User: rbronste

gravatar for rbronste
rbronste380
Reputation:
380
Status:
Trusted
Location:
Last seen:
7 months, 3 weeks ago
Joined:
4 years, 1 month ago
Email:
r************@gmail.com

Posts by rbronste

<prev • 271 results • page 1 of 28 • next >
4
votes
0
answers
238
views
0
answers
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 10 months ago by rbronste380
0
votes
1
answer
333
views
1
answers
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 12 months ago by rbronste380
0
votes
1
answer
333
views
1
answers
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 12 months ago by rbronste380
0
votes
1
answer
333
views
1
answers
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 12 months ago by rbronste380
0
votes
1
answer
333
views
1
answers
Comment: C: grep sorting question
... Just added the `head` output ...
written 12 months ago by rbronste380
3
votes
1
answer
333
views
1
answer
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 12 months ago by rbronste380 • updated 12 months ago by Ram32k
0
votes
1
answer
2.8k
views
1
answers
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 13 months ago by rbronste380
0
votes
0
answers
236
views
0
answers
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 13 months ago by rbronste380
0
votes
1
answer
684
views
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 13 months ago by rbronste380
5
votes
1
answer
684
views
1
answer
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 13 months ago by rbronste380 • updated 13 months ago by zx87549.9k

Latest awards to rbronste

Popular Question 8 months ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 9 months ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 9 months ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 9 months ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 10 months ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 10 months ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 11 months ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 12 months ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 12 months ago, created a question with more than 1,000 views. For BED intersects/overlaps output for Venn diagrams - single column
Popular Question 13 months ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 13 months ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 14 months ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 15 months ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 15 months ago, created a question with more than 1,000 views. For Removing PCR duplicates - fastq or BAM?
Popular Question 15 months ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 16 months ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 16 months ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 17 months ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 18 months ago, created a question with more than 1,000 views. For Figure quality browser tracks
Popular Question 18 months ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 18 months ago, created a question with more than 1,000 views. For Figure quality browser tracks
Popular Question 21 months ago, created a question with more than 1,000 views. For Removing PCR duplicates - fastq or BAM?
Great Question 22 months ago, created a question with more than 5,000 views. For Trouble installing R package Cairo
Popular Question 22 months ago, created a question with more than 1,000 views. For Removing PCR duplicates - fastq or BAM?
Popular Question 22 months ago, created a question with more than 1,000 views. For Comparing open chromatin data to ChromHMM model

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1429 users visited in the last hour
_