User: noorpratap.singh

Reputation:
110
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Trusted
Location:
India
Website:
https://github.com/NPSDC
Last seen:
2 minutes ago
Joined:
2 years, 4 months ago
Email:
n*********@gmail.com

I am currently doing my  MS at IIIT-H where I am enrolled in CND program(Btech in Computer Science and MS by Research in Computational Natural Sciences. My interests lie in interplay of Computer Science and Biology. 

Posts by noorpratap.singh

<prev • 40 results • page 1 of 4 • next >
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Comment: C: Finding Correlation between methylation and RNA-Seq data and their significance
... Hi Charles, Thanks for replying. You are correct to mention that I am describing the strategy of R function cor.test to compute p-value. I have two groups tumor and non-tumor. As such biomodal distribution exists but for correlation I have to use both the groups. So this makes me uncomfortable to e ...
written 7 weeks ago by noorpratap.singh110
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Finding Correlation between methylation and RNA-Seq data and their significance
... I had a couple of questions. First - Is there any specific reason to pick spearman or pearson correlation? Which one is usually the more preferred one and why? Second - For computing significance of the correlation, a common method employed is to compute the t-statistic from the correlation value ...
correlation methylation rna-seq written 7 weeks ago by noorpratap.singh110 • updated 7 weeks ago by Charles Warden5.6k
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Answer: A: GDC portal barcode / metadata
... If you are familiar with R, then things are really easy. There is a package called [TCGABiolinks][1]. For your case examples 3 and 4 are useful. Make sure to use legacy = T, since I am not sure whether the subtypes exist for the updated data. If you are uncomfortable with R then you have to downloa ...
written 3 months ago by noorpratap.singh110
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Answer: A: Tumor grade from miRNA data set from TCGA database
... Hi, You can extract that information from the following link: http://firebrowse.org/?cohort=HNSC&download_dialog=true ...
written 7 months ago by noorpratap.singh110
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Answer: A: single cell RNAseq: From counts or RPKM > PCA > tSNE visualization of PCA
... Hi, Have a go through this link http://satijalab.org/seurat/ ...
written 7 months ago by noorpratap.singh110
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Answer: A: Differentially methylated regions Analysis
... Hi David, For RNA-Seq data use DESeq2. This is the most common package used for analysing RNASeq data and carrying differential analysis with a very helpful documentation and large community to help. For Methylation you can use minfi. Hope it helps. ...
written 8 months ago by noorpratap.singh110
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Answer: A: Gene expression study
... Directly comparing datasets from two studies might impact interpretation because of individual dataset biases. Usually for these there exist packages that enable meta analyses i.e combining data from platforms. [Mtea Seq][1] is one such package. I would urge to you explore on these lines. [1]: h ...
written 9 months ago by noorpratap.singh110
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Answer: A: Intersection 5 sets of genes and retrieval of specific subsets
... get.int.genes <- function(genes.list) { total.genes <- Reduce(union, genes.list) genes.req <- list() for(i in c(paste('only ', c(1:5)), paste("common ", c(2:5)))) genes.req[[i]] <- c() for(gene in total.genes) { count = 0 set. ...
written 9 months ago by noorpratap.singh110
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Answer: A: Differential Expression Gene analysis using normalized data
... I can't help with analysing normalised data but you could use TCGABiolinks for downloading raw count data from TCGA. [1]: https://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html ...
written 9 months ago by noorpratap.singh110
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Comment: C: Detecting error in Ubuntu environment
... Could you share the script. It seems it is trying to create a temp directory which you cannot excess or does not exist. Possibly changing that directory where it stores might help. ...
written 9 months ago by noorpratap.singh110

Latest awards to noorpratap.singh

Popular Question 5 days ago, created a question with more than 1,000 views. For Getting subtypes of cancer from TCGA
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Random forest for gene expression
Scholar 9 months ago, created an answer that has been accepted. For A: Random forest for gene expression
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Random forest for gene expression
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Popular Question 15 months ago, created a question with more than 1,000 views. For Getting subtypes of cancer from TCGA
Popular Question 22 months ago, created a question with more than 1,000 views. For Retrieving data from new data portal of tcga

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