Showing : bsgenome • reset
1
vote
4
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392
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submitting a BSgenome package
BSgenome
14 months ago • updated 1 day ago deisianyufg • 0
1
vote
2
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155
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Building BSgenome package fails - .make_BSgenome_seqinfo error: sequence names found in .2bit file are not identical to 'seqnames'
BSGenome Forge
9 weeks ago geo.vogler ▴ 10
1
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2
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292
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How to make OrgPackage (BSgenome data) package available for R Bioconductor users
BSGenome
updated 8 months ago by 15k • written 8 months ago by • 0
2
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7
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481
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Can I use BSgenome for in-house assemblies?
BSgenome
updated 8 months ago by 15k • written 8 months ago by • 0
3
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5
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386
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unable to forge custom BSgenome after update
BSgenome
updated 9 months ago by 15k • written 9 months ago by ▴ 80
0
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0
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168
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how to construct a SNPlocs-class by myself
BSgenome SNPlocs
9 months ago Guandong Shang ▴ 20
2
votes
4
replies
407
views
BSGenome Forge for non-model organism
BSGenomeForge BSGenome
updated 9 months ago by 15k • written 9 months ago by • 0
0
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3
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550
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Can BSGenome forge from non-UCSC/NCBI assemblies?
BSgenome
updated 12 months ago by ▴ 10 • written 13 months ago by • 0
2
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2
replies
542
views
Forging a BSGenome
BSgenome microtus forging
updated 13 months ago by 15k • written 13 months ago by ▴ 20
1
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4
replies
470
views
forging a BSgenome data package - Seed file issue
seedfiles BSgenome
14 months ago n.mary • 0
2
votes
2
replies
462
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How does one modify a single value of a field in a seqinfo object?
GenomicRanges GenomeInfoDb BSgenome isCircular
updated 14 months ago by 15k • written 16 months ago by ▴ 80
0
votes
3
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540
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Error in Forge the target package (BSgenome)
software error BSgenome
16 months ago • updated 14 months ago jiazhou0116 • 0
1
vote
1
reply
346
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About generating a seed file (DCF format) for forging a BSgenome
software error BSgenome
updated 16 months ago by 15k • written 16 months ago by • 0
0
votes
0
replies
202
views
Error in loading forged BSgenome
BSgenome msgbsR
16 months ago jiazhou0116 • 0
0
votes
1
reply
274
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How can i get repetitive elements genomic ranges in human genome?
repetitive elements IRanges GenomicRanges BSgenome
updated 16 months ago by 58k • written 16 months ago by ▴ 50
0
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1
reply
240
views
error when forging a BSgenome
BSgenome
updated 20 months ago by 2.9k • written 20 months ago by ▴ 10
0
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4
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548
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Error in seqlevelsStyle after creating a BSgenome package
bsgenome MutationalPatterns
22 months ago • updated 21 months ago sibyl.bertrand • 0
0
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2
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309
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vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
21 months ago mb2subi • 0
2
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6
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383
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Can't find library BSgenome.Mmulatta.UCSC for latest genome (mmul10)
annotation mmul10 BSgenome
updated 2.1 years ago by 15k • written 2.1 years ago by ▴ 40
1
vote
0
replies
264
views
News: New BSgenome data packages for bosTau9, rheMac10, danRer11, and galGal6
BSgenome News
2.1 years ago Hervé Pagès 15k
2
votes
1
reply
195
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Does "exclude" argument break BSgenome::vmatchPattern?
BSgenome
updated 2.2 years ago by 58k • written 2.2 years ago by ▴ 120
0
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6
replies
1.5k
views
Error while attempting to forge BSgenome data package
bsgenome ggbio
updated 2.2 years ago by • 0 • written 7.2 years ago by • 0
3
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15
replies
734
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Error in creating BSGenome package
BSGenome
updated 2.2 years ago by 58k • written 2.3 years ago by • 0
0
votes
3
replies
500
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Defining BSgenome -> GRanges S4 coercer without package attaching
BSgenome methods GenomicRanges
2.4 years ago Aditya ▴ 120
2
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3
replies
338
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What is the use of a masked BSgenome?
BSgenome BSgenome.Mmusculus.UCSC.mm10::Mmusculus Biostrings
updated 2.4 years ago by 2.9k • written 2.4 years ago by ▴ 120
1
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2
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380
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Is it useful to define and export a setAs('BSgenome', 'GRanges')
BSgenome GenomicRanges
updated 2.4 years ago by 11k • written 2.4 years ago by ▴ 120
0
votes
2
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413
views
getBSgenome{Bsgenome}: avoid attaching BiocGenerics (and others)
BSgenome Bsgenome.Mmusculus.UCSC.mm10
2.4 years ago Aditya ▴ 120
1
vote
6
replies
995
views
How to subset a BSgenome
BSgenome BSgenome.Mmusculus.UCSC.mm10
updated 2.5 years ago by 2.9k • written 2.5 years ago by ▴ 120
0
votes
6
replies
437
views
error when using matchProbePair with BSgenome.Hsapiens.UCSC.hg19
matchProbePair BSgenome Biostrings BSgenome.Hsapiens.UCSC.hg19
updated 2.7 years ago by 58k • written 2.7 years ago by • 0
0
votes
1
reply
346
views
getSeqSrcpaths (forgeBSgenome) error files not found, but they are right there....
bsgenome forgebsgenome getSeqSrcpaths
2.8 years ago tguerreroa90 • 0
2
votes
1
reply
380
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 2.8 years ago by 58k • written 2.8 years ago by ▴ 40
0
votes
9
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634
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Unable to generate feature vector with custom genome in cleanUpdTSeq
cleanUpdTSeq BSgenome BSgenomeForge
updated 2.9 years ago by ★ 4.3k • written 2.9 years ago by • 0
2
votes
2
replies
706
views
BSgenome package building
bsgenome
updated 3.3 years ago by 58k • written 3.3 years ago by • 0
3
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5
replies
838
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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 3.4 years ago by 15k • written 3.4 years ago by ▴ 780
0
votes
5
replies
633
views
Custom BSgenome with makeTxDbFromGFF
bsgenome genomicfeatures
3.5 years ago michael.weber.1 • 0
6
votes
3
replies
945
views
News: New Bioconductor package for dbSNP151
SNPlocs.Hsapiens.dbSNP151.GRCh38 BSgenome News
3.5 years ago Hervé Pagès 15k
0
votes
1
reply
423
views
extract codon position via BSgenome
bsgenome
updated 3.6 years ago by 15k • written 3.6 years ago by • 0
1
vote
12
replies
1.9k
views
error in loadFun(x,seqname,ranges). BSgenome.Hsapiens.UCSC.hg19
bsgenome
updated 3.6 years ago by 58k • written 3.6 years ago by ▴ 10
1
vote
6
replies
903
views
MEDIP: Problem with MEDIPS.createSet
medips bsgenome medip-seq
updated 3.8 years ago by ▴ 570 • written 3.8 years ago by • 0
2
votes
3
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713
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What's the best way to retrieve the sizes (lengths) of chromosomes for a reference genome assembly?
bsgenome chromosome reference genome
updated 3.9 years ago by 15k • written 3.9 years ago by ▴ 10
2
votes
1
reply
611
views
Using 'BSgenome::export' to write each chromosome of an organism into separate files
bsgenome biocgenerics bsapply export
updated 3.9 years ago by 58k • written 3.9 years ago by • 0
0
votes
1
reply
1.2k
views
How to name the custom genome in karyoploteR ?
software error R bsgenome karyoploter
updated 4.2 years ago by ▴ 130 • written 4.2 years ago by • 0
0
votes
1
reply
864
views
add new genome as Bsgenome object
bsgenome
updated 4.4 years ago by 25k • written 4.4 years ago by • 0
0
votes
2
replies
719
views
BSgenome.Dmelanogaster.UCSC.dm6 annotation issue
bsgenome BSgenome.Dmelanogaster.UCSC.dm6
4.4 years ago jbeira • 0
1
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3
replies
1.3k
views
BSgenome Sscrofa 11.1
sus scrofa bsgenome
updated 4.4 years ago by 25k • written 4.4 years ago by • 0
4
votes
1
reply
1.2k
views
Getting "negative length vectors are not allowed" error in BSgenome::getSeq
BSgenome getSeq
updated 4.5 years ago by 25k • written 4.5 years ago by ▴ 100
4
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3
replies
1.0k
views
Extracting sequences from BSgenomeViews object
sequence bsgenome
updated 4.5 years ago by 25k • written 4.5 years ago by ▴ 10
0
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2
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1.2k
views
add annotation features to BSgenome or txdb package
bsgenome txdb annotation orgdb
4.5 years ago Didi ▴ 10
2
votes
5
replies
1.3k
views
Forge a BSgenome data package
bsgenome bsgenome forge
4.9 years ago • updated 4.5 years ago jodiera • 0
1
vote
8
replies
1.0k
views
CRISPRseek with genome not available in BSgenome
bsgenome crisprseek
updated 4.5 years ago by ★ 4.3k • written 4.8 years ago by • 0
50 results • Page 1 of 1
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Replies
Comment: Cannot install Phyloseq and dada2 by Guido Hooiveld ★ 3.2k
Did you notice this message:? Installation paths not writeable, unable to update packages path: C:/Program Files/R/R-4.0.0/libra…
Comment: Use of shrunken LFCs to address questions about the distribution of LFCs between by i.sudbery ▴ 20
Thanks Mike. I might have a play with stratifying by expression level. One reason I wasn't looking at gene set testing is that its the nul…
Answer: submitting a BSgenome package by deisianyufg • 0
From my Github repository. I am sorry, I thought the package was already released and realize now that is still only in my github reposito…
Comment: PlotPCA in DESeq2 doesn't produce exactly the same result as prcomp by swbarnes2 ▴ 970
Is the one plot a mirror image of the other?
Answer: Use of shrunken LFCs to address questions about the distribution of LFCs between by Michael Love 35k
hi Ian, Great question, and good to be concerned that the mean expression may be a confounder for either analysis, Why not stratify your…
Votes
Answer: Use of shrunken LFCs to address questions about the distribution of LFCs between
Answer: DiffBind dba.count Error in if (sum(tokeep) < length(tokeep))
Comment: submitting a BSgenome package
Answer: rlog vs vst for outlier identification
Answer: DESeq2 median of ratios normalization for signature score calculation
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