago, created a question with more than 1,000 views. For Removing batch effects from RPKM data
Popular Question 21 months ago, created a question with more than 1,000 views. For MACS2 Peak Calling : Different number of peaks for each replicate
Great Question 22 months ago, created a question with more than 5,000 views. For PCA plot of RPKM data from RNA-Seq dataset
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
Scholar 23 months ago, created an answer that has been accepted. For A: Converting narrowpeak files to make it compatible with UCSC trackhub
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 2.3 years ago, created a question with more than 1,000 views. For Removing batch effects from RPKM data

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1363 users visited in the last hour