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User: rbronste

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rbronste • 360
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Posts by rbronste

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Seurat code availability for published papers
... I feel like I already know the answer to my own question, but wondering if there are any journals requiring the submission of exact Seurat code for scRNA-seq containing papers? Just thinking about ways to get exact reconstruction of published clustering on limited data in methods. Seems like all jou ...
scrna-seq seurat written 4 months ago by rbronste • 360
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Comment: C: grep sorting question
... This does seem to work in terms of ordering the sites however the gencode list has 54K rows and my gene list has 14k but I get a final tally of 140K rows. Is that due to alternate promoters? ...
written 7 months ago by rbronste • 360
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Comment: C: grep sorting question
... Yes thats right, Im going to use the resulting BED file for a heatmap where the descending order is important. ...
written 7 months ago by rbronste • 360
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Comment: C: grep sorting question
... The purpose is simple. The genes are in an order of descending normalized signal strength in the txt file, I would like the same in the TSS interval file for those specific genes. ...
written 7 months ago by rbronste • 360
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Comment: C: grep sorting question
... Just added the `head` output ...
written 7 months ago by rbronste • 360
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grep sorting question
... Hi I have the following code: grep -w -F -i -f gene_list.txt gencode.vM18.promoters.bed > gene_list_promoters.bed head gene_list.txt Rn45s Malat1 Sptbn1 head gencode.vM18.promoters.bed chr1 3071252 3075252 ENSMUSG00000102693.1 . + ...
grep awk sed unix bash written 7 months ago by rbronste • 360 • updated 7 months ago by RamRS ♦ 30k
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Comment: C: multiple bed - merge regions IF overlapping more than xx percent of size
... So I have the following code: N=6 bedops --everything \ | bedmap --echo-map --fraction-both 0.1 - \ | awk -vN=${N} '(split($0, a, ";") == N)' - \ | sed 's/\;/\n/g' - \ | sort-bed - \ | uniq - \ | bedops --merge - \ > answer1.bed I ...
written 7 months ago by rbronste • 360
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ggplot2 loess curve application to 2 dataframes
... Hi I am trying to create a loess curve for two dataframes within the same plot with a **different** span value for each, not sure exactly how to go about that, here is my code thus far which adds the loess curve to both sets of data but with the **same** span value. Thanks. ggplot(dplyr::bind_r ...
ggplot2 ggplot written 7 months ago by rbronste • 360
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Comment: C: EnhancedVolcano R pdf export size
... Thanks, very helpful! So my input table in this instance is a DESeqDataSet, would you still use sample() or seq() in that case? I have about 325K variables and would def be able to remove 50% within certain FC and pval constraints, probably FC < 2 and pval > .5 ...
written 7 months ago by rbronste • 360
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EnhancedVolcano R pdf export size
... Hi, I was wondering if anyone knew a way to make the export of pdfs from EnhancedVolcano significantly smaller in terms of file size for plots containing many points (over 100K). Right now they are like 4mb after externally reducing the size of the pdf before manipulating it in Illustrator which i ...
R enhancedvolcano volcano plot written 7 months ago by rbronste • 360 • updated 7 months ago by zx8754 ♦ 9.6k

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