User: patelk26
patelk26 • 140
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Bioinformatics Scientist I working at The Children's Hospital of Philadelphia. I work mainly with ChIP-Seq and RNA-Seq data. I'm proficient in R.
Posts by patelk26
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Comment:
C: More Ensembl IDs than genes
... Thank you for the explanation, this makes sense. ...
written 4 months ago by
patelk26 • 140
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Comment:
C: More Ensembl IDs than genes
... I checked, they all begin from `ENSG*` ...
written 4 months ago by
patelk26 • 140
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... Hello,
This is a very basic question, I am not sure if I understand Ensembl gene IDs.
I have a gene quantification matrix and I can see there are around ~ 60K Ensembl gene IDs.
How can there be more (almost double) gene IDs than total number of genes in human genome?
Can multiple gene IDs map to o ...
written 4 months ago by
patelk26 • 140
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... You can use `GEOquery` R package ([vignette][1]) to get expression matrix and associated phenotypic data.
[1]: https://kasperdanielhansen.github.io/genbioconductor/html/GEOquery.html ...
written 6 months ago by
patelk26 • 140
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... You can try using UCSC treehouse data public data ([link to data][1]). It has gene expression data for various tumor types from publicly available repositories, which includes TCGA.
[1]: https://treehousegenomics.soe.ucsc.edu/public-data/#tumor_v11_polyA ...
written 6 months ago by
patelk26 • 140
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... Hello,
I want to call somatic CNVs for Whole Exome Sequencing data. These are tumor samples, with no normal/control samples available.
I read this [article][1] and tried a couple of tools like ADTEX and ExomeCNV, however they require normal samples to be provided as well. I cannot run with just tu ...
written 7 months ago by
patelk26 • 140
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... You're welcome, I'm glad it worked :) ...
written 11 months ago by
patelk26 • 140
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... There are multiple ways you can do this, I did it in R:
test <- read.csv('test.csv')
res <- data.frame('result'=ifelse(!is.na(test$Method1), test$Method1,
ifelse(!is.na(test$Method2),test$Method2, test$Ensembl))) ...
written 11 months ago by
patelk26 • 140
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... Try this before plotting:
test <- test[order(as.numeric(factor(test$NAME))),]
test$NAME <- factor(test$NAME, levels=rev(unique(test$NAME))) ...
written 12 months ago by
patelk26 • 140
• updated
12 months ago by
Kevin Blighe ♦ 69k
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Answer:
A: Get SVG image of motif
... Since you know the motif name, you could search for it in JASPAR (http://jaspar.genereg.net). JASPAR allows you to download SVG image for a motif.
...
written 14 months ago by
patelk26 • 140
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