Showing : bsgenome • reset
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How to construct a BSgenome object from a custom genome assembly using BSgenomeForge?
BSgenome BSgenomeForge
updated 4 months ago by 68k • written 4 months ago by ▴ 80
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5
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1.1k
views
Package needs internet access
BSgenome BSgenome.Hsapiens.UCSC.hg38 Offline
updated 14 months ago by 68k • written 14 months ago by ▴ 20
0
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4
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9.6k
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Any tools to convert .gff to .gtf format
AnnotationData CrispRdesignR BSgenome
updated 13 months ago by • 0 • written 3.4 years ago by • 0
1
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6
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1.8k
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Help creating BSgenome object for new canine and feline genomes?
BSgenome
updated 23 months ago by 68k • written 24 months ago by • 0
2
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4
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1.7k
views
Need help generating BSgenome and orgdb
OrgDb BSgenome
2.3 years ago • updated 2.0 years ago mat149 ▴ 80
1
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3
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1.5k
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Using injectSNPs with a custom set of SNPs
SNPlocs BSgenome
written 2.3 years ago by • 0
0
votes
3
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1.5k
views
Get Intron Seq
intron BSgenome.Hsapiens.UCSC.hg38 BSgenome
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by • 0
0
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4
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3.6k
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BSgenome for ensembl mm10
BSgenomeForge BSgenome
updated 2.6 years ago by 68k • written 2.7 years ago by • 0
1
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4
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1.4k
views
Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 2.7 years ago by 16k • written 2.7 years ago by • 0
1
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1
reply
945
views
add genome to BSgenome
bsgenome
updated 3.2 years ago by 4.3k • written 3.2 years ago by ▴ 10
2
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2
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3.5k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
3.4 years ago • updated 3.3 years ago Mog • 0
9
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5
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2.5k
views
karyoploteR genome coverage plotting using BSgenome.TAIR10
BSgenome.Athaliana.TAIR.TAIR10. karyoploteR BSgenome
updated 3.4 years ago by 68k • written 3.4 years ago by • 0
2
votes
3
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1.8k
views
Request : Add Chinese Spring Wheat genome to BSgenome
BSgenome
updated 2.1 years ago by • 0 • written 3.8 years ago by ▴ 10
1
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1
reply
1.2k
views
Request: Add Marmoset (calJac4) genome to BSgenome
BSgenome
updated 3.8 years ago by 16k • written 3.8 years ago by • 0
1
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0
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1.4k
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News: BSgenome package for T2T-CHM13v2.0 assembly and SNPlocs package for dbSNP155
BSgenome dbSNP T2T-CHM13v2.0 SNPlocs
3.8 years ago Hervé Pagès 16k
1
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1
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1.5k
views
Fail to install BSgenome and library
BSgenome Celegans
updated 3.8 years ago by 16k • written 3.8 years ago by • 0
1
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0
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1.3k
views
How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
3.8 years ago Charles Plessy ▴ 180
2
votes
4
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2.2k
views
Subset a BSgenome object (keep standard chomosomes) for applying vmatchPattern or vmatchPDict
BSgenome seqinfo
3.9 years ago alain.corvisier • 0
2
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1
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1.4k
views
How to find the BSgenome object that provided the seqinfo of a GRanges object ?
BSgenome
updated 4.0 years ago by 16k • written 4.0 years ago by ▴ 180
1
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5
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2.0k
views
submitting a BSgenome package
BSgenome
5.3 years ago • updated 4.0 years ago deisianyufg • 0
1
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2
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1.6k
views
Building BSgenome package fails - .make_BSgenome_seqinfo error: sequence names found in .2bit file are not identical to 'seqnames'
BSGenome Forge
4.2 years ago geo.vogler ▴ 10
1
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2
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1.4k
views
How to make OrgPackage (BSgenome data) package available for R Bioconductor users
BSGenome
updated 4.7 years ago by 16k • written 4.8 years ago by • 0
2
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7
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2.4k
views
Can I use BSgenome for in-house assemblies?
BSgenome
updated 4.8 years ago by 16k • written 4.8 years ago by • 0
3
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5
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2.0k
views
unable to forge custom BSgenome after update
BSgenome
updated 4.8 years ago by 16k • written 4.8 years ago by ▴ 80
0
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0
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1.0k
views
how to construct a SNPlocs-class by myself
BSgenome SNPlocs
4.8 years ago Guandong Shang ▴ 40
2
votes
4
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2.5k
views
BSGenome Forge for non-model organism
BSGenomeForge BSGenome
updated 4.8 years ago by 16k • written 4.8 years ago by • 0
0
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3
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3.1k
views
Can BSGenome forge from non-UCSC/NCBI assemblies?
BSgenome
updated 5.1 years ago by ▴ 10 • written 5.2 years ago by • 0
3
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2
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3.5k
views
Forging a BSGenome
BSgenome microtus forging
updated 5.2 years ago by 16k • written 5.2 years ago by ▴ 20
1
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4
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2.3k
views
forging a BSgenome data package - Seed file issue
seedfiles BSgenome
5.2 years ago n.mary • 0
2
votes
2
replies
2.4k
views
How does one modify a single value of a field in a seqinfo object?
GenomicRanges GenomeInfoDb BSgenome isCircular
updated 5.2 years ago by 16k • written 5.4 years ago by ▴ 80
0
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3
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2.1k
views
Error in Forge the target package (BSgenome)
software error BSgenome
5.4 years ago • updated 5.3 years ago jiazhou0116 • 0
1
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1
reply
1.6k
views
About generating a seed file (DCF format) for forging a BSgenome
software error BSgenome
updated 5.4 years ago by 16k • written 5.4 years ago by • 0
0
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0
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943
views
Error in loading forged BSgenome
BSgenome msgbsR
5.4 years ago jiazhou0116 • 0
0
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1
reply
2.1k
views
How can i get repetitive elements genomic ranges in human genome?
repetitive elements IRanges GenomicRanges BSgenome
updated 5.4 years ago by 68k • written 5.4 years ago by ▴ 50
0
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1
reply
1.4k
views
error when forging a BSgenome
BSgenome
updated 5.7 years ago by 4.3k • written 5.7 years ago by ▴ 10
0
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4
replies
2.8k
views
Error in seqlevelsStyle after creating a BSgenome package
bsgenome MutationalPatterns
5.9 years ago • updated 5.8 years ago sibyl.bertrand • 0
0
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2
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1.5k
views
vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
5.8 years ago mb2subi • 0
2
votes
6
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1.9k
views
Can't find library BSgenome.Mmulatta.UCSC for latest genome (mmul10)
annotation mmul10 BSgenome
updated 6.2 years ago by 16k • written 6.2 years ago by ▴ 40
1
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0
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1.2k
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News: New BSgenome data packages for bosTau9, rheMac10, danRer11, and galGal6
BSgenome News
6.2 years ago Hervé Pagès 16k
2
votes
1
reply
926
views
Does "exclude" argument break BSgenome::vmatchPattern?
BSgenome
updated 6.2 years ago by 68k • written 6.2 years ago by ▴ 160
0
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6
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3.1k
views
Error while attempting to forge BSgenome data package
bsgenome ggbio
updated 6.3 years ago by • 0 • written 11.3 years ago by • 0
3
votes
16
replies
3.2k
views
Error in creating BSGenome package
BSGenome
updated 22 days ago by 68k • written 6.3 years ago by • 0
0
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3
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2.0k
views
Defining BSgenome -> GRanges S4 coercer without package attaching
BSgenome methods GenomicRanges
6.4 years ago Aditya ▴ 160
2
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3
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2.0k
views
What is the use of a masked BSgenome?
BSgenome BSgenome.Mmusculus.UCSC.mm10::Mmusculus Biostrings
updated 6.4 years ago by 4.3k • written 6.5 years ago by ▴ 160
1
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2
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1.5k
views
Is it useful to define and export a setAs('BSgenome', 'GRanges')
BSgenome GenomicRanges
updated 6.4 years ago by ★ 11k • written 6.4 years ago by ▴ 160
0
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2
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1.5k
views
getBSgenome{Bsgenome}: avoid attaching BiocGenerics (and others)
BSgenome Bsgenome.Mmusculus.UCSC.mm10
6.5 years ago • updated 6.4 years ago Aditya ▴ 160
1
vote
6
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3.7k
views
How to subset a BSgenome
BSgenome BSgenome.Mmusculus.UCSC.mm10
updated 6.5 years ago by 4.3k • written 6.5 years ago by ▴ 160
0
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6
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1.8k
views
error when using matchProbePair with BSgenome.Hsapiens.UCSC.hg19
matchProbePair BSgenome Biostrings BSgenome.Hsapiens.UCSC.hg19
updated 6.7 years ago by 68k • written 6.7 years ago by • 0
0
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1
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1.3k
views
getSeqSrcpaths (forgeBSgenome) error files not found, but they are right there....
bsgenome forgebsgenome getSeqSrcpaths
6.9 years ago tguerreroa90 • 0
2
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1
reply
1.4k
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 6.9 years ago by 68k • written 6.9 years ago by ▴ 40
349 results • Page 1 of 7
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Comment: using limma trend workflow in CAMERA by Gordon Smyth 53k
No, `trend.var=TRUE` and `trend=TRUE` are not needed in any voom pipeline, because the trend is already incorporated into the voom weights.
Comment: Questions about bacon QC and correction on EWAS results by Tikaaa2sahaaaq2c • 0
In the world of mobile games, the 88ef game download has gained traction for its performance driven design [free download][1], similar to …
Comment: using limma trend workflow in CAMERA by A.Barden ▴ 20
Do you need to set trend.var=TRUE when using camera in the limma-voom pipeline with RNA-Seq data (as apposed to limma-trend pipeline)?
Comment: Upcoming Ensembl API and data access changes - new blog post available by Tikaaa2sahaaaq2c • 0
Just as the Ensembl team transitions to a new platform for streamlined data access, diners can benefit from a digital newks menu prices con…
Comment: Error message that there is no package called Biobase by DamionLedner99 • 0
thanks for sharing!!! https://cran.r-project.org/
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Answer: What happens to genes with low dispersion during dispersion shrinkage in DESeq2
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
A: DESeq2 normalization vs VST vs rlog
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