User: patelk26

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patelk26140
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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

<prev • 28 results • page 1 of 3 • next >
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Comment: C: More Ensembl IDs than genes
... Thank you for the explanation, this makes sense. ...
written 4 months ago by patelk26140
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Comment: C: More Ensembl IDs than genes
... I checked, they all begin from `ENSG*` ...
written 4 months ago by patelk26140
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More Ensembl IDs than genes
... 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 ...
genome gene next-gen written 4 months ago by patelk26140
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Answer: A: Obtaining gene expression data from GEO
... 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 patelk26140
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Answer: A: How to get gene and microRNA expression profiles for specific type of cancers fr
... 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 patelk26140
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CNV callers for WES data
... 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 ...
R next-gen cnv wes written 7 months ago by patelk26140
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Comment: C: Merge columns adding conditions for every row
... You're welcome, I'm glad it worked :) ...
written 11 months ago by patelk26140
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Answer: C: Merge columns adding conditions for every row
... 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$Ensembl))) ...
written 11 months ago by patelk26140
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Comment: C: How to order rows in a dot plot with ggplot2
... Try this before plotting: test <- test[order(as.numeric(factor(test$NAME))),] test$NAME <- factor(test$NAME, levels=rev(unique(test$NAME))) ...
written 12 months ago by patelk26140 • updated 12 months ago by Kevin Blighe69k
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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 patelk26140

Latest awards to patelk26

Scholar 6 months ago, created an answer that has been accepted. For A: How to interpret CERES gene scores for genome wide CRISPR-Cas9 knockout screens?
Popular Question 8 months ago, created a question with more than 1,000 views. For How to interpret CERES gene scores for genome wide CRISPR-Cas9 knockout screens?
Autobiographer 16 months ago, has more than 80 characters in the information field of the user's profile.

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