User: patelk26

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patelk26120
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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 • 24 results • page 1 of 3 • next >
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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 2 days ago by patelk26120
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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 20 days ago by patelk26120
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Comment: C: Merge columns adding conditions for every row
... You're welcome, I'm glad it worked :) ...
written 4 months ago by patelk26120
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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$Ensembl))) ...
written 4 months ago by patelk26120
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Comment: C: How to order rows in a dot plot with ggplot2
... Try this before plotting: test <- test[order(as.numeric(factor(test$NAME))),] test$NAME <- factor(test$NAME, levels=rev(unique(test$NAME))) ...
written 5 months ago by patelk26120 • updated 5 months ago by Kevin Blighe61k
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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 8 months ago by patelk26120
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Comment: C: Rename fasta headers using a variable already present in the header?
... Try this: grep '>' LARGE_MSA.fna | sed 's/>.*.gene=/>/' | sed 's/].*//' ...
written 8 months ago by patelk26120
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Answer: A: Affymetrix probesets to Gene symbols
... You can find your answer here: [Annotate Affymetrix probesets to Gene symbols][1] [1]: https://www.biostars.org/p/332461/#332474 ...
written 8 months ago by patelk26120
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Comment: C: How to create matrix for larger data set?
... This can be done in R. library(readxl) library(dplyr) df <- read_excel('data.xlsx') # reading in your data df %>% gather(key = 'genesB', value, -c(genesA)) %>% filter(value > 0) %>% select(genesA, genesB) %>% rename(Protein.B = genesB ...
written 9 months ago by patelk26120
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Answer: A: sed command to extract sequence
... Try this: `sed 's/::g.*(-)//' input.fasta | sed 's/>.*::/>/' > output.fasta` ...
written 9 months ago by patelk26120

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