User: Shaurya Jauhari

Reputation:
40
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New User
Location:
China
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http://www.twitter.com...
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shauryajauhari
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Last seen:
2 months, 4 weeks ago
Joined:
7 years, 9 months ago
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about me

Posts by Shaurya Jauhari

<prev • 40 results • page 1 of 4 • next >
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Comment: A: Inconsistency in shinyFiles output.
... **EDIT:** **server.R** shinyServer(function(input, output, session){ ... dataFolder <- NULL ## directory path ## Validating path and confirming upload output$filepaths <- renderText({ shinyFileChoose(input, "files", ...
written 4 months ago by Shaurya Jauhari40
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(Closed) Inconsistency in shinyFiles output.
... Hi there. My objective is to record a folder path that contains BED files. The user is required to browse to the folder and choose any BED file. On doing that the absolute path to that folder gets recorded. I have a working code below. ui <- shinyUI(bootstrapPage( shinyFilesButton('fil ...
server.r shinyapp shinyfiles written 4 months ago by Shaurya Jauhari40
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Comment: A: plotProfile (deepTools) generated a peak on gene body region
... Hello. Not sure if my problem aligns perfectly to this thread, but I want to share some weird plots from the computeMatrix-plotProfile workflow. Not sure about "flatness" of the plot. computeMatrix scale-regions \ -R LD9783.bed \ -S H3K4me1.bw \ H3K4me2.bw \ H3K4me3.bw \ H3 ...
written 4 months ago by Shaurya Jauhari40
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Comment: A: Mapping reads from a BAM file to a custom BED file.
... To illustrate my point, would something like this be advisable. The "targetBED" is the file for specific sized genomic regions, while "sourceBED" has heterogeneous regions with a score. mappingReadsBins <- function(targetBED, sourceBED) { sourceBED$Chrom <- factor(sourc ...
written 6 months ago by Shaurya Jauhari40
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Comment: C: Mapping reads from a BAM file to a custom BED file.
... I wouldn't say it is a problem, but the layout of the output file I desire is such- scores in homogeneous bins. Secondly, a post-process of the bedGraph file is surely doable. I just want to know if there are any tools already that can help achieve that. In R, I am trying looping over all the lines ...
written 6 months ago by Shaurya Jauhari40
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Mapping reads from a BAM file to a custom BED file.
... Hi. I have a BED file that was engendered with the following: bedtools makewindows -g ../bedtools2/genomes/human.hg19.genome -w 2000 > hg19_2K_bins.bed The goal is to map reads from a BAM file to the intervals as defined, to visualize the distribution of the counts pan-genome, bin-wise. No ...
chip-seq bed file bam file written 7 months ago by Shaurya Jauhari40
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How are the transcription factories and the enhancer-promoter interactions linked?
... The general awareness about gene regulation is that enhancer sequences from a remote location in the genome also (and quite often) interact with the gene promoter thereby triggering transcription. Several other complexes including transcription factors, co-activators, other binders play key roles to ...
transcription factories written 10 months ago by Shaurya Jauhari40
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Answer: A: How To Extract Go Terms From A Given Kegg Id
... Via transitivity; **GO** <-> Orthology (KO terms), Orthology <-> PubmedID, PubmedID <-> **Pathway**; KEGG API/ LinkDB allows for structuring a many-many linkage map between GO and Pathway terms that isn't directly available (although marked 'routed' on the official page). This has ...
written 19 months ago by Shaurya Jauhari40
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Comment: C: Variable definition in R
... Thanks zx8754. Few things here though: 1. I completely dig that **lapply()** usage shall be a viable alternative, and it works; just that the same error is engendered. 2. The question here is not just to read a file, rather also to save it as a R data object for further manipulation. 3. The vari ...
written 20 months ago by Shaurya Jauhari40
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(Closed) Variable definition in R
... Hi everyone. I have the following line of code where R rejects the expression on the left to be treated as an assignee variable. for (i in 1:length(my_list)){ paste(eval(parse(text='names(my_list[i])')),"table",sep="") <- read.table(paste("./foo/",paste(eval(parse(text='names(my_list[i] ...
R written 20 months ago by Shaurya Jauhari40

Latest awards to Shaurya Jauhari

Popular Question 10 months ago, created a question with more than 1,000 views. For SVM for classified gene expression data
Popular Question 18 months ago, created a question with more than 1,000 views. For SVM for classified gene expression data
Popular Question 2.2 years ago, created a question with more than 1,000 views. For SVM for classified gene expression data
Popular Question 2.8 years ago, created a question with more than 1,000 views. For SVM for classified gene expression data
Popular Question 4.6 years ago, created a question with more than 1,000 views. For SVM for classified gene expression data

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