Showing : BSgenome • reset
0
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3
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315
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Get Intron Seq
intron BSgenome.Hsapiens.UCSC.hg38 BSgenome
updated 3 months ago by ★ 3.4k • written 3 months ago by • 0
0
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4
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379
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BSgenome for ensembl mm10
BSgenomeForge BSgenome
updated 3 months ago by 63k • written 3 months ago by • 0
1
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4
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398
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Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 3 months ago by 16k • written 4 months ago by • 0
1
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1
reply
325
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add genome to BSgenome
bsgenome
updated 10 months ago by 3.5k • written 10 months ago by ▴ 10
2
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2
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939
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getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
12 months ago • updated 11 months ago Mog • 0
9
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5
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908
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karyoploteR genome coverage plotting using BSgenome.TAIR10
BSgenome.Athaliana.TAIR.TAIR10. karyoploteR BSgenome
updated 12 months ago by 63k • written 12 months ago by • 0
0
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2
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3.2k
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Any tools to convert .gff to .gtf format
AnnotationData CrispRdesignR BSgenome
updated 12 months ago by ★ 1.6k • written 13 months ago by • 0
2
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2
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567
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Request : Add Chinese Spring Wheat genome to BSgenome
BSgenome
updated 8 months ago by • 0 • written 16 months ago by ▴ 10
1
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1
reply
545
views
Request: Add Marmoset (calJac4) genome to BSgenome
BSgenome
updated 17 months ago by 16k • written 17 months ago by • 0
1
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0
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532
views
News: BSgenome package for T2T-CHM13v2.0 assembly and SNPlocs package for dbSNP155
BSgenome dbSNP T2T-CHM13v2.0 SNPlocs
17 months ago Hervé Pagès 16k
1
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1
reply
695
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Fail to install BSgenome and library
BSgenome Celegans
updated 17 months ago by 16k • written 17 months ago by • 0
1
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0
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534
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How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
17 months ago Charles Plessy ▴ 180
2
votes
4
replies
757
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Subset a BSgenome object (keep standard chomosomes) for applying vmatchPattern or vmatchPDict
BSgenome seqinfo
18 months ago alain.corvisier • 0
2
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1
reply
599
views
How to find the BSgenome object that provided the seqinfo of a GRanges object ?
BSgenome
updated 20 months ago by 16k • written 20 months ago by ▴ 180
1
vote
5
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1.0k
views
submitting a BSgenome package
BSgenome
2.9 years ago • updated 20 months ago deisianyufg • 0
1
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2
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715
views
Building BSgenome package fails - .make_BSgenome_seqinfo error: sequence names found in .2bit file are not identical to 'seqnames'
BSGenome Forge
22 months ago geo.vogler ▴ 10
1
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2
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703
views
How to make OrgPackage (BSgenome data) package available for R Bioconductor users
BSGenome
updated 2.4 years ago by 16k • written 2.4 years ago by • 0
2
votes
7
replies
1.2k
views
Can I use BSgenome for in-house assemblies?
BSgenome
updated 2.4 years ago by 16k • written 2.4 years ago by • 0
3
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5
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950
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unable to forge custom BSgenome after update
BSgenome
updated 2.4 years ago by 16k • written 2.4 years ago by ▴ 80
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0
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484
views
how to construct a SNPlocs-class by myself
BSgenome SNPlocs
2.5 years ago Guandong Shang ▴ 40
2
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4
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1.4k
views
BSGenome Forge for non-model organism
BSGenomeForge BSGenome
updated 2.5 years ago by 16k • written 2.5 years ago by • 0
0
votes
3
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1.4k
views
Can BSGenome forge from non-UCSC/NCBI assemblies?
BSgenome
updated 2.7 years ago by ▴ 10 • written 2.8 years ago by • 0
2
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2
replies
1.5k
views
Forging a BSGenome
BSgenome microtus forging
updated 2.8 years ago by 16k • written 2.8 years ago by ▴ 20
1
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4
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1.2k
views
forging a BSgenome data package - Seed file issue
seedfiles BSgenome
2.9 years ago n.mary • 0
2
votes
2
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1.1k
views
How does one modify a single value of a field in a seqinfo object?
GenomicRanges GenomeInfoDb BSgenome isCircular
updated 2.9 years ago by 16k • written 3.0 years ago by ▴ 80
0
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3
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1.2k
views
Error in Forge the target package (BSgenome)
software error BSgenome
3.1 years ago • updated 2.9 years ago jiazhou0116 • 0
1
vote
1
reply
718
views
About generating a seed file (DCF format) for forging a BSgenome
software error BSgenome
updated 3.0 years ago by 16k • written 3.1 years ago by • 0
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0
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462
views
Error in loading forged BSgenome
BSgenome msgbsR
3.0 years ago jiazhou0116 • 0
0
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1
reply
744
views
How can i get repetitive elements genomic ranges in human genome?
repetitive elements IRanges GenomicRanges BSgenome
updated 3.1 years ago by 63k • written 3.1 years ago by ▴ 50
0
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1
reply
652
views
error when forging a BSgenome
BSgenome
updated 3.4 years ago by 3.5k • written 3.4 years ago by ▴ 10
0
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4
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1.4k
views
Error in seqlevelsStyle after creating a BSgenome package
bsgenome MutationalPatterns
3.5 years ago • updated 3.4 years ago sibyl.bertrand • 0
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2
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719
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vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
3.5 years ago mb2subi • 0
2
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6
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888
views
Can't find library BSgenome.Mmulatta.UCSC for latest genome (mmul10)
annotation mmul10 BSgenome
updated 3.8 years ago by 16k • written 3.8 years ago by ▴ 40
1
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0
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571
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News: New BSgenome data packages for bosTau9, rheMac10, danRer11, and galGal6
BSgenome News
3.8 years ago Hervé Pagès 16k
2
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1
reply
432
views
Does "exclude" argument break BSgenome::vmatchPattern?
BSgenome
updated 3.8 years ago by 63k • written 3.9 years ago by ▴ 160
0
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6
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2.1k
views
Error while attempting to forge BSgenome data package
bsgenome ggbio
updated 3.9 years ago by • 0 • written 8.9 years ago by • 0
3
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15
replies
1.6k
views
Error in creating BSGenome package
BSGenome
updated 3.9 years ago by 63k • written 4.0 years ago by • 0
0
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3
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935
views
Defining BSgenome -> GRanges S4 coercer without package attaching
BSgenome methods GenomicRanges
4.1 years ago Aditya ▴ 160
2
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3
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844
views
What is the use of a masked BSgenome?
BSgenome BSgenome.Mmusculus.UCSC.mm10::Mmusculus Biostrings
updated 4.1 years ago by 3.5k • written 4.1 years ago by ▴ 160
1
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2
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752
views
Is it useful to define and export a setAs('BSgenome', 'GRanges')
BSgenome GenomicRanges
updated 4.1 years ago by 11k • written 4.1 years ago by ▴ 160
0
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2
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779
views
getBSgenome{Bsgenome}: avoid attaching BiocGenerics (and others)
BSgenome Bsgenome.Mmusculus.UCSC.mm10
4.1 years ago Aditya ▴ 160
1
vote
6
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1.9k
views
How to subset a BSgenome
BSgenome BSgenome.Mmusculus.UCSC.mm10
updated 4.1 years ago by 3.5k • written 4.1 years ago by ▴ 160
0
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6
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864
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error when using matchProbePair with BSgenome.Hsapiens.UCSC.hg19
matchProbePair BSgenome Biostrings BSgenome.Hsapiens.UCSC.hg19
updated 4.4 years ago by 63k • written 4.4 years ago by • 0
0
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1
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659
views
getSeqSrcpaths (forgeBSgenome) error files not found, but they are right there....
bsgenome forgebsgenome getSeqSrcpaths
4.5 years ago tguerreroa90 • 0
2
votes
1
reply
699
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 4.5 years ago by 63k • written 4.5 years ago by ▴ 40
0
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9
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1.2k
views
Unable to generate feature vector with custom genome in cleanUpdTSeq
cleanUpdTSeq BSgenome BSgenomeForge
updated 4.6 years ago by ★ 4.3k • written 4.6 years ago by • 0
2
votes
2
replies
1.1k
views
BSgenome package building
bsgenome
updated 5.0 years ago by 63k • written 5.0 years ago by • 0
3
votes
5
replies
1.4k
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 5.1 years ago by 16k • written 5.1 years ago by ▴ 810
0
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5
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1.0k
views
Custom BSgenome with makeTxDbFromGFF
bsgenome genomicfeatures
5.2 years ago michael.weber.1 • 0
6
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3
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1.8k
views
News: New Bioconductor package for dbSNP151
SNPlocs.Hsapiens.dbSNP151.GRCh38 BSgenome News
5.2 years ago Hervé Pagès 16k
50 results • Page 1 of 1
Recent ...
Replies
Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k
Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0
I´m sorry causing confusion here, but the gene matrices I refer to are actually obtained via https://nf-co.re/rnaseq. The problem with the…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
For the reasons outlined in the Soneson paper, I'd prefer this pipeline: https://nf-co.re/rnaseq You cannot use these scaled TPM approach…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0
I get your point as we already starting with TPM. This was more to clarify that I understand the principle correctly. However, further I´m…
Votes
batch effect : comBat or blocking in limma ?
Batch correction and repeated measures
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Comment: Phenotype effect - building a contrast matrix - grouping vs interaction
Answer: Batch correction and repeated measures
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