User: thejustpark

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thejustpark60
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United States
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6 days, 11 hours ago
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5 years, 3 months ago
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Posts by thejustpark

<prev • 27 results • page 1 of 3 • next >
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Comment: C: RNA-Seq database of cancer patients other than TCGA and ICGC?
... I am actually interested in pan cancer study, so does not matter (the more, the better). ...
written 9 weeks ago by thejustpark60
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Comment: C: RNA-Seq database of cancer patients other than TCGA and ICGC?
... I am sorry that I can't understand what you mean by entity. Assuming that you ask about response variable or covariate, I want to have their survival status with RNA-Seq data. If it's not what you asked, please let me know again. Thank you very much. ...
written 9 weeks ago by thejustpark60
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RNA-Seq database of cancer patients other than TCGA and ICGC?
... For my computational cancer model using RNA-Seq data, I am going to use TCGA as a discovery cohort. Since ICGC or GDC have great overlap with TCGA data, I want to find independent databases as validation cohort. I can find several RNA-Seq data on cancer cell lines, such as CTRP, TARGET, CCLE, but c ...
patient rna-seq cancer written 9 weeks ago by thejustpark60 • updated 8 weeks ago by Pappu1.9k
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What to do to identify rare variatns from vcf files resulted from UnifiedGenotyper?
... Hello, I am new to exome sequencing data anslysis and want to ask questions regarding what to do in my situation. I have spent quite a time to figure this out by myself, but since there's no one around me to direct me, I couldn't get much. I am given vcf files suspected to be from GATK UnifiedGe ...
next-gen written 11 months ago by thejustpark60 • updated 11 months ago by rse70
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Large number of breast tumor and matched normal samples other than TCGA
... Hello all, I have generated a hypothesis using RNA-Seq data on ~100 breast tumor and matched normal samples from TCGA. Now, I need to test this hypothesis in a even larger number of breast tumor and matched normal samples other than TCGA. I searched for it and found METABRIC data (http://www.cbi ...
rna-seq sequencing written 13 months ago by thejustpark60
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Comment: C: Co-expression of transcripts in HeLa cell
... Thank you Heriche,  You are providing good examples to start with! ...
written 3.2 years ago by thejustpark60
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Co-expression of transcripts in HeLa cell
... Hello all,    I have to do something using co-expression network of transcripts in HeLa cell.  Since HeLa cell has been widely studied, I think there should be this data out there,  but can't find one.    Can you please help me to locate this data? If I have to build this myself, it would tak ...
rna-seq written 3.2 years ago by thejustpark60 • updated 3.2 years ago by Jean-Karim Heriche18k
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P value for gene set overlap but by edges
... Hello,  I know the question of p value for gene set overlap is answered.  But this is different; In my situation, there are (undirected) edges between genes.  Given pathway A and B, each consisting of gene 1,2,3,4,5 (for A) and 6,7,8,9,10 (for B).  And the edges are as follows: 1<->6, 2< ...
gene overlap edge written 4.0 years ago by thejustpark60
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A statistical test to call group connectivity based on individual connectivities.
... Guys,    I am looking for a statistical test for my purpose.  Although I believe that this test should exist, can't find one.    Given 1000 genes and many connections between them,  suppose you have two subgroups of genes from the population, each consisting of 5 genes, and are asked if the gr ...
connectivity statistical test written 4.2 years ago by thejustpark60
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Comment: C: Correlation of two genes on 2 observations
... Michael,  I appreciate your kind comments.  Yes, many details were buried under the simplification (that I now repent doing), and I did apply multiple testing.  But many thanks, it is always important to check details (and yes it is fun!). HJ.  ...
written 4.5 years ago by thejustpark60

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Popular Question 8 weeks ago, created a question with more than 1,000 views. For A statistical test to call group connectivity based on individual connectivities.
Popular Question 9 months ago, created a question with more than 1,000 views. For A statistical test to call group connectivity based on individual connectivities.
Popular Question 13 months ago, created a question with more than 1,000 views. For Easy Way To Screenshot Whole Region From Igv?
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Popular Question 2.1 years ago, created a question with more than 1,000 views. For A statistical test to call group connectivity based on individual connectivities.
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Popular Question 4.2 years ago, created a question with more than 1,000 views. For A statistical test to call group connectivity based on individual connectivities.

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