User: rjactonspsfcf

gravatar for rjactonspsfcf
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Posts by rjactonspsfcf

<prev • 7 results • page 1 of 1 • next >
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Answer: A: How do I modify default ggplot2 axis?
... just add limits + xlim(-5,5) + ylim(-5,5) see: https://ggplot2.tidyverse.org/reference/lims.html ...
written 13 months ago by rjactonspsfcf90
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Using GenomicDataCommons R package to identify cases with both DNA methylation and gene expression data
... 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 ...
R gdc rna-seq dna methylation written 13 months ago by rjactonspsfcf90
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Answer: A: Merging position of all different CDS of a single gene in one line
... 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 15 months ago by rjactonspsfcf90
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GDC data portal - Tumour and Adjacent normal
... 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 ...
dna methylation tcga gdc rna-seq written 15 months ago by rjactonspsfcf90 • updated 15 months ago by Kevin Blighe52k
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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 2.5 years ago by rjactonspsfcf90 • updated 7 days ago by RamRS25k
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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 2.5 years ago by rjactonspsfcf90 • updated 7 days ago by RamRS25k
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Comment: C: Batch Fetching Fasta Sequences From Bed File
... ".../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 3.1 years ago by rjactonspsfcf90

Latest awards to rjactonspsfcf

Scholar 15 months 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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