Showing : bsgenome • reset
1
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115
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add genome to BSgenome
bsgenome
updated 8 weeks ago by 3.4k • written 9 weeks ago by ▴ 10
2
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2
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315
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getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
3 months ago Mog • 0
9
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5
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363
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karyoploteR genome coverage plotting using BSgenome.TAIR10
BSgenome.Athaliana.TAIR.TAIR10. karyoploteR BSgenome
updated 4 months ago by 62k • written 4 months ago by • 0
0
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2
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1.1k
views
Any tools to convert .gff to .gtf format
AnnotationData CrispRdesignR BSgenome
updated 4 months ago by ★ 1.6k • written 4 months ago by • 0
2
votes
2
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310
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Request : Add Chinese Spring Wheat genome to BSgenome
BSgenome
updated 7 days ago by • 0 • written 8 months ago by ▴ 10
1
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1
reply
282
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Request: Add Marmoset (calJac4) genome to BSgenome
BSgenome
updated 9 months ago by 16k • written 9 months ago by • 0
1
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0
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316
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News: BSgenome package for T2T-CHM13v2.0 assembly and SNPlocs package for dbSNP155
BSgenome dbSNP T2T-CHM13v2.0 SNPlocs
9 months ago Hervé Pagès 16k
1
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1
reply
406
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Fail to install BSgenome and library
BSgenome Celegans
updated 9 months ago by 16k • written 9 months ago by • 0
1
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0
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286
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How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
9 months ago Charles Plessy ▴ 170
2
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4
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416
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Subset a BSgenome object (keep standard chomosomes) for applying vmatchPattern or vmatchPDict
BSgenome seqinfo
10 months ago alain.corvisier • 0
2
votes
1
reply
359
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How to find the BSgenome object that provided the seqinfo of a GRanges object ?
BSgenome
updated 12 months ago by 16k • written 12 months ago by ▴ 170
1
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5
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786
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submitting a BSgenome package
BSgenome
2.2 years ago • updated 12 months ago deisianyufg • 0
1
vote
2
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490
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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
14 months ago geo.vogler ▴ 10
1
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2
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511
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How to make OrgPackage (BSgenome data) package available for R Bioconductor users
BSGenome
updated 20 months ago by 16k • written 21 months ago by • 0
2
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7
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871
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Can I use BSgenome for in-house assemblies?
BSgenome
updated 21 months ago by 16k • written 21 months ago by • 0
3
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5
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650
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unable to forge custom BSgenome after update
BSgenome
updated 21 months ago by 16k • written 21 months ago by ▴ 80
0
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0
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333
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how to construct a SNPlocs-class by myself
BSgenome SNPlocs
21 months ago Guandong Shang ▴ 40
2
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4
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863
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BSGenome Forge for non-model organism
BSGenomeForge BSGenome
updated 21 months ago by 16k • written 21 months ago by • 0
0
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3
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980
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Can BSGenome forge from non-UCSC/NCBI assemblies?
BSgenome
updated 2.1 years ago by ▴ 10 • written 2.2 years ago by • 0
2
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2
replies
1.1k
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Forging a BSGenome
BSgenome microtus forging
updated 2.1 years ago by 16k • written 2.1 years ago by ▴ 20
1
vote
4
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793
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forging a BSgenome data package - Seed file issue
seedfiles BSgenome
2.2 years ago n.mary • 0
2
votes
2
replies
792
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How does one modify a single value of a field in a seqinfo object?
GenomicRanges GenomeInfoDb BSgenome isCircular
updated 2.2 years ago by 16k • written 2.3 years ago by ▴ 80
0
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3
replies
917
views
Error in Forge the target package (BSgenome)
software error BSgenome
2.4 years ago • updated 2.2 years ago jiazhou0116 • 0
1
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1
reply
536
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About generating a seed file (DCF format) for forging a BSgenome
software error BSgenome
updated 2.4 years ago by 16k • written 2.4 years ago by • 0
0
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0
replies
328
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Error in loading forged BSgenome
BSgenome msgbsR
2.4 years ago jiazhou0116 • 0
0
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1
reply
500
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How can i get repetitive elements genomic ranges in human genome?
repetitive elements IRanges GenomicRanges BSgenome
updated 2.4 years ago by 62k • written 2.4 years ago by ▴ 50
0
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1
reply
444
views
error when forging a BSgenome
BSgenome
updated 2.7 years ago by 3.4k • written 2.7 years ago by ▴ 10
0
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4
replies
969
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Error in seqlevelsStyle after creating a BSgenome package
bsgenome MutationalPatterns
2.8 years ago sibyl.bertrand • 0
0
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2
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484
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vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
2.8 years ago mb2subi • 0
2
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6
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601
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Can't find library BSgenome.Mmulatta.UCSC for latest genome (mmul10)
annotation mmul10 BSgenome
updated 3.1 years ago by 16k • written 3.1 years ago by ▴ 40
1
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0
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414
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News: New BSgenome data packages for bosTau9, rheMac10, danRer11, and galGal6
BSgenome News
3.1 years ago Hervé Pagès 16k
2
votes
1
reply
301
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Does "exclude" argument break BSgenome::vmatchPattern?
BSgenome
updated 3.2 years ago by 62k • written 3.2 years ago by ▴ 140
0
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6
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1.9k
views
Error while attempting to forge BSgenome data package
bsgenome ggbio
updated 3.2 years ago by • 0 • written 8.3 years ago by • 0
3
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15
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1.1k
views
Error in creating BSGenome package
BSGenome
updated 3.3 years ago by 62k • written 3.3 years ago by • 0
0
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3
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725
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Defining BSgenome -> GRanges S4 coercer without package attaching
BSgenome methods GenomicRanges
3.4 years ago Aditya ▴ 140
2
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3
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546
views
What is the use of a masked BSgenome?
BSgenome BSgenome.Mmusculus.UCSC.mm10::Mmusculus Biostrings
updated 3.4 years ago by 3.4k • written 3.4 years ago by ▴ 140
1
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2
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538
views
Is it useful to define and export a setAs('BSgenome', 'GRanges')
BSgenome GenomicRanges
updated 3.4 years ago by 11k • written 3.4 years ago by ▴ 140
0
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2
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572
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getBSgenome{Bsgenome}: avoid attaching BiocGenerics (and others)
BSgenome Bsgenome.Mmusculus.UCSC.mm10
3.5 years ago • updated 3.4 years ago Aditya ▴ 140
1
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6
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1.4k
views
How to subset a BSgenome
BSgenome BSgenome.Mmusculus.UCSC.mm10
updated 3.5 years ago by 3.4k • written 3.5 years ago by ▴ 140
0
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6
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639
views
error when using matchProbePair with BSgenome.Hsapiens.UCSC.hg19
matchProbePair BSgenome Biostrings BSgenome.Hsapiens.UCSC.hg19
updated 3.7 years ago by 62k • written 3.7 years ago by • 0
0
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1
reply
498
views
getSeqSrcpaths (forgeBSgenome) error files not found, but they are right there....
bsgenome forgebsgenome getSeqSrcpaths
3.8 years ago tguerreroa90 • 0
2
votes
1
reply
534
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 3.9 years ago by 62k • written 3.9 years ago by ▴ 40
0
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9
replies
855
views
Unable to generate feature vector with custom genome in cleanUpdTSeq
cleanUpdTSeq BSgenome BSgenomeForge
updated 3.9 years ago by ★ 4.3k • written 3.9 years ago by • 0
2
votes
2
replies
947
views
BSgenome package building
bsgenome
updated 4.3 years ago by 62k • written 4.3 years ago by • 0
3
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5
replies
1.1k
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 4.4 years ago by 16k • written 4.4 years ago by ▴ 800
0
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5
replies
821
views
Custom BSgenome with makeTxDbFromGFF
bsgenome genomicfeatures
4.5 years ago michael.weber.1 • 0
6
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3
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1.3k
views
News: New Bioconductor package for dbSNP151
SNPlocs.Hsapiens.dbSNP151.GRCh38 BSgenome News
4.6 years ago Hervé Pagès 16k
0
votes
1
reply
599
views
extract codon position via BSgenome
bsgenome
updated 4.6 years ago by 16k • written 4.6 years ago by • 0
1
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12
replies
2.8k
views
error in loadFun(x,seqname,ranges). BSgenome.Hsapiens.UCSC.hg19
bsgenome
updated 4.7 years ago by 62k • written 4.7 years ago by ▴ 10
1
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6
replies
1.1k
views
MEDIP: Problem with MEDIPS.createSet
medips bsgenome medip-seq
updated 4.9 years ago by ▴ 570 • written 4.9 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: transcript name mapping between human and mouse by Eric • 0
It works very well, and thanks for such a great answer! Because I use the old version gtf from GENECODE (vM12), the id version does not mat…
Comment: How to normalize long-read RNA-seq data for comparison with short-reads by Bernardo • 0
Just did that, thank you for the suggestion.
Comment: Empty ChipQC Report by Okan • 0
Hi, I have the same issue. Have you found any solution or any reason why this is happening?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
Am I understanding correctly that you have 24 RNA-seq libraries in total, 6 from the pooled samples and 18 from regular samples with biolog…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
I'm sorry, I know it is kinda confusing... We have 6 pools in total: Phenotype A: T1a, T2, T1b, T1c Phenotype B: T1, T2 Each pool consist…
Votes
Answer: transcript name mapping between human and mouse
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Volcano Plot in R
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
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