User: j.lunger18

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j.lunger1810
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Posts by j.lunger18

<prev • 13 results • page 1 of 2 • next >
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Comment: C: GENCODE and untranslated regions
... Great, thank yoU! ...
written 6 weeks ago by j.lunger1810
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GENCODE and untranslated regions
... I want to pull variants from a specific gene and for that I need chromosomal locations. I'm using the UCSC browser to get a range of positions for my gene. I want to include untranslated regions that flank the transcript. I found that the GENCODE transcripts are easy to click on to find their chromo ...
utr gencode written 6 weeks ago by j.lunger1810 • updated 6 weeks ago by Emily_Ensembl20k
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Extracting VCF of all variants in TCGA exomes from all cancer types
... Hi. Ideally, I would like to get a single VCF file from all the exomes sequences that TCGA has from all cancer types. Even more ideally, I would do this for only a certain region in the genome. Is there any way to do this? I have GDC-client downloaded and loaded in the command line at the moment, bu ...
vcf tcga written 9 weeks ago by j.lunger1810 • updated 9 weeks ago by Kevin Blighe53k
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Add error bars to barplot that uses melted dataframe in R
... I'm attempting to add error bars to my barchart. In order to plot it, I had to melt my dataframe, which originally contained a "plus" column and a "minus" column, which indicated the top and bottom of my error bars respectively for that group of replicates. I don't know how to add in my error bars o ...
R ggplot2 ddct qpcr written 10 weeks ago by j.lunger1810
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Comment: C: Extract variants from genomic range from gnomAD GRCh38
... Y = chromosome, X = genomic positions --> for p53 this would be something like 17:7661779-7687550 ...
written 11 weeks ago by j.lunger1810
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Extract variants from genomic range from gnomAD GRCh38
... With the new release of gnomAD, I want to pull variants from several genes for which I have their genomic coordinates. I was successfully able to do this for gnomad GRCh37, so I'm trying to do the same with the following terminal command: module load google-cloud-sdk tabix -h gs://gnomad-p ...
genome exome gnomad variants written 11 weeks ago by j.lunger1810
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select() not working in R
... Trying to make a new dataframe with a subset of columns in an existing dataframe. This worked for me before, not sure what's going wrong now... **head(mt_coding_variants[1:3]) # A tibble: 6 x 3 POS ID REF 1 119606751 rs751351167 A 2 1196 ...
R written 12 weeks ago by j.lunger1810 • updated 12 weeks ago by antonioggsousa90
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Using joiningdata/lollipops to make lollipop chart
... I'm having trouble downloading and using pbnjay's [lollipop][1] [1]: https://github.com/joiningdata/lollipops I went and downloaded the mac version and opened up "lollipops" in the command line. I closed the terminal and then opened it again, and tried: lollipops TP53 R273C R175H T125 R24 ...
genome annotation mutation lollipop written 12 weeks ago by j.lunger1810
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New Column based on another data frame
... Hi, I am trying to apply this problem to a data frame with variants so that I can say within which domain each variant is found. > ranges start end domain_name 1 1 3 beginning 2 4 6 middle1 3 7 8 middle2 4 9 11 end > pos ...
genome R domains written 12 weeks ago by j.lunger1810 • updated 12 weeks ago by Brice Sarver3.3k
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problem using UniprotR's " GetFamily_Domains() "
... I'm having trouble using the GetFamily_Domains() function in Uniprot R. Here is my code after installing the package and adding it to my library: uniprot_ID <- "Q9HCE5" domain_list <- GetFamily_Domains(uniprot_ID) "Warning message:In file(file, "rt") : cannot open URL 'http://w ...
R functional domains protein domains uniprot written 12 weeks ago by j.lunger1810

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