Showing : BSGenome • reset
1
vote
6
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780
views
Help creating BSgenome object for new canine and feline genomes?
BSgenome
updated 3 months ago by 66k • written 3 months ago by • 0
2
votes
4
replies
575
views
Need help generating BSgenome and orgdb
OrgDb BSgenome
7 months ago • updated 3 months ago mat149 ▴ 70
1
vote
3
replies
625
views
Using injectSNPs with a custom set of SNPs
SNPlocs BSgenome
written 7 months ago by • 0
0
votes
3
replies
742
views
Get Intron Seq
intron BSgenome.Hsapiens.UCSC.hg38 BSgenome
updated 11 months ago by ★ 4.2k • written 11 months ago by • 0
0
votes
4
replies
1.1k
views
BSgenome for ensembl mm10
BSgenomeForge BSgenome
updated 11 months ago by 66k • written 11 months ago by • 0
1
vote
4
replies
787
views
Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 12 months ago by 16k • written 12 months ago by • 0
1
vote
1
reply
548
views
add genome to BSgenome
bsgenome
updated 18 months ago by 3.9k • written 18 months ago by ▴ 10
2
votes
2
replies
1.9k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
20 months ago Mog • 0
9
votes
5
replies
1.5k
views
karyoploteR genome coverage plotting using BSgenome.TAIR10
BSgenome.Athaliana.TAIR.TAIR10. karyoploteR BSgenome
updated 20 months ago by 66k • written 20 months ago by • 0
0
votes
2
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5.4k
views
Any tools to convert .gff to .gtf format
AnnotationData CrispRdesignR BSgenome
updated 21 months ago by ★ 1.6k • written 21 months ago by • 0
2
votes
3
replies
886
views
Request : Add Chinese Spring Wheat genome to BSgenome
BSgenome
updated 4 months ago by • 0 • written 2.1 years ago by ▴ 10
1
vote
1
reply
786
views
Request: Add Marmoset (calJac4) genome to BSgenome
BSgenome
updated 2.1 years ago by 16k • written 2.1 years ago by • 0
1
vote
0
replies
857
views
News: BSgenome package for T2T-CHM13v2.0 assembly and SNPlocs package for dbSNP155
BSgenome dbSNP T2T-CHM13v2.0 SNPlocs
2.1 years ago Hervé Pagès 16k
1
vote
1
reply
985
views
Fail to install BSgenome and library
BSgenome Celegans
updated 2.1 years ago by 16k • written 2.1 years ago by • 0
1
vote
0
replies
803
views
How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
2.1 years ago Charles Plessy ▴ 180
2
votes
4
replies
1.2k
views
Subset a BSgenome object (keep standard chomosomes) for applying vmatchPattern or vmatchPDict
BSgenome seqinfo
2.2 years ago alain.corvisier • 0
2
votes
1
reply
844
views
How to find the BSgenome object that provided the seqinfo of a GRanges object ?
BSgenome
updated 2.3 years ago by 16k • written 2.3 years ago by ▴ 180
1
vote
5
replies
1.3k
views
submitting a BSgenome package
BSgenome
3.6 years ago • updated 2.4 years ago deisianyufg • 0
1
vote
2
replies
1.0k
views
Building BSgenome package fails - .make_BSgenome_seqinfo error: sequence names found in .2bit file are not identical to 'seqnames'
BSGenome Forge
2.6 years ago geo.vogler ▴ 10
1
vote
2
replies
930
views
How to make OrgPackage (BSgenome data) package available for R Bioconductor users
BSGenome
updated 3.0 years ago by 16k • written 3.1 years ago by • 0
2
votes
7
replies
1.6k
views
Can I use BSgenome for in-house assemblies?
BSgenome
updated 3.1 years ago by 16k • written 3.1 years ago by • 0
3
votes
5
replies
1.2k
views
unable to forge custom BSgenome after update
BSgenome
updated 3.1 years ago by 16k • written 3.1 years ago by ▴ 80
0
votes
0
replies
676
views
how to construct a SNPlocs-class by myself
BSgenome SNPlocs
3.1 years ago Guandong Shang ▴ 40
2
votes
4
replies
1.7k
views
BSGenome Forge for non-model organism
BSGenomeForge BSGenome
updated 3.1 years ago by 16k • written 3.2 years ago by • 0
0
votes
3
replies
1.8k
views
Can BSGenome forge from non-UCSC/NCBI assemblies?
BSgenome
updated 3.4 years ago by ▴ 10 • written 3.5 years ago by • 0
3
votes
2
replies
2.2k
views
Forging a BSGenome
BSgenome microtus forging
updated 3.5 years ago by 16k • written 3.5 years ago by ▴ 20
1
vote
4
replies
1.5k
views
forging a BSgenome data package - Seed file issue
seedfiles BSgenome
3.6 years ago • updated 3.5 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 3.6 years ago by 16k • written 3.7 years ago by ▴ 80
0
votes
3
replies
1.5k
views
Error in Forge the target package (BSgenome)
software error BSgenome
3.7 years ago • updated 3.6 years ago jiazhou0116 • 0
1
vote
1
reply
998
views
About generating a seed file (DCF format) for forging a BSgenome
software error BSgenome
updated 3.7 years ago by 16k • written 3.7 years ago by • 0
0
votes
0
replies
647
views
Error in loading forged BSgenome
BSgenome msgbsR
3.7 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 3.8 years ago by 66k • written 3.8 years ago by ▴ 50
0
votes
1
reply
953
views
error when forging a BSgenome
BSgenome
updated 4.0 years ago by 3.9k • written 4.0 years ago by ▴ 10
0
votes
4
replies
1.9k
views
Error in seqlevelsStyle after creating a BSgenome package
bsgenome MutationalPatterns
4.2 years ago • updated 4.1 years ago sibyl.bertrand • 0
0
votes
2
replies
999
views
vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
4.2 years ago mb2subi • 0
2
votes
6
replies
1.2k
views
Can't find library BSgenome.Mmulatta.UCSC for latest genome (mmul10)
annotation mmul10 BSgenome
updated 4.5 years ago by 16k • written 4.5 years ago by ▴ 40
1
vote
0
replies
773
views
News: New BSgenome data packages for bosTau9, rheMac10, danRer11, and galGal6
BSgenome News
4.5 years ago Hervé Pagès 16k
2
votes
1
reply
611
views
Does "exclude" argument break BSgenome::vmatchPattern?
BSgenome
updated 4.5 years ago by 66k • written 4.5 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 4.6 years ago by • 0 • written 9.6 years ago by • 0
3
votes
15
replies
2.1k
views
Error in creating BSGenome package
BSGenome
updated 4.6 years ago by 66k • written 4.6 years ago by • 0
0
votes
3
replies
1.2k
views
Defining BSgenome -> GRanges S4 coercer without package attaching
BSgenome methods GenomicRanges
4.7 years ago Aditya ▴ 160
2
votes
3
replies
1.3k
views
What is the use of a masked BSgenome?
BSgenome BSgenome.Mmusculus.UCSC.mm10::Mmusculus Biostrings
updated 4.7 years ago by 3.9k • written 4.8 years ago by ▴ 160
1
vote
2
replies
969
views
Is it useful to define and export a setAs('BSgenome', 'GRanges')
BSgenome GenomicRanges
updated 4.7 years ago by ★ 11k • written 4.7 years ago by ▴ 160
0
votes
2
replies
1.0k
views
getBSgenome{Bsgenome}: avoid attaching BiocGenerics (and others)
BSgenome Bsgenome.Mmusculus.UCSC.mm10
4.8 years ago Aditya ▴ 160
1
vote
6
replies
2.5k
views
How to subset a BSgenome
BSgenome BSgenome.Mmusculus.UCSC.mm10
updated 4.8 years ago by 3.9k • written 4.8 years ago by ▴ 160
0
votes
6
replies
1.1k
views
error when using matchProbePair with BSgenome.Hsapiens.UCSC.hg19
matchProbePair BSgenome Biostrings BSgenome.Hsapiens.UCSC.hg19
updated 5.0 years ago by 66k • written 5.0 years ago by • 0
0
votes
1
reply
912
views
getSeqSrcpaths (forgeBSgenome) error files not found, but they are right there....
bsgenome forgebsgenome getSeqSrcpaths
5.2 years ago tguerreroa90 • 0
2
votes
1
reply
905
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 5.2 years ago by 66k • written 5.2 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 5.2 years ago by ★ 4.3k • written 5.2 years ago by • 0
2
votes
2
replies
1.3k
views
BSgenome package building
bsgenome
updated 5.6 years ago by 66k • written 5.6 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to compare subset of samples from VCF files by Gordon Smyth 50k
Welcome to Bioconductor support. Did you know that you can delete your old postings if they haven't received an answer yet? Instead of ap…
Comment: How to compare subset of samples from VCF files by Marco • 0
Here's the vcf file as code block ``` ##fileformat=VCFv4.2 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth"> ##FOR…
Comment: Gviz and custom database by James W. MacDonald 66k
The vignette for `Gviz` says you can use a `DNAStringSet`, generated using `Biostrings`. Have you tried that?
Comment: Gviz and custom database by luigi.faino • 0
Dear, this is not what I need. I need to transform a fasta sequence in a genome track usable in Gviz. L
Answer: Gviz and custom database by James W. MacDonald 66k
https://bioconductor.org/packages/release/bioc/vignettes/txdbmaker/inst/doc/txdbmaker.html
Votes
Answer: makeExampleDESeqDataSet using pilot data
Answer: Checking/updating package versions
Answer: Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)?
convert data frame of Entrez IDs to Gene Symbols
Answer: LRT, pairwise comparisons and p-value adjustment
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