Showing : bsgenome • reset
1
vote
6
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780
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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
623
views
Using injectSNPs with a custom set of SNPs
SNPlocs BSgenome
written 7 months ago by • 0
0
votes
3
replies
739
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
786
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
547
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
881
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
785
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
853
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
0
replies
802
views
How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
2.1 years ago Charles Plessy ▴ 180
1
vote
1
reply
983
views
Fail to install BSgenome and library
BSgenome Celegans
updated 2.1 years ago by 16k • written 2.1 years ago by • 0
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
843
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
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 • updated 2.5 years ago geo.vogler ▴ 10
1
vote
2
replies
929
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
675
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 3.1 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
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
1
vote
4
replies
1.5k
views
forging a BSgenome data package - Seed file issue
seedfiles BSgenome
3.5 years ago n.mary • 0
1
vote
5
replies
1.3k
views
submitting a BSgenome package
BSgenome
3.6 years ago • updated 2.4 years ago deisianyufg • 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 3.7 years ago by ▴ 80
0
votes
0
replies
646
views
Error in loading forged BSgenome
BSgenome msgbsR
3.7 years ago jiazhou0116 • 0
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
995
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
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
951
views
error when forging a BSgenome
BSgenome
updated 4.0 years ago by 3.9k • written 4.0 years ago by ▴ 10
0
votes
2
replies
997
views
vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
4.2 years ago mb2subi • 0
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
1
vote
0
replies
770
views
News: New BSgenome data packages for bosTau9, rheMac10, danRer11, and galGal6
BSgenome News
4.5 years ago Hervé Pagès 16k
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
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
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
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
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
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
910
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
904
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
3
votes
5
replies
1.9k
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 5.8 years ago by 16k • written 5.8 years ago by ▴ 830
50 results • Page 1 of 1
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Comment: Deseq2 by Ram ▴ 210
Cross-posted on biostars: https://www.biostars.org/p/9596031/
Comment: SpliceWiz collateData error by giulia.nicoletto.1 • 0
Hi there, I am facing a similar error. When I try the collateData command collateData( Experiment = expr, reference_path = "./Referen…
Answer: Best way to describe DEseq2 design by SamGG ▴ 350
Hi, My own opinion. In the design `~ Batch`, ChemicalA_t1 is the intercept. So, all coefficients refer to this level as a reference. …
Answer: Deseq2 by ATpoint ★ 4.2k
Ser the vignette https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html It covers prefiltering (and everyt…
Comment: Counter-directional LFC shrinkage by Michael Love 42k
Gene 1 is hard to predict given the paucity of data for the comparison of interest. What is happening is that the relatively low dispersion…
Votes
Answer: Deseq2
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: When should I correct for batch effects
Answer: When should I correct for batch effects
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