User: rbronste
rbronste • 360
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Posts by rbronste
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4
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... 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 ...
written 4 weeks ago by
rbronste • 360
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193
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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 3 months ago by
rbronste • 360
0
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1
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193
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1
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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 3 months ago by
rbronste • 360
0
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1
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193
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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 3 months ago by
rbronste • 360
0
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1
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193
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1
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Comment:
C: grep sorting question
... Just added the `head` output ...
written 3 months ago by
rbronste • 360
3
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193
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1
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... 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 . + ...
0
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... 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 3 months ago by
rbronste • 360
0
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0
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119
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... 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 ...
written 4 months ago by
rbronste • 360
0
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1
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231
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1
answers
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 4 months ago by
rbronste • 360
5
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1
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231
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1
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... 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 ...
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