Showing : BSGenome • reset
3
votes
2
replies
220
views
Need help generating BSgenome and orgdb
OrgDb BSgenome
updated 5 weeks ago by 16k • written 5 weeks ago by ▴ 70
1
vote
3
replies
321
views
Using injectSNPs with a custom set of SNPs
SNPlocs BSgenome
written 6 weeks ago by • 0
0
votes
3
replies
414
views
Get Intron Seq
intron BSgenome.Hsapiens.UCSC.hg38 BSgenome
updated 5 months ago by ★ 3.6k • written 5 months ago by • 0
0
votes
4
replies
525
views
BSgenome for ensembl mm10
BSgenomeForge BSgenome
updated 5 months ago by 64k • written 5 months ago by • 0
1
vote
4
replies
526
views
Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 6 months ago by 16k • written 6 months ago by • 0
1
vote
1
reply
392
views
add genome to BSgenome
bsgenome
updated 12 months ago by 3.6k • written 12 months ago by ▴ 10
2
votes
2
replies
1.2k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
14 months ago Mog • 0
9
votes
5
replies
1.1k
views
karyoploteR genome coverage plotting using BSgenome.TAIR10
BSgenome.Athaliana.TAIR.TAIR10. karyoploteR BSgenome
updated 14 months ago by 64k • written 14 months ago by • 0
0
votes
2
replies
3.8k
views
Any tools to convert .gff to .gtf format
AnnotationData CrispRdesignR BSgenome
updated 15 months ago by ★ 1.6k • written 15 months ago by • 0
2
votes
2
replies
666
views
Request : Add Chinese Spring Wheat genome to BSgenome
BSgenome
updated 10 months ago by • 0 • written 19 months ago by ▴ 10
1
vote
1
reply
622
views
Request: Add Marmoset (calJac4) genome to BSgenome
BSgenome
updated 19 months ago by 16k • written 19 months ago by • 0
1
vote
0
replies
617
views
News: BSgenome package for T2T-CHM13v2.0 assembly and SNPlocs package for dbSNP155
BSgenome dbSNP T2T-CHM13v2.0 SNPlocs
19 months ago Hervé Pagès 16k
1
vote
1
reply
780
views
Fail to install BSgenome and library
BSgenome Celegans
updated 19 months ago by 16k • written 19 months ago by • 0
1
vote
0
replies
617
views
How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
19 months ago Charles Plessy ▴ 180
2
votes
4
replies
882
views
Subset a BSgenome object (keep standard chomosomes) for applying vmatchPattern or vmatchPDict
BSgenome seqinfo
20 months ago alain.corvisier • 0
2
votes
1
reply
674
views
How to find the BSgenome object that provided the seqinfo of a GRanges object ?
BSgenome
updated 22 months ago by 16k • written 22 months ago by ▴ 180
1
vote
5
replies
1.1k
views
submitting a BSgenome package
BSgenome
3.1 years ago • updated 22 months ago deisianyufg • 0
1
vote
2
replies
798
views
Building BSgenome package fails - .make_BSgenome_seqinfo error: sequence names found in .2bit file are not identical to 'seqnames'
BSGenome Forge
2.1 years ago geo.vogler ▴ 10
1
vote
2
replies
767
views
How to make OrgPackage (BSgenome data) package available for R Bioconductor users
BSGenome
updated 2.6 years ago by 16k • written 2.6 years ago by • 0
2
votes
7
replies
1.3k
views
Can I use BSgenome for in-house assemblies?
BSgenome
updated 2.6 years ago by 16k • written 2.6 years ago by • 0
3
votes
5
replies
1.0k
views
unable to forge custom BSgenome after update
BSgenome
updated 2.6 years ago by 16k • written 2.6 years ago by ▴ 80
0
votes
0
replies
540
views
how to construct a SNPlocs-class by myself
BSgenome SNPlocs
2.6 years ago Guandong Shang ▴ 40
2
votes
4
replies
1.5k
views
BSGenome Forge for non-model organism
BSGenomeForge BSGenome
updated 2.6 years ago by 16k • written 2.7 years ago by • 0
0
votes
3
replies
1.5k
views
Can BSGenome forge from non-UCSC/NCBI assemblies?
BSgenome
updated 2.9 years ago by ▴ 10 • written 3.0 years ago by • 0
3
votes
2
replies
1.8k
views
Forging a BSGenome
BSgenome microtus forging
updated 3.0 years ago by 16k • written 3.0 years ago by ▴ 20
1
vote
4
replies
1.3k
views
forging a BSgenome data package - Seed file issue
seedfiles BSgenome
3.0 years ago n.mary • 0
2
votes
2
replies
1.2k
views
How does one modify a single value of a field in a seqinfo object?
GenomicRanges GenomeInfoDb BSgenome isCircular
updated 3.1 years ago by 16k • written 3.2 years ago by ▴ 80
0
votes
3
replies
1.3k
views
Error in Forge the target package (BSgenome)
software error BSgenome
3.2 years ago • updated 3.1 years ago jiazhou0116 • 0
1
vote
1
reply
788
views
About generating a seed file (DCF format) for forging a BSgenome
software error BSgenome
updated 3.2 years ago by 16k • written 3.2 years ago by • 0
0
votes
0
replies
509
views
Error in loading forged BSgenome
BSgenome msgbsR
3.2 years ago jiazhou0116 • 0
0
votes
1
reply
846
views
How can i get repetitive elements genomic ranges in human genome?
repetitive elements IRanges GenomicRanges BSgenome
updated 3.3 years ago by 64k • written 3.3 years ago by ▴ 50
0
votes
1
reply
730
views
error when forging a BSgenome
BSgenome
updated 3.5 years ago by 3.6k • written 3.5 years ago by ▴ 10
0
votes
4
replies
1.5k
views
Error in seqlevelsStyle after creating a BSgenome package
bsgenome MutationalPatterns
3.7 years ago • updated 3.6 years ago sibyl.bertrand • 0
0
votes
2
replies
802
views
vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
3.7 years ago mb2subi • 0
2
votes
6
replies
970
views
Can't find library BSgenome.Mmulatta.UCSC for latest genome (mmul10)
annotation mmul10 BSgenome
updated 4.0 years ago by 16k • written 4.0 years ago by ▴ 40
1
vote
0
replies
622
views
News: New BSgenome data packages for bosTau9, rheMac10, danRer11, and galGal6
BSgenome News
4.0 years ago Hervé Pagès 16k
2
votes
1
reply
491
views
Does "exclude" argument break BSgenome::vmatchPattern?
BSgenome
updated 4.0 years ago by 64k • written 4.0 years ago by ▴ 160
0
votes
6
replies
2.2k
views
Error while attempting to forge BSgenome data package
bsgenome ggbio
updated 4.1 years ago by • 0 • written 9.1 years ago by • 0
3
votes
15
replies
1.7k
views
Error in creating BSGenome package
BSGenome
updated 4.1 years ago by 64k • written 4.1 years ago by • 0
0
votes
3
replies
1.0k
views
Defining BSgenome -> GRanges S4 coercer without package attaching
BSgenome methods GenomicRanges
4.2 years ago Aditya ▴ 160
2
votes
3
replies
940
views
What is the use of a masked BSgenome?
BSgenome BSgenome.Mmusculus.UCSC.mm10::Mmusculus Biostrings
updated 4.2 years ago by 3.6k • written 4.3 years ago by ▴ 160
1
vote
2
replies
820
views
Is it useful to define and export a setAs('BSgenome', 'GRanges')
BSgenome GenomicRanges
updated 4.2 years ago by 11k • written 4.2 years ago by ▴ 160
0
votes
2
replies
859
views
getBSgenome{Bsgenome}: avoid attaching BiocGenerics (and others)
BSgenome Bsgenome.Mmusculus.UCSC.mm10
4.3 years ago Aditya ▴ 160
1
vote
6
replies
2.1k
views
How to subset a BSgenome
BSgenome BSgenome.Mmusculus.UCSC.mm10
updated 4.3 years ago by 3.6k • written 4.3 years ago by ▴ 160
0
votes
6
replies
955
views
error when using matchProbePair with BSgenome.Hsapiens.UCSC.hg19
matchProbePair BSgenome Biostrings BSgenome.Hsapiens.UCSC.hg19
updated 4.5 years ago by 64k • written 4.5 years ago by • 0
0
votes
1
reply
733
views
getSeqSrcpaths (forgeBSgenome) error files not found, but they are right there....
bsgenome forgebsgenome getSeqSrcpaths
4.7 years ago tguerreroa90 • 0
2
votes
1
reply
768
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 4.7 years ago by 64k • written 4.7 years ago by ▴ 40
0
votes
9
replies
1.3k
views
Unable to generate feature vector with custom genome in cleanUpdTSeq
cleanUpdTSeq BSgenome BSgenomeForge
updated 4.7 years ago by ★ 4.3k • written 4.7 years ago by • 0
2
votes
2
replies
1.2k
views
BSgenome package building
bsgenome
updated 5.1 years ago by 64k • written 5.1 years ago by • 0
3
votes
5
replies
1.6k
views
Include and implement a new reference genome option in the R package BSgenome for downstream variant calling analysis
bsgenome variant calling whole exome sequence gencode reference genome
updated 5.3 years ago by 16k • written 5.3 years ago by ▴ 820
50 results • Page 1 of 1
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Comment: GOslim missing GO term by amanda • 0
Thank you for the advice and many thanks! It is WGCNA analysis. I will try your method today and see if there are some consistencies.
Comment: GOslim missing GO term by James W. MacDonald 64k
Is this a WGCNA analysis (multiple co-expression clusters sounds like WGCNA)? If so, none of that is inferential or easily interpreted. It …
Comment: GOslim missing GO term by amanda • 0
For each group, I generated multiple co-expression clusters, and within each cluster, cluster PC1 was correlated with PC1 of multiple clini…
Comment: GOslim missing GO term by James W. MacDonald 64k
What do you mean by 'enriched with ... GO terms from their correlations with clinical traits'? Are you doing a GO hypergeometric or somethi…
Comment: GOslim missing GO term by amanda • 0
I have multiple groups to compare with, and each enriched with hundreds of GO terms from their correlations with clinical traits (top1 pval…
Votes
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: limma::voom vs edgeR::voomLmFit - when to use?
Answer: limma::voom vs edgeR::voomLmFit - when to use?
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