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promoter
•
reset
0
votes
2
replies
1.4k
views
Failed to get promoters using promoters() in R 4.0.3.
promoter
GenomicRanges
rtracklayer
GRanges
3.6 years ago
Arslan
• 0
3
votes
6
replies
1.6k
views
Better way to find head to head GRanges?
promoter
updated 4.9 years ago by
Hervé Pagès
16k • written 4.9 years ago by
Charles Plessy
▴ 180
1
vote
3
replies
1.6k
views
Obtain coordinates of 5' upstream region up to closest coding region
r
granges
promoter
updated 6.1 years ago by
Hervé Pagès
16k • written 6.1 years ago by
eggrandio
• 0
0
votes
0
replies
1.2k
views
CAGEr get TSS in bed file
TSS
promoter
cage
cager
6.4 years ago
bharata1803
▴ 60
0
votes
0
replies
1.6k
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
6.6 years ago
Wojeff
• 0
0
votes
3
replies
2.5k
views
How to handle multi-TSS genes in Repitools?
repitools
promoter
tss
annotation
7.1 years ago
Ryan C. Thompson
★ 7.9k
1
vote
5
replies
2.4k
views
Extract genomic features from a TxDb-like object
TxDB
genomicfeatures
promoter
getpromoterseq
updated 7.1 years ago by
Hervé Pagès
16k • written 7.1 years ago by
rbenel
▴ 40
1
vote
2
replies
1.4k
views
DEXseq for alternate promoter usage
dexseq
promoter
utr
updated 8.9 years ago by
Alejandro Reyes
★ 1.9k • written 8.9 years ago by
joan.hooper
• 0
1
vote
6
replies
2.3k
views
problem creating txdb object and bsgenome for solanum pennellii
bsgenome
txdb
promoter
updated 9.2 years ago by
Martin Morgan
25k • written 9.2 years ago by
sekawaiwai2006
▴ 20
2
votes
2
replies
3.4k
views
using the "promoters" function with an "OrganismDb" to generate "GRanges" with "REFSEQ" rather than UCSC gene names
promoter
granges
refseq
ucsc
organismdb
updated 9.4 years ago by
Robert Castelo
★ 3.4k • written 9.4 years ago by
efoss
▴ 10
2
votes
2
replies
1.6k
views
promoter definition in VariantAnnotation
VariantAnnotation
promoter
drosophila melanogaster
updated 10.3 years ago by
Valerie Obenchain
★ 6.8k • written 10.3 years ago by
lidia.mateo
▴ 30
11 results • Page
1 of 1
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Comment: GSEA preranked analysis downstream of DEseq2
by
Ajay
• 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file
by
janwilseo
• 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped"
by
James W. MacDonald
68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
by
donnycrimson
• 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender
by
donnycrimson
• 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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