Showing : bsgenome • reset
1
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6
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724
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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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517
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Need help generating BSgenome and orgdb
OrgDb BSgenome
6 months ago • updated 11 weeks ago mat149 ▴ 70
1
vote
3
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575
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Using injectSNPs with a custom set of SNPs
SNPlocs BSgenome
written 6 months ago by • 0
0
votes
3
replies
677
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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918
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BSgenome for ensembl mm10
BSgenomeForge BSgenome
updated 10 months ago by 65k • written 10 months ago by • 0
1
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4
replies
728
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
521
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 Mog • 0
9
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5
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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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851
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
746
views
Request: Add Marmoset (calJac4) genome to BSgenome
BSgenome
updated 2.0 years ago by 16k • written 2.0 years ago by • 0
1
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0
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793
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
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1
reply
947
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
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774
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
817
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
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974
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
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905
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
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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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648
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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
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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
962
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
604
views
Error in loading forged BSgenome
BSgenome msgbsR
3.6 years ago jiazhou0116 • 0
0
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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
918
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
970
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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
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0
replies
746
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News: New BSgenome data packages for bosTau9, rheMac10, danRer11, and galGal6
BSgenome News
4.4 years ago Hervé Pagès 16k
2
votes
1
reply
591
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
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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
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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
943
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
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2
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1000
views
getBSgenome{Bsgenome}: avoid attaching BiocGenerics (and others)
BSgenome Bsgenome.Mmusculus.UCSC.mm10
4.7 years ago Aditya ▴ 160
1
vote
6
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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
votes
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
882
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
880
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
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
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?
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