User: rjactonspsfcf
rjactonspsfcf • 130
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Posts by rjactonspsfcf
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2
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1
answer
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... just add limits
+ xlim(-5,5) + ylim(-5,5)
see: https://ggplot2.tidyverse.org/reference/lims.html ...
written 2.1 years ago by
rjactonspsfcf • 130
3
votes
1
answer
707
views
1
answer
... I'm trying to get a list of cases for which there is DNA methylation and gene expression data available for both normal and cancer tissue samples using the GenomicDataCommons R package (which I am using for the first time).
qCases <- cases() %>%
filter( ~ samples.sample_type == "Solid Tiss ...
written 2.1 years ago by
rjactonspsfcf • 130
3
votes
1
answer
737
views
1
answers
... There are a number of tool you could use to do that and i'm not sure what you would prefer, but here is a solution in R using tools from the 'tidyverse':
library(tidyverse)
data <- read_delim("~/Documents/tmp/cds.txt",delim="\t",col_names = c("contig","name","start","end"))
# get th ...
written 2.2 years ago by
rjactonspsfcf • 130
0
votes
1
answer
813
views
1
answer
... Hi,
I'm trying to use the python API from https://portal.gdc.cancer.gov/ to select samples with DNA methylation data and/or RNA-seq data from tumour and adjacent normal tissue. I can't seem to find a metadata tag that I can use to filter the samples based on the criterion of the data being from tum ...
written 2.2 years ago by
rjactonspsfcf • 130
• updated
2.2 years ago by
Kevin Blighe ♦ 67k
0
votes
11
answers
37k
views
11
answers
Comment:
C: How To Sort Bed Format File
... This only crops up when you have a bed file with overlapping features e.g.
chr1 1 10
chr1 1 5
would not be ordered as:
chr1 1 5
chr1 1 10
without sorting on `-k3,3n` ...
written 3.5 years ago by
rjactonspsfcf • 130
• updated
12 months ago by
_r_am ♦ 31k
6
votes
11
answers
37k
views
11
answers
Answer:
A: How To Sort Bed Format File
... Example Bed file:
chr3 1 20
chr4 20 30
chr1 2 10
chr3 10 15
chrX 20 30
chrY 20 40
chrX 5 25
chr3 10 40
chr1 1 9
chr10 20 30
chr22 12 24
chr11 10 90
Sort Command:
sort -k1,1V -k2,2n -k3,3n "file"
- `-k1,1V`: Sort 1st field alphabetically, recog ...
written 3.5 years ago by
rjactonspsfcf • 130
• updated
12 months ago by
_r_am ♦ 31k
1
vote
4
answers
18k
views
4
answers
... ".../chr1.fa.gz ..." produced a fasta file with the chr1 sequence concatenated 24 times, I needed to put the variable name in place of the 1 ".../chr1$chr.fa.gz..." to get this to work:
```
BED=$1
for chr in `seq 1 22` X Y
do
wget -O - -q http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromoso ...
written 4.0 years ago by
rjactonspsfcf • 130
Latest awards to rjactonspsfcf
Appreciated
2.1 years ago,
created a post with more than 5 votes.
For A: How To Sort Bed Format File
Good Answer
2.1 years ago,
created an answer that was upvoted at least 5 times.
For A: How To Sort Bed Format File
Teacher
2.1 years ago,
created an answer with at least 3 up-votes.
For A: How To Sort Bed Format File
Teacher
2.1 years ago,
created an answer with at least 3 up-votes.
For A: Merging position of all different CDS of a single gene in one line
Scholar
2.2 years ago,
created an answer that has been accepted.
For A: Merging position of all different CDS of a single gene in one line
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