User: patelk26

gravatar for patelk26
patelk26100
Reputation:
100
Status:
Trusted
Location:
Scholar ID:
Google Scholar Page
Last seen:
1 day, 11 hours ago
Joined:
1 year, 1 month ago
Email:
p*******@email.chop.edu

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 >
0
votes
0
answers
88
views
0
answers
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 patelk26100 • updated 3 days ago by Kevin Blighe53k
0
votes
3
answers
168
views
3
answers
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 patelk26100
0
votes
0
answers
178
views
0
answers
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 patelk26100
1
vote
1
answer
140
views
1
answers
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 patelk26100
1
vote
0
answers
107
views
0
answers
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 patelk26100
2
votes
1
answer
137
views
1
answers
Answer: A: sed command to extract sequence
... Try this: `sed 's/::g.*(-)//' input.fasta | sed 's/>.*::/>/' > output.fasta` ...
written 3 months ago by patelk26100
1
vote
2
answers
198
views
2
answers
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 patelk26100
1
vote
1
answer
578
views
1
answers
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 patelk26100
0
votes
0
answers
301
views
0
answers
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 patelk26100
0
votes
0
answers
301
views
0
answers
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 patelk26100

Latest awards to patelk26

Autobiographer 4 months ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1172 users visited in the last hour