User: noorpratap.singh
noorpratap.singh • 110
- Reputation:
- 110
- Status:
- 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
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... 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.singh • 110
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... 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 ...
written 7 weeks ago by
noorpratap.singh • 110
• updated
7 weeks ago by
Charles Warden ♦ 5.6k
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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.singh • 110
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... Hi,
You can extract that information from the following link:
http://firebrowse.org/?cohort=HNSC&download_dialog=true ...
written 7 months ago by
noorpratap.singh • 110
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... Hi,
Have a go through this link
http://satijalab.org/seurat/ ...
written 7 months ago by
noorpratap.singh • 110
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... 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.singh • 110
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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.singh • 110
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... 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.singh • 110
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... 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.singh • 110
0
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... 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.singh • 110
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