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promoter
•
reset
0
votes
2
replies
1.0k
views
Failed to get promoters using promoters() in R 4.0.3.
promoter
GenomicRanges
rtracklayer
GRanges
2.6 years ago
Arslan
• 0
3
votes
6
replies
1.2k
views
Better way to find head to head GRanges?
promoter
updated 3.9 years ago by
Hervé Pagès
16k • written 3.9 years ago by
Charles Plessy
▴ 180
1
vote
3
replies
1.2k
views
Obtain coordinates of 5' upstream region up to closest coding region
r
granges
promoter
updated 5.1 years ago by
Hervé Pagès
16k • written 5.1 years ago by
eggrandio
• 0
0
votes
0
replies
898
views
CAGEr get TSS in bed file
TSS
promoter
cage
cager
5.4 years ago
bharata1803
▴ 60
0
votes
0
replies
1.3k
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
5.6 years ago
Wojeff
• 0
0
votes
3
replies
1.8k
views
How to handle multi-TSS genes in Repitools?
repitools
promoter
tss
annotation
6.1 years ago
Ryan C. Thompson
★ 7.9k
1
vote
5
replies
1.9k
views
Extract genomic features from a TxDb-like object
TxDB
genomicfeatures
promoter
getpromoterseq
updated 6.1 years ago by
Hervé Pagès
16k • written 6.1 years ago by
rbenel
▴ 40
1
vote
2
replies
1.1k
views
DEXseq for alternate promoter usage
dexseq
promoter
utr
updated 7.9 years ago by
Alejandro Reyes
★ 1.9k • written 7.9 years ago by
joan.hooper
• 0
1
vote
6
replies
1.8k
views
problem creating txdb object and bsgenome for solanum pennellii
bsgenome
txdb
promoter
updated 8.2 years ago by
Martin Morgan
25k • written 8.2 years ago by
sekawaiwai2006
▴ 20
2
votes
2
replies
2.6k
views
using the "promoters" function with an "OrganismDb" to generate "GRanges" with "REFSEQ" rather than UCSC gene names
promoter
granges
refseq
ucsc
organismdb
updated 8.4 years ago by
Robert Castelo
★ 3.3k • written 8.4 years ago by
efoss
▴ 10
2
votes
2
replies
1.4k
views
promoter definition in VariantAnnotation
VariantAnnotation
promoter
drosophila melanogaster
updated 9.3 years ago by
Valerie Obenchain
★ 6.8k • written 9.3 years ago by
lidia.mateo
▴ 30
11 results • Page
1 of 1
Recent ...
Replies
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
Gayatri
• 0
Hello James, How to generate the db? By running the makeOrgPackageFromNCBI() command? I have tried doing that, first by just deleting the …
Answer: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param
by
Tim Peters
▴ 170
Hi Jose and Russ, Apologies to Jose for not seeing this earlier. Sometimes the loess smoother in the bottom panel will throw this error …
Comment: Trying to use enrichGO
by
fernanda.backsouza
• 0
Sure, I changed it but still NULL G0 <- enrichGO( gene = ortologos_filtrados$Gene.ID, OrgDb = org.Cs.eg.db, keyType = "ENTREZID",…
Answer: limma-voom: Calculate the log-fold change in gene expression within a sample
by
Gordon Smyth
50k
No, you cannot use residuals to compute logFCs. From the information you give, I guess that you need to add individual-specific condition …
Comment: Error EPICv2 ChAMP
by
James W. MacDonald
65k
You don't need to do either of the above suggestions. ``` library(BiocManager) install("YuanTian1991/ChAMPdata") ``` will install without…
Votes
Comment: Cannabis and KEGGgraph
Comment: Cannabis and KEGGgraph
Answer: Cannabis and KEGGgraph
Answer: Differentially expressed genes in monocle pseudotime
Answer: DESeq2 - dispersion estimation when there is none
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