Showing : BSgenome • reset
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Package needs internet access
BSgenome BSgenome.Hsapiens.UCSC.hg38 Offline
updated 4 months ago by 68k • written 4 months ago by ▴ 20
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4
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7.9k
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Any tools to convert .gff to .gtf format
AnnotationData CrispRdesignR BSgenome
updated 12 weeks ago by • 0 • written 2.6 years ago by • 0
1
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6
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1.4k
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Help creating BSgenome object for new canine and feline genomes?
BSgenome
updated 13 months ago by 68k • written 13 months ago by • 0
2
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4
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1.1k
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Need help generating BSgenome and orgdb
OrgDb BSgenome
17 months ago • updated 13 months ago mat149 ▴ 80
1
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3
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1.1k
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Using injectSNPs with a custom set of SNPs
SNPlocs BSgenome
written 17 months ago by • 0
0
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3
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1.2k
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Get Intron Seq
intron BSgenome.Hsapiens.UCSC.hg38 BSgenome
updated 21 months ago by ★ 4.8k • written 21 months ago by • 0
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4
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2.3k
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BSgenome for ensembl mm10
BSgenomeForge BSgenome
updated 21 months ago by 68k • written 21 months ago by • 0
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4
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1.1k
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Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 22 months ago by 16k • written 22 months ago by • 0
1
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1
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753
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add genome to BSgenome
bsgenome
updated 2.3 years ago by 4.1k • written 2.3 years ago by ▴ 10
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2
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2.8k
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getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
2.5 years ago Mog • 0
9
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5
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2.0k
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karyoploteR genome coverage plotting using BSgenome.TAIR10
BSgenome.Athaliana.TAIR.TAIR10. karyoploteR BSgenome
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
2
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3
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1.3k
views
Request : Add Chinese Spring Wheat genome to BSgenome
BSgenome
updated 14 months ago by • 0 • written 2.9 years ago by ▴ 10
1
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1
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1.0k
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Request: Add Marmoset (calJac4) genome to BSgenome
BSgenome
updated 2.9 years ago by 16k • written 2.9 years ago by • 0
1
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0
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1.1k
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News: BSgenome package for T2T-CHM13v2.0 assembly and SNPlocs package for dbSNP155
BSgenome dbSNP T2T-CHM13v2.0 SNPlocs
2.9 years ago Hervé Pagès 16k
1
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1
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1.3k
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Fail to install BSgenome and library
BSgenome Celegans
updated 3.0 years ago by 16k • written 3.0 years ago by • 0
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0
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1.1k
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How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
3.0 years ago Charles Plessy ▴ 180
2
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4
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1.7k
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Subset a BSgenome object (keep standard chomosomes) for applying vmatchPattern or vmatchPDict
BSgenome seqinfo
3.0 years ago alain.corvisier • 0
2
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1
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1.1k
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How to find the BSgenome object that provided the seqinfo of a GRanges object ?
BSgenome
updated 3.2 years ago by 16k • written 3.2 years ago by ▴ 180
1
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5
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1.7k
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submitting a BSgenome package
BSgenome
4.4 years ago • updated 3.2 years ago deisianyufg • 0
1
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2
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1.3k
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Building BSgenome package fails - .make_BSgenome_seqinfo error: sequence names found in .2bit file are not identical to 'seqnames'
BSGenome Forge
3.4 years ago geo.vogler ▴ 10
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2
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1.2k
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How to make OrgPackage (BSgenome data) package available for R Bioconductor users
BSGenome
updated 3.9 years ago by 16k • written 3.9 years ago by • 0
2
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7
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2.0k
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Can I use BSgenome for in-house assemblies?
BSgenome
updated 3.9 years ago by 16k • written 3.9 years ago by • 0
3
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5
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1.6k
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unable to forge custom BSgenome after update
BSgenome
updated 3.9 years ago by 16k • written 3.9 years ago by ▴ 80
0
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0
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865
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how to construct a SNPlocs-class by myself
BSgenome SNPlocs
4.0 years ago Guandong Shang ▴ 40
2
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4
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2.1k
views
BSGenome Forge for non-model organism
BSGenomeForge BSGenome
updated 4.0 years ago by 16k • written 4.0 years ago by • 0
0
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3
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2.4k
views
Can BSGenome forge from non-UCSC/NCBI assemblies?
BSgenome
updated 4.2 years ago by ▴ 10 • written 4.3 years ago by • 0
3
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2
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2.9k
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Forging a BSGenome
BSgenome microtus forging
updated 4.3 years ago by 16k • written 4.3 years ago by ▴ 20
1
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4
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1.9k
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forging a BSgenome data package - Seed file issue
seedfiles BSgenome
4.4 years ago n.mary • 0
2
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2
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1.9k
views
How does one modify a single value of a field in a seqinfo object?
GenomicRanges GenomeInfoDb BSgenome isCircular
updated 4.4 years ago by 16k • written 4.5 years ago by ▴ 80
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3
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1.8k
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Error in Forge the target package (BSgenome)
software error BSgenome
4.6 years ago • updated 4.4 years ago jiazhou0116 • 0
1
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1
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1.3k
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About generating a seed file (DCF format) for forging a BSgenome
software error BSgenome
updated 4.5 years ago by 16k • written 4.6 years ago by • 0
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0
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793
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Error in loading forged BSgenome
BSgenome msgbsR
4.5 years ago jiazhou0116 • 0
0
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1
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1.6k
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How can i get repetitive elements genomic ranges in human genome?
repetitive elements IRanges GenomicRanges BSgenome
updated 4.6 years ago by 68k • written 4.6 years ago by ▴ 50
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1
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1.2k
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error when forging a BSgenome
BSgenome
updated 4.9 years ago by 4.1k • written 4.9 years ago by ▴ 10
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4
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2.4k
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Error in seqlevelsStyle after creating a BSgenome package
bsgenome MutationalPatterns
5.0 years ago • updated 4.9 years ago sibyl.bertrand • 0
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2
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1.3k
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vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
5.0 years ago mb2subi • 0
2
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6
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1.5k
views
Can't find library BSgenome.Mmulatta.UCSC for latest genome (mmul10)
annotation mmul10 BSgenome
updated 5.3 years ago by 16k • written 5.3 years ago by ▴ 40
1
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0
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976
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News: New BSgenome data packages for bosTau9, rheMac10, danRer11, and galGal6
BSgenome News
5.3 years ago Hervé Pagès 16k
2
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1
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776
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Does "exclude" argument break BSgenome::vmatchPattern?
BSgenome
updated 5.3 years ago by 68k • written 5.3 years ago by ▴ 160
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6
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2.7k
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Error while attempting to forge BSgenome data package
bsgenome ggbio
updated 5.4 years ago by • 0 • written 10.4 years ago by • 0
3
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15
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2.6k
views
Error in creating BSGenome package
BSGenome
updated 5.4 years ago by 68k • written 5.5 years ago by • 0
0
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3
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1.6k
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Defining BSgenome -> GRanges S4 coercer without package attaching
BSgenome methods GenomicRanges
5.6 years ago • updated 5.5 years ago Aditya ▴ 160
2
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3
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1.7k
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What is the use of a masked BSgenome?
BSgenome BSgenome.Mmusculus.UCSC.mm10::Mmusculus Biostrings
updated 5.6 years ago by 4.1k • written 5.6 years ago by ▴ 160
1
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2
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1.3k
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Is it useful to define and export a setAs('BSgenome', 'GRanges')
BSgenome GenomicRanges
updated 5.6 years ago by ★ 11k • written 5.6 years ago by ▴ 160
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2
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1.3k
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getBSgenome{Bsgenome}: avoid attaching BiocGenerics (and others)
BSgenome Bsgenome.Mmusculus.UCSC.mm10
5.6 years ago Aditya ▴ 160
1
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6
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3.1k
views
How to subset a BSgenome
BSgenome BSgenome.Mmusculus.UCSC.mm10
updated 5.6 years ago by 4.1k • written 5.6 years ago by ▴ 160
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6
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1.4k
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error when using matchProbePair with BSgenome.Hsapiens.UCSC.hg19
matchProbePair BSgenome Biostrings BSgenome.Hsapiens.UCSC.hg19
updated 5.9 years ago by 68k • written 5.9 years ago by • 0
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1
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1.1k
views
getSeqSrcpaths (forgeBSgenome) error files not found, but they are right there....
bsgenome forgebsgenome getSeqSrcpaths
6.0 years ago tguerreroa90 • 0
2
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1
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1.1k
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Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 6.0 years ago by 68k • written 6.0 years ago by ▴ 40
0
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9
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1.9k
views
Unable to generate feature vector with custom genome in cleanUpdTSeq
cleanUpdTSeq BSgenome BSgenomeForge
updated 6.1 years ago by ★ 4.3k • written 6.1 years ago by • 0
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Comment: Annotation package for Manduca sexta by GA ▴ 10
Thank you!
Comment: Improving performance of edgeR and limma while adjusting for multiple confounder by ATpoint ★ 4.8k
If 2 minutes is inacceptable to you then you can still fall back to limma-trend which should give a dramatic speedup and finish in seconds.…
Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k
Great, thanks for the update from Ensembl. So the most relevant part of 'Location: Scaffold HG1277_PATCH: 137,021-141,806 forward strand' …
Answer: Improving performance of edgeR and limma while adjusting for multiple confounder by Gordon Smyth 52k
We recommend that you use voomLmFit() instead of voom+lmFit. We are pretty proud of the speed of glmQLFit and voom, and we hadn't expected…
Answer: Merging EPICV1 and V2 betas by James W. MacDonald 68k
It appears that [SeSAMe][1] has functions meant to do that sort of thing. [1]: https://bioconductor.org/packages/release/bioc/vignet…
Votes
Looking for equivalent EPIC chip v1 vs. v2 annotation variables
Properly constructing a hypergeometric test
A: Is logFC a log2 fold change or some other base in scran::findMarkers
Comment: Error in retrieving clinical data
What is the cheapest day to fly on American Airlines? {Ask_Expert}
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