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Showing :
promoter
•
reset
0
votes
2
replies
535
views
Failed to get promoters using promoters() in R 4.0.3.
promoter
GenomicRanges
rtracklayer
GRanges
17 months ago
Arslan
• 0
3
votes
6
replies
645
views
Better way to find head to head GRanges?
promoter
updated 2.7 years ago by
Hervé Pagès
16k • written 2.7 years ago by
Charles Plessy
▴ 170
1
vote
3
replies
757
views
Obtain coordinates of 5' upstream region up to closest coding region
r
granges
promoter
updated 3.9 years ago by
Hervé Pagès
16k • written 3.9 years ago by
eggrandio
• 0
0
votes
0
replies
533
views
CAGEr get TSS in bed file
TSS
promoter
cage
cager
4.2 years ago
bharata1803
▴ 40
0
votes
0
replies
990
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
4.4 years ago
Wojeff
• 0
0
votes
3
replies
1.2k
views
How to handle multi-TSS genes in Repitools?
repitools
promoter
tss
annotation
4.9 years ago
Ryan C. Thompson
7.8k
1
vote
5
replies
1.2k
views
Extract genomic features from a TxDb-like object
TxDB
genomicfeatures
promoter
getpromoterseq
updated 4.9 years ago by
Hervé Pagès
16k • written 4.9 years ago by
rbenel
▴ 20
1
vote
2
replies
817
views
DEXseq for alternate promoter usage
dexseq
promoter
utr
updated 6.6 years ago by
Alejandro Reyes
★ 1.8k • written 6.6 years ago by
joan.hooper
• 0
1
vote
6
replies
1.3k
views
problem creating txdb object and bsgenome for solanum pennellii
bsgenome
txdb
promoter
updated 7.0 years ago by
Martin Morgan
25k • written 7.0 years ago by
sekawaiwai2006
▴ 20
2
votes
2
replies
1.8k
views
using the "promoters" function with an "OrganismDb" to generate "GRanges" with "REFSEQ" rather than UCSC gene names
promoter
granges
refseq
ucsc
organismdb
updated 7.2 years ago by
Robert Castelo
★ 3.0k • written 7.2 years ago by
efoss
▴ 10
2
votes
2
replies
1.1k
views
promoter definition in VariantAnnotation
VariantAnnotation
promoter
drosophila melanogaster
updated 8.1 years ago by
Valerie Obenchain
★ 6.7k • written 8.1 years ago by
lidia.mateo
▴ 30
11 results • Page
1 of 1
Recent ...
Replies
Comment: mas5calls function doesn't work; mirna40cdf problem
by
James W. MacDonald
62k
Yes. Follow the recommendation in the link that was provided to you by Lori Shepherd.
Comment: mas5calls function doesn't work; mirna40cdf problem
by
Berna
• 0
Thank you for the information. I did not know that. Would you have a tip how I could proceed differently?
Comment: Correct use of Likelihood Ratio Test and LFC Shrinkage
by
ayabalbaa1990
• 0
Hi Michael, So I use this res_LRT <- results(dds_lrt) r2=lfcShrink(dds_lrt, coef=7, res=res_LRT) tu run lfcshrink with LRT, is that oko?…
Comment: Combat and dds Object
by
shaimaa
• 0
I used the combat-seq but the deseq complain as its not integer what should i do
Answer: Different summary() and results() values in DeSeq2
by
Basti
▴ 540
summary() tells you the number of genes with low counts, see independant filtering of results in the DESeq2 vignette : https://www.biocondu…
Votes
Answer: mas5calls function doesn't work; mirna40cdf problem
Issue with bumphunter and TxDb.Hsapiens.UCSC.hg38.knownGene that could be due to S4Vectors or an installation problem
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
A: How to translate FASTA file of DNA sequence to protein sequence using Biostrings
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Guido Hooiveld
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James W. MacDonald
62k
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Michael Love
39k
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twtoal
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