User: noorpratap.singh

Reputation:
240
Status:
Trusted
Location:
India
Website:
https://github.com/NPSDC
Last seen:
4 hours ago
Joined:
2 years, 7 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 • 50 results • page 1 of 5 • next >
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Comment: C: Error in GDCprepare
... Updated. Thanks for the advise. ...
written 14 days ago by noorpratap.singh240
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Comment: C: Difficulty Converting lncRNA gene symbol to Ensembl
... The following website might help https://genealacart.genecards.org/Query You need create an account. In addition directly going to genecards website and typing the RNA in query is also a way around if you have a very limited set of genes ...
written 14 days ago by noorpratap.singh240
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Comment: C: Error in GDCprepare
... Hi, Few things. Coming specifically to your query, the returned object of GDCPrepare is a data.frame (not an object of any other class). Thus you cannot apply assay function. Raw counts are present in the data.frame along with the other elements. To extract them use following: ``` Matrix.C1 <- ...
written 14 days ago by noorpratap.singh240
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Answer: C: Error in GDCprepare
... Could you please write the query, otherwise its hard to speculate. Further at times errors occur using this package owing to updates. Make sure you update it by typing the following command in R/Rstudio. ``` devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks") ``` ...
written 15 days ago by noorpratap.singh240
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Comment: C: RNAseq differential expression analysis : learning design matrix
... I have gone through these courses and these actually provide a solid intuition behind the same. ...
written 19 days ago by noorpratap.singh240
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Answer: C: RNA-seq Differential Gene Analysis
... It depends on the needs. Ideally first a FDR (mostly 0.05 but this can also change) is set and then the fold change is applied. Start with a lower threshold (say 0.5 or 1) and observe the total number of genes derived. Do an enrichment and see the key processes arrived at. Then increase the threshol ...
written 19 days ago by noorpratap.singh240
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Comment: C: Is it fine to run SVM on RNA-seq read counts?
... If I interpret correctly you are implying you are get 100% accuracy on the test data. As such there is no problem in running SVM on RNA-seq read counts but the results you seem to get are not believable. It is hard to comment without looking at your code snippet. As such it seems, there is some ov ...
written 4 weeks ago by noorpratap.singh240
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Answer: A: Beginner: looking for suggestions
... Being from a CS background my self, I can perhaps provides some insights. Bioinformatics as such is a vast field, covering different areas. Since programming wont be much of issue, biology and statistics background is something you need to pick up. Following two repositories provides a comprehensive ...
written 7 weeks ago by noorpratap.singh240
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Comment: C: Annotation of Methylation data in GDC Portal
... Thanks for the reply. I knew this but often in papers I come across Open Seas so thats why this question. ...
written 11 weeks ago by noorpratap.singh240
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Annotation of Methylation data in GDC Portal
... I was specifically looking at rowData of the SummarizedExperiment object that is obtained after downloading from TCGABiolinks package. So in this data.frame, a particular column called '*Feature type*' exists. It contains information about S_Shore, N_Shore, CGI, N_Shelf, S_Shelf. However I also see ...
dna methylation tcga illumina 450k gdc written 12 weeks ago by noorpratap.singh240

Latest awards to noorpratap.singh

Scholar 14 days ago, created an answer that has been accepted. For A: Random forest for gene expression
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: Random forest for gene expression
Supporter 14 days ago, voted at least 25 times.
Popular Question 16 days ago, created a question with more than 1,000 views. For Getting subtypes of cancer from TCGA
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: Random forest for gene expression
Scholar 7 weeks ago, created an answer that has been accepted. For A: Random forest for gene expression
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Random forest for gene expression
Popular Question 3 months ago, created a question with more than 1,000 views. For Getting subtypes of cancer from TCGA
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Random forest for gene expression
Scholar 12 months ago, created an answer that has been accepted. For A: Random forest for gene expression
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Random forest for gene expression
Autobiographer 17 months ago, has more than 80 characters in the information field of the user's profile.
Popular Question 18 months ago, created a question with more than 1,000 views. For Getting subtypes of cancer from TCGA
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Retrieving data from new data portal of tcga

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