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User: patelk26

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patelk26 • 100
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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 • 20 results • page 1 of 2 • next >
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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 days ago by patelk26 • 100 • updated 3 days ago by Kevin Blighe ♦ 53k
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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 11 weeks ago by patelk26 • 100
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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 3 months ago by patelk26 • 100
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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 3 months ago by patelk26 • 100
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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 3 months ago by patelk26 • 100
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Answer: A: sed command to extract sequence
... Try this: `sed 's/::g.*(-)//' input.fasta | sed 's/>.*::/>/' > output.fasta` ...
written 3 months ago by patelk26 • 100
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Answer: A: How to identify Transcript Factors (TF) binding to my target sequence
... You can use Homer's `findMotifs.pl ` to find motifs in your sequences. Homer outputs known motifs (motifs matching with the database of motifs) as well as de novo motifs. ...
written 3 months ago by patelk26 • 100
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Comment: C: convert rows to columns in r
... Error indicates you must be having duplicate depmap_ids for same gene. For example: You must be having something like this: ACH-000840 TP53 4.75 ACH-000840 TP53 3.23 So when you try spreading your data frame, it does not know which value to put for gene TP53 depmap_id ACH-000840. Your k ...
written 3 months ago by patelk26 • 100
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Comment: C: snakemake and Star aligner code issue
... May be it should be {wildcards.samples} since you have `SAMPLES= ['A','B','C']` at the beginning of your config file and you are trying to refer to that. ...
written 4 months ago by patelk26 • 100
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Comment: C: snakemake and Star aligner code issue
... Have you tried running by changing {sample} to {wildcards.sample} in your shell commands? ...
written 4 months ago by patelk26 • 100

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