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promoter
•
reset
0
votes
2
replies
1.7k
views
Failed to get promoters using promoters() in R 4.0.3.
promoter
GenomicRanges
rtracklayer
GRanges
4.5 years ago
Arslan
• 0
3
votes
6
replies
2.0k
views
Better way to find head to head GRanges?
promoter
updated 5.8 years ago by
Hervé Pagès
16k • written 5.8 years ago by
Charles Plessy
▴ 180
1
vote
3
replies
2.0k
views
Obtain coordinates of 5' upstream region up to closest coding region
r
granges
promoter
updated 7.0 years ago by
Hervé Pagès
16k • written 7.0 years ago by
eggrandio
• 0
0
votes
0
replies
1.5k
views
CAGEr get TSS in bed file
TSS
promoter
cage
cager
7.3 years ago
bharata1803
▴ 60
0
votes
0
replies
1.9k
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
7.4 years ago
Wojeff
• 0
0
votes
3
replies
3.0k
views
How to handle multi-TSS genes in Repitools?
repitools
promoter
tss
annotation
8.0 years ago
Ryan C. Thompson
★ 7.9k
1
vote
5
replies
2.7k
views
Extract genomic features from a TxDb-like object
TxDB
genomicfeatures
promoter
getpromoterseq
updated 8.0 years ago by
Hervé Pagès
16k • written 8.0 years ago by
rbenel
▴ 50
1
vote
2
replies
1.7k
views
DEXseq for alternate promoter usage
dexseq
promoter
utr
updated 9.7 years ago by
Alejandro Reyes
★ 1.9k • written 9.7 years ago by
joan.hooper
• 0
1
vote
6
replies
2.7k
views
problem creating txdb object and bsgenome for solanum pennellii
bsgenome
txdb
promoter
updated 10.1 years ago by
Martin Morgan
25k • written 10.1 years ago by
sekawaiwai2006
▴ 20
2
votes
2
replies
3.8k
views
using the "promoters" function with an "OrganismDb" to generate "GRanges" with "REFSEQ" rather than UCSC gene names
promoter
granges
refseq
ucsc
organismdb
updated 10.3 years ago by
Robert Castelo
★ 3.4k • written 10.3 years ago by
efoss
▴ 10
2
votes
2
replies
2.0k
views
promoter definition in VariantAnnotation
VariantAnnotation
promoter
drosophila melanogaster
updated 11.1 years ago by
Valerie Obenchain
★ 6.8k • written 11.1 years ago by
lidia.mateo
▴ 30
11 results • Page
1 of 1
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Answer: tximeta cannot open annotation gtf?
by
ATpoint
★ 5.0k
> Timeout of 60 seconds was reached You have to increase the default timeout limits for downloads, `options(timeout=3600)`. GENCODE serve…
Answer: GSEA error
by
James W. MacDonald
68k
At a very high level, the way non-model organisms are annotated is by using blast to find orthologs in other species that are well annotate…
Comment: Unable to find ENTREZ IDs
by
Adithi
• 0
Hi James, Thank you so much for your reply. My main goal is to find ortholog genes from chinese hamster gene symbols to mouse gene symbols…
Comment: Unable to find ENTREZ IDs
by
Adithi
• 0
Hi James, Thank you so much for your reply. My main goal is to find ortholog genes from chinese hamster gene symbols to mouse gene symbols…
Answer: Unable to find ENTREZ IDs
by
James W. MacDonald
68k
Those are the 'symbols', and are a concatenation of LOC and the NCBI Gene ID (what used to be called an Entrez Gene ID). As an example:http…
Votes
Answer: GSEA error
Answer: OrgDb for maize
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
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