Showing : bsgenome • reset
1
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3
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278
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How to construct a BSgenome object from a custom genome assembly using BSgenomeForge?
BSgenome BSgenomeForge
updated 23 days ago by 68k • written 27 days ago by ▴ 80
1
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5
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842
views
Package needs internet access
BSgenome BSgenome.Hsapiens.UCSC.hg38 Offline
updated 10 months ago by 68k • written 10 months ago by ▴ 20
0
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4
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8.8k
views
Any tools to convert .gff to .gtf format
AnnotationData CrispRdesignR BSgenome
updated 9 months ago by • 0 • written 3.1 years ago by • 0
1
vote
6
replies
1.6k
views
Help creating BSgenome object for new canine and feline genomes?
BSgenome
updated 19 months ago by 68k • written 20 months ago by • 0
2
votes
4
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1.4k
views
Need help generating BSgenome and orgdb
OrgDb BSgenome
23 months ago • updated 20 months ago mat149 ▴ 80
1
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3
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1.3k
views
Using injectSNPs with a custom set of SNPs
SNPlocs BSgenome
written 24 months ago by • 0
0
votes
3
replies
1.3k
views
Get Intron Seq
intron BSgenome.Hsapiens.UCSC.hg38 BSgenome
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
0
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4
replies
2.9k
views
BSgenome for ensembl mm10
BSgenomeForge BSgenome
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
1
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4
replies
1.3k
views
Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 2.4 years ago by 16k • written 2.4 years ago by • 0
1
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1
reply
856
views
add genome to BSgenome
bsgenome
updated 2.9 years ago by 4.2k • written 2.9 years ago by ▴ 10
2
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2
replies
3.2k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
3.0 years ago Mog • 0
9
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5
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2.3k
views
karyoploteR genome coverage plotting using BSgenome.TAIR10
BSgenome.Athaliana.TAIR.TAIR10. karyoploteR BSgenome
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
2
votes
3
replies
1.5k
views
Request : Add Chinese Spring Wheat genome to BSgenome
BSgenome
updated 21 months ago by • 0 • written 3.4 years ago by ▴ 10
1
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1
reply
1.1k
views
Request: Add Marmoset (calJac4) genome to BSgenome
BSgenome
updated 3.5 years ago by 16k • written 3.5 years ago by • 0
1
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0
replies
1.3k
views
News: BSgenome package for T2T-CHM13v2.0 assembly and SNPlocs package for dbSNP155
BSgenome dbSNP T2T-CHM13v2.0 SNPlocs
3.5 years ago Hervé Pagès 16k
1
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1
reply
1.4k
views
Fail to install BSgenome and library
BSgenome Celegans
updated 3.5 years ago by 16k • written 3.5 years ago by • 0
1
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0
replies
1.2k
views
How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
3.5 years ago Charles Plessy ▴ 180
2
votes
4
replies
2.0k
views
Subset a BSgenome object (keep standard chomosomes) for applying vmatchPattern or vmatchPDict
BSgenome seqinfo
3.6 years ago alain.corvisier • 0
2
votes
1
reply
1.3k
views
How to find the BSgenome object that provided the seqinfo of a GRanges object ?
BSgenome
updated 3.7 years ago by 16k • written 3.7 years ago by ▴ 180
1
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5
replies
1.8k
views
submitting a BSgenome package
BSgenome
4.9 years ago • updated 3.7 years ago deisianyufg • 0
1
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2
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1.5k
views
Building BSgenome package fails - .make_BSgenome_seqinfo error: sequence names found in .2bit file are not identical to 'seqnames'
BSGenome Forge
3.9 years ago geo.vogler ▴ 10
1
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2
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1.3k
views
How to make OrgPackage (BSgenome data) package available for R Bioconductor users
BSGenome
updated 4.4 years ago by 16k • written 4.4 years ago by • 0
2
votes
7
replies
2.2k
views
Can I use BSgenome for in-house assemblies?
BSgenome
updated 4.4 years ago by 16k • written 4.4 years ago by • 0
3
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5
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1.8k
views
unable to forge custom BSgenome after update
BSgenome
updated 4.5 years ago by 16k • written 4.5 years ago by ▴ 80
0
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0
replies
972
views
how to construct a SNPlocs-class by myself
BSgenome SNPlocs
4.5 years ago Guandong Shang ▴ 40
2
votes
4
replies
2.4k
views
BSGenome Forge for non-model organism
BSGenomeForge BSGenome
updated 4.5 years ago by 16k • written 4.5 years ago by • 0
0
votes
3
replies
2.9k
views
Can BSGenome forge from non-UCSC/NCBI assemblies?
BSgenome
updated 4.8 years ago by ▴ 10 • written 4.9 years ago by • 0
3
votes
2
replies
3.3k
views
Forging a BSGenome
BSgenome microtus forging
updated 4.8 years ago by 16k • written 4.8 years ago by ▴ 20
1
vote
4
replies
2.1k
views
forging a BSgenome data package - Seed file issue
seedfiles BSgenome
4.9 years ago n.mary • 0
2
votes
2
replies
2.1k
views
How does one modify a single value of a field in a seqinfo object?
GenomicRanges GenomeInfoDb BSgenome isCircular
updated 4.9 years ago by 16k • written 5.0 years ago by ▴ 80
0
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3
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2.0k
views
Error in Forge the target package (BSgenome)
software error BSgenome
5.1 years ago • updated 4.9 years ago jiazhou0116 • 0
1
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1
reply
1.4k
views
About generating a seed file (DCF format) for forging a BSgenome
software error BSgenome
updated 5.1 years ago by 16k • written 5.1 years ago by • 0
0
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0
replies
874
views
Error in loading forged BSgenome
BSgenome msgbsR
5.1 years ago jiazhou0116 • 0
0
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1
reply
1.9k
views
How can i get repetitive elements genomic ranges in human genome?
repetitive elements IRanges GenomicRanges BSgenome
updated 5.1 years ago by 68k • written 5.1 years ago by ▴ 50
0
votes
1
reply
1.3k
views
error when forging a BSgenome
BSgenome
updated 5.4 years ago by 4.2k • written 5.4 years ago by ▴ 10
0
votes
4
replies
2.6k
views
Error in seqlevelsStyle after creating a BSgenome package
bsgenome MutationalPatterns
5.5 years ago sibyl.bertrand • 0
0
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2
replies
1.4k
views
vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
5.5 years ago mb2subi • 0
2
votes
6
replies
1.7k
views
Can't find library BSgenome.Mmulatta.UCSC for latest genome (mmul10)
annotation mmul10 BSgenome
updated 5.8 years ago by 16k • written 5.8 years ago by ▴ 40
1
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0
replies
1.1k
views
News: New BSgenome data packages for bosTau9, rheMac10, danRer11, and galGal6
BSgenome News
5.8 years ago Hervé Pagès 16k
2
votes
1
reply
868
views
Does "exclude" argument break BSgenome::vmatchPattern?
BSgenome
updated 5.9 years ago by 68k • written 5.9 years ago by ▴ 160
0
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6
replies
2.9k
views
Error while attempting to forge BSgenome data package
bsgenome ggbio
updated 5.9 years ago by • 0 • written 11.0 years ago by • 0
3
votes
15
replies
2.9k
views
Error in creating BSGenome package
BSGenome
updated 6.0 years ago by 68k • written 6.0 years ago by • 0
0
votes
3
replies
1.9k
views
Defining BSgenome -> GRanges S4 coercer without package attaching
BSgenome methods GenomicRanges
6.1 years ago Aditya ▴ 160
2
votes
3
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1.9k
views
What is the use of a masked BSgenome?
BSgenome BSgenome.Mmusculus.UCSC.mm10::Mmusculus Biostrings
updated 6.1 years ago by 4.2k • written 6.2 years ago by ▴ 160
1
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2
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1.4k
views
Is it useful to define and export a setAs('BSgenome', 'GRanges')
BSgenome GenomicRanges
updated 6.1 years ago by ★ 11k • written 6.1 years ago by ▴ 160
0
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2
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1.4k
views
getBSgenome{Bsgenome}: avoid attaching BiocGenerics (and others)
BSgenome Bsgenome.Mmusculus.UCSC.mm10
6.2 years ago • updated 6.1 years ago Aditya ▴ 160
1
vote
6
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3.4k
views
How to subset a BSgenome
BSgenome BSgenome.Mmusculus.UCSC.mm10
updated 6.2 years ago by 4.2k • written 6.2 years ago by ▴ 160
0
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6
replies
1.6k
views
error when using matchProbePair with BSgenome.Hsapiens.UCSC.hg19
matchProbePair BSgenome Biostrings BSgenome.Hsapiens.UCSC.hg19
updated 6.4 years ago by 68k • written 6.4 years ago by • 0
0
votes
1
reply
1.2k
views
getSeqSrcpaths (forgeBSgenome) error files not found, but they are right there....
bsgenome forgebsgenome getSeqSrcpaths
6.5 years ago tguerreroa90 • 0
2
votes
1
reply
1.3k
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 6.6 years ago by 68k • written 6.6 years ago by ▴ 40
349 results • Page 1 of 7
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Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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