Showing : BSgenome • reset
0
votes
3
replies
6.6k
views
Any tools to convert .gff to .gtf format
AnnotationData CrispRdesignR BSgenome
updated 4 months ago by • 0 • written 2.2 years ago by • 0
1
vote
6
replies
1.1k
views
Help creating BSgenome object for new canine and feline genomes?
BSgenome
updated 8 months ago by 67k • written 9 months ago by • 0
2
votes
4
replies
826
views
Need help generating BSgenome and orgdb
OrgDb BSgenome
12 months ago • updated 9 months ago mat149 ▴ 80
1
vote
3
replies
908
views
Using injectSNPs with a custom set of SNPs
SNPlocs BSgenome
written 12 months ago by • 0
0
votes
3
replies
985
views
Get Intron Seq
intron BSgenome.Hsapiens.UCSC.hg38 BSgenome
updated 16 months ago by ★ 4.5k • written 16 months ago by • 0
0
votes
4
replies
1.8k
views
BSgenome for ensembl mm10
BSgenomeForge BSgenome
updated 17 months ago by 67k • written 17 months ago by • 0
1
vote
4
replies
974
views
Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 17 months ago by 16k • written 17 months ago by • 0
1
vote
1
reply
685
views
add genome to BSgenome
bsgenome
updated 23 months ago by 4.1k • written 23 months ago by ▴ 10
2
votes
2
replies
2.4k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
2.1 years ago Mog • 0
9
votes
5
replies
1.8k
views
karyoploteR genome coverage plotting using BSgenome.TAIR10
BSgenome.Athaliana.TAIR.TAIR10. karyoploteR BSgenome
updated 2.1 years ago by 67k • written 2.1 years ago by • 0
2
votes
3
replies
1.1k
views
Request : Add Chinese Spring Wheat genome to BSgenome
BSgenome
updated 10 months ago by • 0 • written 2.5 years ago by ▴ 10
1
vote
1
reply
911
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
1.2k
views
Fail to install BSgenome and library
BSgenome Celegans
updated 2.6 years ago by 16k • written 2.6 years ago by • 0
1
vote
0
replies
946
views
How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
2.6 years ago Charles Plessy ▴ 180
2
votes
4
replies
1.5k
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
1.0k
views
How to find the BSgenome object that provided the seqinfo of a GRanges object ?
BSgenome
updated 2.8 years ago by 16k • written 2.8 years ago by ▴ 180
1
vote
5
replies
1.5k
views
submitting a BSgenome package
BSgenome
4.0 years ago • updated 2.8 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
3.0 years ago geo.vogler ▴ 10
1
vote
2
replies
1.1k
views
How to make OrgPackage (BSgenome data) package available for R Bioconductor users
BSGenome
updated 3.5 years ago by 16k • written 3.5 years ago by • 0
2
votes
7
replies
1.8k
views
Can I use BSgenome for in-house assemblies?
BSgenome
updated 3.5 years ago by 16k • written 3.5 years ago by • 0
3
votes
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
votes
0
replies
793
views
how to construct a SNPlocs-class by myself
BSgenome SNPlocs
3.6 years ago Guandong Shang ▴ 40
2
votes
4
replies
2.0k
views
BSGenome Forge for non-model organism
BSGenomeForge BSGenome
updated 3.6 years ago by 16k • written 3.6 years ago by • 0
0
votes
3
replies
2.1k
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 3.9 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
4.0 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 4.0 years ago by 16k • written 4.1 years ago by ▴ 80
0
votes
3
replies
1.7k
views
Error in Forge the target package (BSgenome)
software error BSgenome
4.2 years ago • updated 4.0 years ago jiazhou0116 • 0
1
vote
1
reply
1.2k
views
About generating a seed file (DCF format) for forging a BSgenome
software error BSgenome
updated 4.1 years ago by 16k • written 4.2 years ago by • 0
0
votes
0
replies
738
views
Error in loading forged BSgenome
BSgenome msgbsR
4.1 years ago jiazhou0116 • 0
0
votes
1
reply
1.3k
views
How can i get repetitive elements genomic ranges in human genome?
repetitive elements IRanges GenomicRanges BSgenome
updated 4.2 years ago by 67k • written 4.2 years ago by ▴ 50
0
votes
1
reply
1.1k
views
error when forging a BSgenome
BSgenome
updated 4.5 years ago by 4.1k • written 4.5 years ago by ▴ 10
0
votes
4
replies
2.2k
views
Error in seqlevelsStyle after creating a BSgenome package
bsgenome MutationalPatterns
4.6 years ago • updated 4.5 years ago sibyl.bertrand • 0
0
votes
2
replies
1.2k
views
vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
4.6 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
vote
0
replies
878
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
708
views
Does "exclude" argument break BSgenome::vmatchPattern?
BSgenome
updated 5.0 years ago by 67k • written 5.0 years ago by ▴ 160
0
votes
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
votes
15
replies
2.4k
views
Error in creating BSGenome package
BSGenome
updated 5.1 years ago by 67k • written 5.1 years ago by • 0
0
votes
3
replies
1.5k
views
Defining BSgenome -> GRanges S4 coercer without package attaching
BSgenome methods GenomicRanges
5.2 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 5.2 years ago by 4.1k • written 5.2 years ago by ▴ 160
1
vote
2
replies
1.2k
views
Is it useful to define and export a setAs('BSgenome', 'GRanges')
BSgenome GenomicRanges
updated 5.2 years ago by ★ 11k • written 5.2 years ago by ▴ 160
0
votes
2
replies
1.2k
views
getBSgenome{Bsgenome}: avoid attaching BiocGenerics (and others)
BSgenome Bsgenome.Mmusculus.UCSC.mm10
5.2 years ago Aditya ▴ 160
1
vote
6
replies
2.8k
views
How to subset a BSgenome
BSgenome BSgenome.Mmusculus.UCSC.mm10
updated 5.3 years ago by 4.1k • written 5.3 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 5.5 years ago by 67k • written 5.5 years ago by • 0
0
votes
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 5.7 years ago by ★ 4.3k • written 5.7 years ago by • 0
2
votes
2
replies
1.5k
views
BSgenome package building
bsgenome
updated 6.1 years ago by 67k • written 6.1 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Consistent Decimals In Data After Antibody Array Background Correction Using Lim by Gordon Smyth 51k
`nec` computes one set of negative control parameters (mu, sigma, alpha) for each sample.
Comment: DESeq Input from Salmon + tximport/tximeta by LuciaNhu • 0
Thank you to the author for the quick reply. If I use `gene_counts_length_scaled.tsv` as a metric that has already normalized for library s…
Answer: DESeq Input from Salmon + tximport/tximeta by Michael Love 42k
Given nf-core's pipeline here, you can use rounded counts from `gene_counts_length_scaled.tsv`.
Comment: Question about using LRT test for time course experiments with DESeq2 by James W. MacDonald 67k
You don't want to add a logFC on top like that, as it invalidates the p-value. Maybe I wasn't clear before. The LRT gives you all the gene…
Comment: Question about using LRT test for time course experiments with DESeq2 by Denise • 0
Hi James, Thank you very much for your very detailed explanation! I guess my question is simpler than that, I just want to union, across…
Votes
Answer: DESeq Input from Salmon + tximport/tximeta
Answer: featureCounts segmentation fault with large chromosomes
Answer: Supercells with Basilisk fails for dtype('float64') to dtype('int64') conversion
Comment: Extension to knitr/Rmarkdown to ignore only specific warnings (not all) in a chu
Comment: Extension to knitr/Rmarkdown to ignore only specific warnings (not all) in a chu
Awards • All
Popular Question to john • 0
Popular Question to Gordon Smyth 51k
Popular Question to James W. MacDonald 67k
Popular Question to abadgerw • 0
Commentator to Mike Smith ★ 6.6k
Locations • All
Denmark, 1 minute ago
Germany, 2 minutes ago
Austria, 15 minutes ago
Germany, 27 minutes ago
WEHI, Melbourne, Australia, 28 minutes ago
Traffic: 827 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6