Showing : BSGenome • reset
0
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3
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6.5k
views
Any tools to convert .gff to .gtf format
AnnotationData CrispRdesignR BSgenome
updated 3 months ago by • 0 • written 2.1 years ago by • 0
1
vote
6
replies
1.1k
views
Help creating BSgenome object for new canine and feline genomes?
BSgenome
updated 7 months ago by 67k • written 8 months ago by • 0
2
votes
4
replies
789
views
Need help generating BSgenome and orgdb
OrgDb BSgenome
11 months ago • updated 8 months ago mat149 ▴ 80
1
vote
3
replies
870
views
Using injectSNPs with a custom set of SNPs
SNPlocs BSgenome
written 11 months ago by • 0
0
votes
3
replies
954
views
Get Intron Seq
intron BSgenome.Hsapiens.UCSC.hg38 BSgenome
updated 16 months ago by ★ 4.5k • written 16 months ago by • 0
0
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4
replies
1.7k
views
BSgenome for ensembl mm10
BSgenomeForge BSgenome
updated 16 months ago by 67k • written 16 months ago by • 0
1
vote
4
replies
959
views
Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 16 months ago by 16k • written 16 months ago by • 0
1
vote
1
reply
675
views
add genome to BSgenome
bsgenome
updated 22 months ago by 4.0k • written 23 months ago by ▴ 10
2
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2
replies
2.4k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
2.0 years ago Mog • 0
9
votes
5
replies
1.7k
views
karyoploteR genome coverage plotting using BSgenome.TAIR10
BSgenome.Athaliana.TAIR.TAIR10. karyoploteR BSgenome
updated 2.0 years ago by 67k • written 2.0 years ago by • 0
2
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3
replies
1.1k
views
Request : Add Chinese Spring Wheat genome to BSgenome
BSgenome
updated 9 months ago by • 0 • written 2.4 years ago by ▴ 10
1
vote
1
reply
900
views
Request: Add Marmoset (calJac4) genome to BSgenome
BSgenome
updated 2.5 years ago by 16k • written 2.5 years ago by • 0
1
vote
0
replies
1.0k
views
News: BSgenome package for T2T-CHM13v2.0 assembly and SNPlocs package for dbSNP155
BSgenome dbSNP T2T-CHM13v2.0 SNPlocs
2.5 years ago Hervé Pagès 16k
1
vote
1
reply
1.1k
views
Fail to install BSgenome and library
BSgenome Celegans
updated 2.5 years ago by 16k • written 2.5 years ago by • 0
1
vote
0
replies
921
views
How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
2.5 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
2.6 years ago alain.corvisier • 0
2
votes
1
reply
994
views
How to find the BSgenome object that provided the seqinfo of a GRanges object ?
BSgenome
updated 2.7 years ago by 16k • written 2.7 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
1.2k
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 geo.vogler ▴ 10
1
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2
replies
1.1k
views
How to make OrgPackage (BSgenome data) package available for R Bioconductor users
BSGenome
updated 3.4 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 3.5 years ago by • 0
3
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5
replies
1.4k
views
unable to forge custom BSgenome after update
BSgenome
updated 3.5 years ago by 16k • written 3.5 years ago by ▴ 80
0
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0
replies
777
views
how to construct a SNPlocs-class by myself
BSgenome SNPlocs
3.5 years ago Guandong Shang ▴ 40
2
votes
4
replies
1.9k
views
BSGenome Forge for non-model organism
BSGenomeForge BSGenome
updated 3.5 years ago by 16k • written 3.5 years ago by • 0
0
votes
3
replies
2.0k
views
Can BSGenome forge from non-UCSC/NCBI assemblies?
BSgenome
updated 3.8 years ago by ▴ 10 • written 3.9 years ago by • 0
3
votes
2
replies
2.5k
views
Forging a BSGenome
BSgenome microtus forging
updated 3.8 years ago by 16k • written 3.9 years ago by ▴ 20
1
vote
4
replies
1.7k
views
forging a BSgenome data package - Seed file issue
seedfiles BSgenome
3.9 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 3.9 years ago by 16k • written 4.1 years ago by ▴ 80
0
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3
replies
1.6k
views
Error in Forge the target package (BSgenome)
software error BSgenome
4.1 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 4.1 years ago by 16k • written 4.1 years ago by • 0
0
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0
replies
724
views
Error in loading forged BSgenome
BSgenome msgbsR
4.1 years ago jiazhou0116 • 0
0
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1
reply
1.3k
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 4.4 years ago by 4.0k • written 4.4 years ago by ▴ 10
0
votes
4
replies
2.1k
views
Error in seqlevelsStyle after creating a BSgenome package
bsgenome MutationalPatterns
4.6 years ago • updated 4.5 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 4.9 years ago by 16k • written 4.9 years ago by ▴ 40
1
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0
replies
866
views
News: New BSgenome data packages for bosTau9, rheMac10, danRer11, and galGal6
BSgenome News
4.9 years ago Hervé Pagès 16k
2
votes
1
reply
696
views
Does "exclude" argument break BSgenome::vmatchPattern?
BSgenome
updated 4.9 years ago by 67k • written 4.9 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 5.0 years ago by • 0 • written 10.0 years ago by • 0
3
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15
replies
2.3k
views
Error in creating BSGenome package
BSGenome
updated 5.0 years ago by 67k • written 5.0 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
5.1 years ago Aditya ▴ 160
2
votes
3
replies
1.5k
views
What is the use of a masked BSgenome?
BSgenome BSgenome.Mmusculus.UCSC.mm10::Mmusculus Biostrings
updated 5.1 years ago by 4.0k • written 5.2 years ago by ▴ 160
1
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2
replies
1.1k
views
Is it useful to define and export a setAs('BSgenome', 'GRanges')
BSgenome GenomicRanges
updated 5.1 years ago by ★ 11k • written 5.1 years ago by ▴ 160
0
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2
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1.2k
views
getBSgenome{Bsgenome}: avoid attaching BiocGenerics (and others)
BSgenome Bsgenome.Mmusculus.UCSC.mm10
5.2 years ago • updated 5.1 years ago Aditya ▴ 160
1
vote
6
replies
2.8k
views
How to subset a BSgenome
BSgenome BSgenome.Mmusculus.UCSC.mm10
updated 5.2 years ago by 4.0k • written 5.2 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 5.4 years ago by 67k • written 5.4 years ago by • 0
0
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1
reply
1.0k
views
getSeqSrcpaths (forgeBSgenome) error files not found, but they are right there....
bsgenome forgebsgenome getSeqSrcpaths
5.6 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 5.6 years ago by 67k • written 5.6 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 5.6 years ago by ★ 4.3k • written 5.6 years ago by • 0
2
votes
2
replies
1.5k
views
BSgenome package building
bsgenome
updated 6.0 years ago by 67k • written 6.0 years ago by • 0
50 results • Page 1 of 1
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Answer: featureCounts fails to load annotation file by Yang Liao ▴ 440
Hi Yasmin, I'm following up on the issue you're having with featureCounts and the GRCh38 RefSeq annotation. I've been testing featureCounts…
Answer: How to adjust the DESeq2 formula when there is no control group for one factor? by swbarnes2 ★ 1.4k
You are overthinking this. You have two time points, you compare them to each other. You can't compare them to a time point you don't hav…
Answer: Biostrings: Error writing long reads (>200kbps) with writeQualityScaledXStringSe by Aidan ▴ 40
As far as I am aware, the restriction is historical..having a fixed buffer size in the internal C methods makes the algorithms a little sim…
Comment: Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ? by rohitsatyam102 ▴ 20
I am facing a similar issue.
Answer: How to subset voomLmFit (MArrayLM) object? by Gordon Smyth 51k
Yes, the current behaviour is absolutely intentional. It doesn't seem to me to be meaningful or useful to try to subset the EList object au…
Votes
A: eBayes warning: zero sample variances
A: eBayes warning: zero sample variances
Answer: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
Comment: Are transformed values from rlog /vst log2 normalized counts?
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