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promoter
•
reset
0
votes
2
replies
1.1k
views
Failed to get promoters using promoters() in R 4.0.3.
promoter
GenomicRanges
rtracklayer
GRanges
2.8 years ago
Arslan
• 0
3
votes
6
replies
1.3k
views
Better way to find head to head GRanges?
promoter
updated 4.1 years ago by
Hervé Pagès
16k • written 4.1 years ago by
Charles Plessy
▴ 180
1
vote
3
replies
1.3k
views
Obtain coordinates of 5' upstream region up to closest coding region
r
granges
promoter
updated 5.3 years ago by
Hervé Pagès
16k • written 5.3 years ago by
eggrandio
• 0
0
votes
0
replies
941
views
CAGEr get TSS in bed file
TSS
promoter
cage
cager
5.6 years ago
bharata1803
▴ 60
0
votes
0
replies
1.4k
views
GenomicFeatures: How to extract a gene's upstream region of TSS up to the end position of the flanking (nearby) gene.
genomicranges
genomicfeatures
promoter
upstream_flank
5.8 years ago
Wojeff
• 0
0
votes
3
replies
1.9k
views
How to handle multi-TSS genes in Repitools?
repitools
promoter
tss
annotation
6.3 years ago
Ryan C. Thompson
★ 7.9k
1
vote
5
replies
2.0k
views
Extract genomic features from a TxDb-like object
TxDB
genomicfeatures
promoter
getpromoterseq
updated 6.3 years ago by
Hervé Pagès
16k • written 6.3 years ago by
rbenel
▴ 40
1
vote
2
replies
1.2k
views
DEXseq for alternate promoter usage
dexseq
promoter
utr
updated 8.1 years ago by
Alejandro Reyes
★ 1.9k • written 8.1 years ago by
joan.hooper
• 0
1
vote
6
replies
1.9k
views
problem creating txdb object and bsgenome for solanum pennellii
bsgenome
txdb
promoter
updated 8.4 years ago by
Martin Morgan
25k • written 8.4 years ago by
sekawaiwai2006
▴ 20
2
votes
2
replies
2.7k
views
using the "promoters" function with an "OrganismDb" to generate "GRanges" with "REFSEQ" rather than UCSC gene names
promoter
granges
refseq
ucsc
organismdb
updated 8.6 years ago by
Robert Castelo
★ 3.3k • written 8.6 years ago by
efoss
▴ 10
2
votes
2
replies
1.4k
views
promoter definition in VariantAnnotation
VariantAnnotation
promoter
drosophila melanogaster
updated 9.5 years ago by
Valerie Obenchain
★ 6.8k • written 9.5 years ago by
lidia.mateo
▴ 30
11 results • Page
1 of 1
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Comment: Trouble Installing DADA2 (warning: R new user)
by
shepherl
3.9k
As far as this ERROR for Bioc requires R version, Bioconductor is closely tied to an R release. Depending if you tried to use a premade s…
Answer: LRT test for different timepoints (one tissue types vs. many tissue types)
by
Michael Love
42k
No, this is a contrast of estimated coefficient (e.g. the Wald test).
Comment: Ranking the GSEA Results
by
Michael Love
42k
Got it. So then I'll take off DESeq2 as its mostly a downstream question. You may need to direct the fgsea developer to the thread. When yo…
Comment: Ranking the GSEA Results
by
V_Vibes
• 0
I have actually used the "fgsea" Bioconductor package which is used for GSEA. Thanks for pointing that out. I have edited that in the origi…
Comment: Ranking the GSEA Results
by
V_Vibes
• 0
The idea was inspired by people ranking the DEGs for preranked GSEA using their log2FC * (-log10 p-value). Also, the GSEA results I am gett…
Votes
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
Comment: How to get the DMR?
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
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ATpoint
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WouterDeCoster
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▴ 20
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Jitendra
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