Showing : BSgenome • reset
1
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6
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723
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Help creating BSgenome object for new canine and feline genomes?
BSgenome
updated 8 weeks ago by 65k • written 10 weeks ago by • 0
2
votes
4
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515
views
Need help generating BSgenome and orgdb
OrgDb BSgenome
6 months ago • updated 11 weeks ago mat149 ▴ 70
1
vote
3
replies
574
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Using injectSNPs with a custom set of SNPs
SNPlocs BSgenome
written 6 months ago by • 0
0
votes
3
replies
675
views
Get Intron Seq
intron BSgenome.Hsapiens.UCSC.hg38 BSgenome
updated 10 months ago by ★ 4.0k • written 10 months ago by • 0
0
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4
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917
views
BSgenome for ensembl mm10
BSgenomeForge BSgenome
updated 10 months ago by 65k • written 10 months ago by • 0
1
vote
4
replies
727
views
Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 10 months ago by 16k • written 11 months ago by • 0
1
vote
1
reply
520
views
add genome to BSgenome
bsgenome
updated 17 months ago by 3.8k • written 17 months ago by ▴ 10
2
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2
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1.8k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
19 months ago • updated 18 months ago Mog • 0
9
votes
5
replies
1.4k
views
karyoploteR genome coverage plotting using BSgenome.TAIR10
BSgenome.Athaliana.TAIR.TAIR10. karyoploteR BSgenome
updated 19 months ago by 65k • written 19 months ago by • 0
0
votes
2
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5.1k
views
Any tools to convert .gff to .gtf format
AnnotationData CrispRdesignR BSgenome
updated 20 months ago by ★ 1.6k • written 20 months ago by • 0
2
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3
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850
views
Request : Add Chinese Spring Wheat genome to BSgenome
BSgenome
updated 3 months ago by • 0 • written 24 months ago by ▴ 10
1
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1
reply
745
views
Request: Add Marmoset (calJac4) genome to BSgenome
BSgenome
updated 2.0 years ago by 16k • written 2.0 years ago by • 0
1
vote
0
replies
792
views
News: BSgenome package for T2T-CHM13v2.0 assembly and SNPlocs package for dbSNP155
BSgenome dbSNP T2T-CHM13v2.0 SNPlocs
2.0 years ago Hervé Pagès 16k
1
vote
1
reply
946
views
Fail to install BSgenome and library
BSgenome Celegans
updated 2.0 years ago by 16k • written 2.0 years ago by • 0
1
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0
replies
773
views
How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
2.0 years ago Charles Plessy ▴ 180
2
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4
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1.1k
views
Subset a BSgenome object (keep standard chomosomes) for applying vmatchPattern or vmatchPDict
BSgenome seqinfo
2.1 years ago alain.corvisier • 0
2
votes
1
reply
816
views
How to find the BSgenome object that provided the seqinfo of a GRanges object ?
BSgenome
updated 2.2 years ago by 16k • written 2.2 years ago by ▴ 180
1
vote
5
replies
1.3k
views
submitting a BSgenome package
BSgenome
3.5 years ago • updated 2.3 years ago deisianyufg • 0
1
vote
2
replies
970
views
Building BSgenome package fails - .make_BSgenome_seqinfo error: sequence names found in .2bit file are not identical to 'seqnames'
BSGenome Forge
2.5 years ago geo.vogler ▴ 10
1
vote
2
replies
904
views
How to make OrgPackage (BSgenome data) package available for R Bioconductor users
BSGenome
updated 2.9 years ago by 16k • written 3.0 years ago by • 0
2
votes
7
replies
1.5k
views
Can I use BSgenome for in-house assemblies?
BSgenome
updated 3.0 years ago by 16k • written 3.0 years ago by • 0
3
votes
5
replies
1.2k
views
unable to forge custom BSgenome after update
BSgenome
updated 3.0 years ago by 16k • written 3.0 years ago by ▴ 80
0
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0
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647
views
how to construct a SNPlocs-class by myself
BSgenome SNPlocs
3.0 years ago Guandong Shang ▴ 40
2
votes
4
replies
1.7k
views
BSGenome Forge for non-model organism
BSGenomeForge BSGenome
updated 3.0 years ago by 16k • written 3.0 years ago by • 0
0
votes
3
replies
1.7k
views
Can BSGenome forge from non-UCSC/NCBI assemblies?
BSgenome
updated 3.3 years ago by ▴ 10 • written 3.4 years ago by • 0
3
votes
2
replies
2.1k
views
Forging a BSGenome
BSgenome microtus forging
updated 3.4 years ago by 16k • written 3.4 years ago by ▴ 20
1
vote
4
replies
1.5k
views
forging a BSgenome data package - Seed file issue
seedfiles BSgenome
3.4 years ago n.mary • 0
2
votes
2
replies
1.5k
views
How does one modify a single value of a field in a seqinfo object?
GenomicRanges GenomeInfoDb BSgenome isCircular
updated 3.5 years ago by 16k • written 3.6 years ago by ▴ 80
0
votes
3
replies
1.4k
views
Error in Forge the target package (BSgenome)
software error BSgenome
3.6 years ago • updated 3.5 years ago jiazhou0116 • 0
1
vote
1
reply
961
views
About generating a seed file (DCF format) for forging a BSgenome
software error BSgenome
updated 3.6 years ago by 16k • written 3.6 years ago by • 0
0
votes
0
replies
603
views
Error in loading forged BSgenome
BSgenome msgbsR
3.6 years ago jiazhou0116 • 0
0
votes
1
reply
1.1k
views
How can i get repetitive elements genomic ranges in human genome?
repetitive elements IRanges GenomicRanges BSgenome
updated 3.7 years ago by 65k • written 3.7 years ago by ▴ 50
0
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1
reply
916
views
error when forging a BSgenome
BSgenome
updated 3.9 years ago by 3.8k • written 3.9 years ago by ▴ 10
0
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4
replies
1.8k
views
Error in seqlevelsStyle after creating a BSgenome package
bsgenome MutationalPatterns
4.1 years ago • updated 4.0 years ago sibyl.bertrand • 0
0
votes
2
replies
969
views
vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
4.1 years ago mb2subi • 0
2
votes
6
replies
1.1k
views
Can't find library BSgenome.Mmulatta.UCSC for latest genome (mmul10)
annotation mmul10 BSgenome
updated 4.4 years ago by 16k • written 4.4 years ago by ▴ 40
1
vote
0
replies
745
views
News: New BSgenome data packages for bosTau9, rheMac10, danRer11, and galGal6
BSgenome News
4.4 years ago Hervé Pagès 16k
2
votes
1
reply
590
views
Does "exclude" argument break BSgenome::vmatchPattern?
BSgenome
updated 4.4 years ago by 65k • written 4.4 years ago by ▴ 160
0
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6
replies
2.4k
views
Error while attempting to forge BSgenome data package
bsgenome ggbio
updated 4.5 years ago by • 0 • written 9.5 years ago by • 0
3
votes
15
replies
2.1k
views
Error in creating BSGenome package
BSGenome
updated 4.5 years ago by 65k • written 4.5 years ago by • 0
0
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3
replies
1.2k
views
Defining BSgenome -> GRanges S4 coercer without package attaching
BSgenome methods GenomicRanges
4.6 years ago Aditya ▴ 160
2
votes
3
replies
1.2k
views
What is the use of a masked BSgenome?
BSgenome BSgenome.Mmusculus.UCSC.mm10::Mmusculus Biostrings
updated 4.6 years ago by 3.8k • written 4.7 years ago by ▴ 160
1
vote
2
replies
940
views
Is it useful to define and export a setAs('BSgenome', 'GRanges')
BSgenome GenomicRanges
updated 4.6 years ago by ★ 11k • written 4.6 years ago by ▴ 160
0
votes
2
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999
views
getBSgenome{Bsgenome}: avoid attaching BiocGenerics (and others)
BSgenome Bsgenome.Mmusculus.UCSC.mm10
4.7 years ago Aditya ▴ 160
1
vote
6
replies
2.4k
views
How to subset a BSgenome
BSgenome BSgenome.Mmusculus.UCSC.mm10
updated 4.7 years ago by 3.8k • written 4.7 years ago by ▴ 160
0
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6
replies
1.1k
views
error when using matchProbePair with BSgenome.Hsapiens.UCSC.hg19
matchProbePair BSgenome Biostrings BSgenome.Hsapiens.UCSC.hg19
updated 4.9 years ago by 65k • written 4.9 years ago by • 0
0
votes
1
reply
881
views
getSeqSrcpaths (forgeBSgenome) error files not found, but they are right there....
bsgenome forgebsgenome getSeqSrcpaths
5.1 years ago tguerreroa90 • 0
2
votes
1
reply
879
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 5.1 years ago by 65k • written 5.1 years ago by ▴ 40
0
votes
9
replies
1.5k
views
Unable to generate feature vector with custom genome in cleanUpdTSeq
cleanUpdTSeq BSgenome BSgenomeForge
updated 5.1 years ago by ★ 4.3k • written 5.1 years ago by • 0
2
votes
2
replies
1.3k
views
BSgenome package building
bsgenome
updated 5.5 years ago by 65k • written 5.5 years ago by • 0
50 results • Page 1 of 1
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Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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