User: raunakms

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raunakms980
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Vancouver, BC, Canada
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https://github.com/rau...
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raunakms
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Bioinformatician | Data Scientist | Cancer Genomics| Systems Biology | PhD Candidate | University of British Columbia | Vancouver | Canada | A Nepali

Posts by raunakms

<prev • 60 results • page 1 of 6 • next >
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Answer: A: Matched Normal Tissue Sample of RNAseq data from TCGA
... You may use data from GTEx Project selecting the appropriate tissue type. [https://gtexportal.org/][1] [1]: https://gtexportal.org/ ...
written 7 weeks ago by raunakms980
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Answer: A: problem for gene survival analysis through "Survival" package in R
... The main strategy here is to first use the information of the gene to stratify the patients into different groups (for example: High gene expression group vs. Low gene expression group, or Mutated gene group vs. Non-mutated gene group, etc)and only then perform the survival analysis. Then call the f ...
written 3 months ago by raunakms980
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Comment: C: HIT'nDRIVE: Network based cancer driver genes prioritization algorithm using Hit
... Yes, there could possibly be many approaches to solve the problem. We wanted to use maximum parsimony based combinatorial optimization approach. Here, we want to find the most parsimonious set of driver genes which can have maximum impact (i.e. cover) on a user defined proportion of expression-outli ...
written 19 months ago by raunakms980
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Comment: C: HIT'nDRIVE: Network based cancer driver genes prioritization algorithm using Hit
... In a very general sense, MCL clustering algorithm uses graph flow (i.e. network propagation) to cluster the graph. In case of HIT'nDRIVE, we also use network propagation (random walk) on graph to measure (or quantify) distant interactions. Our main contribution is the use of distance measure - "Mul ...
written 19 months ago by raunakms980
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Comment: C: HIT'nDRIVE: Network based cancer driver genes prioritization algorithm using Hit
... That would be great. ...
written 19 months ago by raunakms980
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Comment: C: HIT'nDRIVE: Network based cancer driver genes prioritization algorithm using Hit
... We have not used proteomics data yet. You can get proteomics data for the samples used in TCGA from CPTAC project [https://cptac-data-portal.georgetown.edu/cptacPublic/][1] [1]: https://cptac-data-portal.georgetown.edu/cptacPublic/ ...
written 19 months ago by raunakms980
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Tool: HIT'nDRIVE: Network based cancer driver genes prioritization algorithm using Hitting Time
... HIT'nDRIVE is a network based cancer driver gene prioritization algorithm. It is a combinatorial optimization method that integrates genomic changes with changes in transcriptome (expression outliers) to identify a set of patient-specific, sequence-altered genes, with sufficient collective influence ...
software driver gene network tool written 19 months ago by raunakms980 • updated 19 months ago by inambioinfo90
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Answer: A: Get feature from location from gff3
... Your BLAST hits must have the sequence location coordinates. Now match those coordinates with the gff annotation. ...
written 23 months ago by raunakms980
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Answer: A: CYP2D6 haplotype reconstruction
... Refer to this paper: Cypiripi [https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btv232][1] [1]: https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btv232 ...
written 2.0 years ago by raunakms980
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Comment: C: How can I get control RNAseq data?
... Look at the download section in the GTEx website (http://www.gtexportal.org/home/), look at the sample ID that matches to kidney tissues and download it !!! ...
written 2.0 years ago by raunakms980

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Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Detecting Polymorphic Sites In Multiple Sequence Aligned Files
Appreciated 22 months ago, created a post with more than 5 votes. For A: Detecting Polymorphic Sites In Multiple Sequence Aligned Files
Guru 2.2 years ago, received more than 100 upvotes.
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Bootstrapping In Clustalw
Scholar 3.5 years ago, created an answer that has been accepted. For A: How to match and reorder these vectors in R
Scholar 3.9 years ago, created an answer that has been accepted. For A: How to match and reorder these vectors in R
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: Detecting Polymorphic Sites In Multiple Sequence Aligned Files
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: Detecting Polymorphic Sites In Multiple Sequence Aligned Files
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: Detecting Polymorphic Sites In Multiple Sequence Aligned Files
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