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bedtools
•
reset
5
votes
9
replies
8.9k
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subsetByOverlaps : comparing GRANGES and keeping all the information in the METACOLUMNS
granges
bedtools
intersect
updated 5.7 years ago by
lee.s
▴ 70 • written 5.7 years ago by
Bogdan
▴ 670
2
votes
3
replies
2.3k
views
Counting reads in fixed width peaks with DiffBind::dba.count without re-centering?
diffbind
chipseq
counts
peaks
bedtools
updated 3.0 years ago by
Rory Stark
★ 5.1k • written 6.0 years ago by
Ni-Ar
▴ 10
0
votes
0
replies
970
views
I need to measure distance of PAR-CLIP data to RNA regions
parclip
bedtools
bed files
gff3
6.2 years ago
linuxborg2
• 0
1
vote
1
reply
1.5k
views
Filtering a BED file according to genomic annotation
bed files
bedtools
filtering
chipseq
updated 6.3 years ago by
Aaron Lun
★ 28k • written 6.3 years ago by
rbronste
▴ 60
0
votes
4
replies
1.3k
views
Error: HelloRanges eval
HelloRanges
bedtools
6.9 years ago
bioinf
▴ 10
2
votes
7
replies
2.0k
views
Minimum overlap for summarizeOverlaps() to call hit
summarizeoverlaps
bedtools
8.1 years ago
tmartinez
• 0
6 results • Page
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Robert Castelo
★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
lonn
• 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph
by
deeenes
▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches
by
Gordon Smyth
50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param
by
russ.bainer
▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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★ 3.2k
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James W. MacDonald
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shepherl
3.8k
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▴ 30
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to
Gordon Smyth
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