User: noorpratap.singh

Reputation:
80
Status:
Trusted
Location:
India
Website:
https://github.com/NPSDC
Last seen:
3 hours ago
Joined:
1 year, 7 months ago
Email:
n***************@research.iiit.ac.in

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 • 33 results • page 1 of 4 • next >
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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 1 day ago by noorpratap.singh80
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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 1 day ago by noorpratap.singh80
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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 2 days ago by noorpratap.singh80
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Comment: C: gene expression anti-correlation data?
... Just find the correlation among the genes of interest and if its negative it means they are anti-correlated. Assuming you are using R, you can use the cor function which would return you a g*g matrix where g are the number of genes. Now if there is strong anticorrelation. then you can keep a thresho ...
written 3 days ago by noorpratap.singh80
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Comment: C: RNA-Seq DGE using PCA components as covariate
... Hi Kevin, I understand your point that family wide variations are not that big but they definitely seem to bigger than case vs control and they seem to cluster more than families as such for patient 20 and and 30. ...
written 5 days ago by noorpratap.singh80
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Comment: C: Can DNA Methylation data of different samples from Human Methylation 27 and 450
... I apparently don't have a reference but coming to the first question the data matrices should be converted into an RGChannelSet, a MethylSet, a RatioSet, a GemomicMethylSet or a GenomicRatioSet. These terms are clearly explained here https://www.bioconductor.org/help/course-materials/2015/BioC2015/m ...
written 6 days ago by noorpratap.singh80
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Answer: A: Can DNA Methylation data of different samples from Human Methylation 27 and 450
... Yes, simple combining can be done. However I would suggest use existing implementations in packages such as minfi or MethylMix. In minfi there exists a function called 'combineArrays'. ...
written 6 days ago by noorpratap.singh80
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Comment: C: technical problem with R and GO terms
... I dont understand exactly the pattern but following is the code snippet: add_col <- c() df #data.frame containing the two columns for(i in df[,1]) { if(i matches pattern) add_col <- c(add_col, 'yes') else add_col <- c(add_col, 'no') } cbind(df, add_col) If pattern i ...
written 8 days ago by noorpratap.singh80
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Comment: C: Illumina 450K array manifest for hg38?
... So did you get any success. Even today I am struggling to find hg38 CpG probes. ...
written 9 days ago by noorpratap.singh80
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Comment: C: Random forest for gene expression
... Well for starters you can do a 10-fold cross validation. There exists functions in any language for doing it. ...
written 10 days ago by noorpratap.singh80

Latest awards to noorpratap.singh

Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Random forest for gene expression
Scholar 10 days ago, created an answer that has been accepted. For A: Random forest for gene expression
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Random forest for gene expression
Autobiographer 5 months ago, has more than 80 characters in the information field of the user's profile.
Popular Question 6 months ago, created a question with more than 1,000 views. For Getting subtypes of cancer from TCGA
Popular Question 13 months ago, created a question with more than 1,000 views. For Retrieving data from new data portal of tcga

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