User: patelk26
patelk26 • 120
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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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... 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
patelk26 • 120
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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 20 days ago by
patelk26 • 120
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... You're welcome, I'm glad it worked :) ...
written 4 months ago by
patelk26 • 120
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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$Ensembl))) ...
written 4 months ago by
patelk26 • 120
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... Try this before plotting:
test <- test[order(as.numeric(factor(test$NAME))),]
test$NAME <- factor(test$NAME, levels=rev(unique(test$NAME))) ...
written 5 months ago by
patelk26 • 120
• updated
5 months ago by
Kevin Blighe ♦ 61k
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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
patelk26 • 120
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... Try this:
grep '>' LARGE_MSA.fna | sed 's/>.*.gene=/>/' | sed 's/].*//' ...
written 8 months ago by
patelk26 • 120
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... 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
patelk26 • 120
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... 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
patelk26 • 120
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... Try this: `sed 's/::g.*(-)//' input.fasta | sed 's/>.*::/>/' > output.fasta` ...
written 9 months ago by
patelk26 • 120
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