User: patelk26
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
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... Try this:
grep '>' LARGE_MSA.fna | sed 's/>.*.gene=/>/' | sed 's/].*//' ...
written 12 days ago by
patelk26 • 100
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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 12 days ago by
patelk26 • 100
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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 20 days ago by
patelk26 • 100
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... Try this: `sed 's/::g.*(-)//' input.fasta | sed 's/>.*::/>/' > output.fasta` ...
written 21 days ago by
patelk26 • 100
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... 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 21 days 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 22 days ago by
patelk26 • 100
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... 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 5 weeks ago by
patelk26 • 100
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... Have you tried running by changing {sample} to {wildcards.sample} in your shell commands? ...
written 5 weeks ago by
patelk26 • 100
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... Hi Fabienne,
I deal with similar issue, of having multiple expression measurements for a single gene while dealing with microarray data from GEO. I usually deal with it by grouping the gene symbols and calculating the row means, keeping only the row with measurements which has the maximum row mean.
...
written 5 weeks ago by
patelk26 • 100
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... You can try two things (assuming your dataset used Affymetrix Human Genome U133 Plus 2.0 Array):
Use `BioMaRt`
library(biomaRt)
ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")
probeids=c('200007_at', '200011_s_at', '200012_x_at')
getBM(attributes=c('affy_hg_u133_plus_2 ...
written 5 weeks ago by
patelk26 • 100
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