Showing : BSgenome • reset
0
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3
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6.3k
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Any tools to convert .gff to .gtf format
AnnotationData CrispRdesignR BSgenome
updated 10 weeks ago by • 0 • written 2.0 years ago by • 0
1
vote
6
replies
1.0k
views
Help creating BSgenome object for new canine and feline genomes?
BSgenome
updated 6 months ago by 67k • written 7 months ago by • 0
2
votes
4
replies
745
views
Need help generating BSgenome and orgdb
OrgDb BSgenome
10 months ago • updated 7 months ago mat149 ▴ 80
1
vote
3
replies
806
views
Using injectSNPs with a custom set of SNPs
SNPlocs BSgenome
written 11 months ago by • 0
0
votes
3
replies
918
views
Get Intron Seq
intron BSgenome.Hsapiens.UCSC.hg38 BSgenome
updated 15 months ago by ★ 4.4k • written 15 months ago by • 0
0
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4
replies
1.6k
views
BSgenome for ensembl mm10
BSgenomeForge BSgenome
updated 15 months ago by 67k • written 15 months ago by • 0
1
vote
4
replies
918
views
Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 15 months ago by 16k • written 15 months ago by • 0
1
vote
1
reply
656
views
add genome to BSgenome
bsgenome
updated 21 months ago by 4.0k • written 22 months ago by ▴ 10
2
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2
replies
2.2k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
23 months ago Mog • 0
9
votes
5
replies
1.7k
views
karyoploteR genome coverage plotting using BSgenome.TAIR10
BSgenome.Athaliana.TAIR.TAIR10. karyoploteR BSgenome
updated 23 months ago by 67k • written 23 months ago by • 0
2
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3
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1.0k
views
Request : Add Chinese Spring Wheat genome to BSgenome
BSgenome
updated 8 months ago by • 0 • written 2.4 years ago by ▴ 10
1
vote
1
reply
883
views
Request: Add Marmoset (calJac4) genome to BSgenome
BSgenome
updated 2.4 years ago by 16k • written 2.4 years ago by • 0
1
vote
0
replies
976
views
News: BSgenome package for T2T-CHM13v2.0 assembly and SNPlocs package for dbSNP155
BSgenome dbSNP T2T-CHM13v2.0 SNPlocs
2.4 years ago Hervé Pagès 16k
1
vote
1
reply
1.1k
views
Fail to install BSgenome and library
BSgenome Celegans
updated 2.4 years ago by 16k • written 2.4 years ago by • 0
1
vote
0
replies
892
views
How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
2.4 years ago Charles Plessy ▴ 180
2
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4
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1.4k
views
Subset a BSgenome object (keep standard chomosomes) for applying vmatchPattern or vmatchPDict
BSgenome seqinfo
2.5 years ago alain.corvisier • 0
2
votes
1
reply
973
views
How to find the BSgenome object that provided the seqinfo of a GRanges object ?
BSgenome
updated 2.6 years ago by 16k • written 2.6 years ago by ▴ 180
1
vote
5
replies
1.5k
views
submitting a BSgenome package
BSgenome
3.9 years ago • updated 2.7 years ago deisianyufg • 0
1
vote
2
replies
1.1k
views
Building BSgenome package fails - .make_BSgenome_seqinfo error: sequence names found in .2bit file are not identical to 'seqnames'
BSGenome Forge
2.9 years ago • updated 2.8 years ago geo.vogler ▴ 10
1
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2
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1.0k
views
How to make OrgPackage (BSgenome data) package available for R Bioconductor users
BSGenome
updated 3.3 years ago by 16k • written 3.4 years ago by • 0
2
votes
7
replies
1.8k
views
Can I use BSgenome for in-house assemblies?
BSgenome
updated 3.4 years ago by 16k • written 3.4 years ago by • 0
3
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5
replies
1.4k
views
unable to forge custom BSgenome after update
BSgenome
updated 3.4 years ago by 16k • written 3.4 years ago by ▴ 80
0
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0
replies
763
views
how to construct a SNPlocs-class by myself
BSgenome SNPlocs
3.4 years ago Guandong Shang ▴ 40
2
votes
4
replies
1.9k
views
BSGenome Forge for non-model organism
BSGenomeForge BSGenome
updated 3.4 years ago by 16k • written 3.4 years ago by • 0
0
votes
3
replies
2.0k
views
Can BSGenome forge from non-UCSC/NCBI assemblies?
BSgenome
updated 3.7 years ago by ▴ 10 • written 3.8 years ago by • 0
3
votes
2
replies
2.4k
views
Forging a BSGenome
BSgenome microtus forging
updated 3.8 years ago by 16k • written 3.8 years ago by ▴ 20
1
vote
4
replies
1.7k
views
forging a BSgenome data package - Seed file issue
seedfiles BSgenome
3.8 years ago n.mary • 0
2
votes
2
replies
1.7k
views
How does one modify a single value of a field in a seqinfo object?
GenomicRanges GenomeInfoDb BSgenome isCircular
updated 3.8 years ago by 16k • written 4.0 years ago by ▴ 80
0
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3
replies
1.6k
views
Error in Forge the target package (BSgenome)
software error BSgenome
4.0 years ago • updated 3.9 years ago jiazhou0116 • 0
1
vote
1
reply
1.1k
views
About generating a seed file (DCF format) for forging a BSgenome
software error BSgenome
updated 4.0 years ago by 16k • written 4.0 years ago by • 0
0
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0
replies
711
views
Error in loading forged BSgenome
BSgenome msgbsR
4.0 years ago jiazhou0116 • 0
0
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1
reply
1.2k
views
How can i get repetitive elements genomic ranges in human genome?
repetitive elements IRanges GenomicRanges BSgenome
updated 4.1 years ago by 67k • written 4.1 years ago by ▴ 50
0
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1
reply
1.1k
views
error when forging a BSgenome
BSgenome
updated 4.3 years ago by 4.0k • written 4.3 years ago by ▴ 10
0
votes
4
replies
2.1k
views
Error in seqlevelsStyle after creating a BSgenome package
bsgenome MutationalPatterns
4.5 years ago • updated 4.4 years ago sibyl.bertrand • 0
0
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2
replies
1.1k
views
vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
4.5 years ago mb2subi • 0
2
votes
6
replies
1.3k
views
Can't find library BSgenome.Mmulatta.UCSC for latest genome (mmul10)
annotation mmul10 BSgenome
updated 4.8 years ago by 16k • written 4.8 years ago by ▴ 40
1
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0
replies
847
views
News: New BSgenome data packages for bosTau9, rheMac10, danRer11, and galGal6
BSgenome News
4.8 years ago Hervé Pagès 16k
2
votes
1
reply
679
views
Does "exclude" argument break BSgenome::vmatchPattern?
BSgenome
updated 4.8 years ago by 67k • written 4.8 years ago by ▴ 160
0
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6
replies
2.5k
views
Error while attempting to forge BSgenome data package
bsgenome ggbio
updated 4.9 years ago by • 0 • written 9.9 years ago by • 0
3
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15
replies
2.3k
views
Error in creating BSGenome package
BSGenome
updated 4.9 years ago by 67k • written 4.9 years ago by • 0
0
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3
replies
1.4k
views
Defining BSgenome -> GRanges S4 coercer without package attaching
BSgenome methods GenomicRanges
5.0 years ago Aditya ▴ 160
2
votes
3
replies
1.4k
views
What is the use of a masked BSgenome?
BSgenome BSgenome.Mmusculus.UCSC.mm10::Mmusculus Biostrings
updated 5.0 years ago by 4.0k • written 5.1 years ago by ▴ 160
1
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2
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1.1k
views
Is it useful to define and export a setAs('BSgenome', 'GRanges')
BSgenome GenomicRanges
updated 5.0 years ago by ★ 11k • written 5.0 years ago by ▴ 160
0
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2
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1.1k
views
getBSgenome{Bsgenome}: avoid attaching BiocGenerics (and others)
BSgenome Bsgenome.Mmusculus.UCSC.mm10
5.1 years ago • updated 5.0 years ago Aditya ▴ 160
1
vote
6
replies
2.7k
views
How to subset a BSgenome
BSgenome BSgenome.Mmusculus.UCSC.mm10
updated 5.1 years ago by 4.0k • written 5.1 years ago by ▴ 160
0
votes
6
replies
1.3k
views
error when using matchProbePair with BSgenome.Hsapiens.UCSC.hg19
matchProbePair BSgenome Biostrings BSgenome.Hsapiens.UCSC.hg19
updated 5.3 years ago by 67k • written 5.3 years ago by • 0
0
votes
1
reply
988
views
getSeqSrcpaths (forgeBSgenome) error files not found, but they are right there....
bsgenome forgebsgenome getSeqSrcpaths
5.5 years ago tguerreroa90 • 0
2
votes
1
reply
1.0k
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 5.5 years ago by 67k • written 5.5 years ago by ▴ 40
0
votes
9
replies
1.7k
views
Unable to generate feature vector with custom genome in cleanUpdTSeq
cleanUpdTSeq BSgenome BSgenomeForge
updated 5.5 years ago by ★ 4.3k • written 5.5 years ago by • 0
2
votes
2
replies
1.4k
views
BSgenome package building
bsgenome
updated 5.9 years ago by 67k • written 5.9 years ago by • 0
50 results • Page 1 of 1
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Comment: When doing differential methylation using the sesame package, seems to only go by James W. MacDonald 67k
The odds ratio, not log FC. My bad.
Comment: When doing differential methylation using the sesame package, seems to only go by James W. MacDonald 67k
``` testResult$Eff_Condition > 0.1 ```
Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th by Fatima • 0
I identified 3804 genes with GO annotations. I put my liste of genes in this link [enter link description here][1] universe <- mapIds…
Comment: When doing differential methylation using the sesame package, seems to only go by ramiro.barrantes ▴ 10
Hello, Thank you. I absolutely respect what you mention about p-values and logFC, I was just going to tackle that soon and thank you for po…
Comment: QSEA:Error in h(simpleError(msg, call)) by kf • 0
genome(qseaSet@regions)<-"BSgenome.Hsapiens.UCSC.hg38" solve the problem
Votes
Answer: Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjus
Answer: Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjus
Answer: clusterProfiler: BgRatio N value does not match the size of the gene universe th
Answer: object 'hdac_targets' not found
Answer: object 'hdac_targets' not found
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