User: raunakms

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raunakms1.1k
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Post-doctoral scholar | PhD in Bioinformatics | Data Scientist | Cancer Genomics | Systems Medicine | University of British Columbia | Vancouver | Canada

Posts by raunakms

<prev • 63 results • page 1 of 7 • next >
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Answer: A: How do I assess quality of hierarchical clustering?
... You could perform bootstrapping experiment (i.e. permuting the data for a large number of times) and then compute the bootstrap p-values for the dendogram. This will provide you p-values of each nodes in the dendogram indicating the confidence on the dendogram structure. If you are using R, the R-pa ...
written 3 months ago by raunakms1.1k
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Comment: C: How to check if first two components of PCA are separated without visualisation?
... Think of the eigenvalues of PC1 and PC2 as x and y coordinates defining each dot in the plot above. The dots highlighted with Red and Blue colors in the plot above are your two sample classes. (1) In-class distance: pair-wise Euclidean distance between each dots highlighted in Red (or Blue). (2) O ...
written 3 months ago by raunakms1.1k
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Answer: A: How to check if first two components of PCA are separated without visualisation?
... First get the PCA eigenvalues of the first two Principal Components (PC1 & PC2) using `pca$x[,1:2]`. Then calculate **in-class distance** (i.e. the pairwise distance between the samples belonging to the same class) as well as **out-class distance** (i.e. the pairwise distance between a sample be ...
written 4 months ago by raunakms1.1k
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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 5 months ago by raunakms1.1k
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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 7 months ago by raunakms1.1k
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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 23 months ago by raunakms1.1k
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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 23 months ago by raunakms1.1k
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Comment: C: HIT'nDRIVE: Network based cancer driver genes prioritization algorithm using Hit
... That would be great. ...
written 23 months ago by raunakms1.1k
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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 23 months ago by raunakms1.1k
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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 24 months ago by raunakms1.1k • updated 23 months ago by inambioinfo90

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Great Question 4 weeks ago, created a question with more than 5,000 views. For Bootstrapping In Clustalw
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Detecting Polymorphic Sites In Multiple Sequence Aligned Files
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: Detecting Polymorphic Sites In Multiple Sequence Aligned Files
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: Detecting Polymorphic Sites In Multiple Sequence Aligned Files
Appreciated 2.1 years ago, created a post with more than 5 votes. For A: Detecting Polymorphic Sites In Multiple Sequence Aligned Files
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Popular Question 2.9 years ago, created a question with more than 1,000 views. For Bootstrapping In Clustalw
Scholar 3.9 years ago, created an answer that has been accepted. For A: How to match and reorder these vectors in R
Scholar 4.2 years ago, created an answer that has been accepted. For A: How to match and reorder these vectors in R
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Detecting Polymorphic Sites In Multiple Sequence Aligned Files
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Detecting Polymorphic Sites In Multiple Sequence Aligned Files
Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: Detecting Polymorphic Sites In Multiple Sequence Aligned Files
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Multiple Color Values For A Single Node In Igraph
Teacher 4.9 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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Appreciated 5.4 years ago, created a post with more than 5 votes. For A: Detecting Polymorphic Sites In Multiple Sequence Aligned Files
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Good Answer 5.4 years ago, created an answer that was upvoted at least 5 times. For A: Detecting Polymorphic Sites In Multiple Sequence Aligned Files
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