User: Vasu

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Vasu320
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Posts by Vasu

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Comment: C: Question about ClinicalData discrepancies b/w cbioportal data and GDC data?
... I see the patients are same in both the portals. From the same place where I downloaded patient clinical data for both colon and rectal in GDC, I have also downloaded the following files nationwidechildrens.org_clinical_follow_up_v1.0_coad.txt nationwidechildrens.org_clinical_follow_ ...
written 21 days ago by Vasu320
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Comment: C: Question about ClinicalData discrepancies b/w cbioportal data and GDC data?
... I second your suggestion (y) Yes, there may be different patients in both cbioportal and GDC, but in my question there is one patient `TCGA-A6-2671` which is alive in `GDC` and dead in `cbioportal`. ...
written 21 days ago by Vasu320
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Comment: C: Question about ClinicalData discrepancies b/w cbioportal data and GDC data?
... If you say GDC is most updated one compared to cbioportal, I see 65 Dead in GDC and 130 Dead in cbioportal. This cannot be a small difference. Should I ask GDC community ppl about this? ...
written 21 days ago by Vasu320
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Question about ClinicalData discrepancies b/w cbioportal data and GDC data?
... I recently downloaded the TCGA colorectal clinical data information from [GDC portal][1]. From this I got the following files. nationwidechildrens.org_clinical_patient_coad.txt nationwidechildrens.org_clinical_patient_read.txt I combined both the files and a total of 628 patients dat ...
clinicaldata survival tcga gdc cbioportal written 21 days ago by Vasu320
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Comment: C: Error with merge_result with dataframes using clusterprofiler
... Coercing a dataframe results again into enrichmentresult object is not possible I guess. But Anyways from [GuangchuangYu github][1] I see an example showing Upregulated and downregulated dotplots side by side. So, I followed that. First I created a new column `Dataset` in both dataframes `A4` and ...
written 4 weeks ago by Vasu320
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Comment: C: Error with merge_result with dataframes using clusterprofiler
... After using `enrichr` function from [clusterprofiler][1] I saved the result in a dataframe. class(A4) and class(B4) is "data.frame". But I see that `merge_result` function from `clusterprofiler` uses only enrichmentresult for plotting. [1]: http://bioconductor.org/packages/release/bioc/vignet ...
written 4 weeks ago by Vasu320
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Error with merge_result with dataframes using clusterprofiler
... I'm using `clusterprofiler` for pathway analysis for two datasets and want to plot the results both in same plot. I have seen an example to merge the results here from [GuangchuangYu github][1] But here it is merging of `enrichmentesults`. In my case I have results in dataframes. Below I gave a n ...
R clusterprofiler rna-seq enrichment written 4 weeks ago by Vasu320
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Comment: C: WGCNA and corAndPvalue
... You have to create your matrix, samples as rows and Genes as columns. Lets say you have matrix "A" like this: 5S_rRNA A1BG A1BG-AS1 A2M A2M-AS1 Sample1 3.008018 4.291537 7.417708 12.42879 8.332809 Sample2 2.725616 5.751250 8.880903 12.53955 8.452564 Sample3 2.1 ...
written 5 weeks ago by Vasu320
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Comment: C: can lnc-RNA target coding RNA?
... What I mean is, MEG3 has multiple transcript IDs right. Do I need to use all or any specific transcript sequence is fine? ...
written 5 weeks ago by Vasu320
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Comment: C: WGCNA and corAndPvalue
... Transpose your data. Follow this [link][1] [1]: https://www.biostars.org/p/307330/ ...
written 5 weeks ago by Vasu320

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Popular Question 20 days ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
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Popular Question 3 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
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Appreciated 5 months ago, created a post with more than 5 votes. For C: Sample names for TCGA data from GDC-legacy archive
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Popular Question 6 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
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