User: raunakms

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Post-doctoral scholar | PhD in Bioinformatics | Data Scientist | Cancer Genomics | University of California, San Francisco | USA

Posts by raunakms

<prev • 65 results • page 1 of 7 • next >
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Comment: C: Infer CNV from ATAC-seq data
... This is from the supplementary text (page-15) of TCGA ATAC-seq paper by [Corces et al. Science 2018][1] "**ATAC-seq data analysis – Inferring copy number amplification** To infer DNA copy number amplifications from ATAC-seq data, we first tiled the genome into 2-Mbp windows using “tile” of genomi ...
written 12 weeks ago by raunakms1.1k
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Comment: C: Infer CNV from ATAC-seq data
... Do you mean correcting ATAC-seq peaks count by Copy Number ? ...
written 3 months ago by raunakms1.1k
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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 15 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 15 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 15 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 17 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 19 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 2.9 years 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 2.9 years 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 2.9 years ago by raunakms1.1k

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Great Question 4 months ago, created a question with more than 5,000 views. For Bootstrapping In Clustalw
Great Question 12 months ago, created a question with more than 5,000 views. For Bootstrapping In Clustalw
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Detecting Polymorphic Sites In Multiple Sequence Aligned Files
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Popular Question 3.9 years ago, created a question with more than 1,000 views. For Bootstrapping In Clustalw
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