Showing : BSgenome • reset
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Package needs internet access
BSgenome BSgenome.Hsapiens.UCSC.hg38 Offline
updated 8 weeks ago by 67k • written 9 weeks ago by ▴ 20
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4
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7.3k
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Any tools to convert .gff to .gtf format
AnnotationData CrispRdesignR BSgenome
updated 24 days ago by • 0 • written 2.4 years ago by • 0
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6
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1.2k
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Help creating BSgenome object for new canine and feline genomes?
BSgenome
updated 10 months ago by 67k • written 11 months ago by • 0
2
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4
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946
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Need help generating BSgenome and orgdb
OrgDb BSgenome
15 months ago • updated 11 months ago mat149 ▴ 80
1
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3
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1.0k
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Using injectSNPs with a custom set of SNPs
SNPlocs BSgenome
written 15 months ago by • 0
0
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3
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1.1k
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Get Intron Seq
intron BSgenome.Hsapiens.UCSC.hg38 BSgenome
updated 19 months ago by ★ 4.6k • written 19 months ago by • 0
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4
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2.0k
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BSgenome for ensembl mm10
BSgenomeForge BSgenome
updated 19 months ago by 67k • written 19 months ago by • 0
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4
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1.0k
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Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 19 months ago by 16k • written 20 months ago by • 0
1
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1
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716
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add genome to BSgenome
bsgenome
updated 2.1 years ago by 4.1k • written 2.2 years ago by ▴ 10
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2
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2.6k
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getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
2.3 years ago Mog • 0
9
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5
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1.9k
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karyoploteR genome coverage plotting using BSgenome.TAIR10
BSgenome.Athaliana.TAIR.TAIR10. karyoploteR BSgenome
updated 2.3 years ago by 67k • written 2.3 years ago by • 0
2
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3
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1.2k
views
Request : Add Chinese Spring Wheat genome to BSgenome
BSgenome
updated 12 months ago by • 0 • written 2.7 years ago by ▴ 10
1
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1
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958
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Request: Add Marmoset (calJac4) genome to BSgenome
BSgenome
updated 2.7 years ago by 16k • written 2.8 years ago by • 0
1
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0
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1.1k
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News: BSgenome package for T2T-CHM13v2.0 assembly and SNPlocs package for dbSNP155
BSgenome dbSNP T2T-CHM13v2.0 SNPlocs
2.8 years ago Hervé Pagès 16k
1
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1
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1.2k
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Fail to install BSgenome and library
BSgenome Celegans
updated 2.8 years ago by 16k • written 2.8 years ago by • 0
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0
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1.0k
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How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
2.8 years ago Charles Plessy ▴ 180
2
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4
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1.6k
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Subset a BSgenome object (keep standard chomosomes) for applying vmatchPattern or vmatchPDict
BSgenome seqinfo
2.9 years ago alain.corvisier • 0
2
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1
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1.1k
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How to find the BSgenome object that provided the seqinfo of a GRanges object ?
BSgenome
updated 3.0 years ago by 16k • written 3.0 years ago by ▴ 180
1
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5
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1.6k
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submitting a BSgenome package
BSgenome
4.2 years ago • updated 3.0 years ago deisianyufg • 0
1
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2
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1.2k
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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
3.2 years ago geo.vogler ▴ 10
1
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2
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1.1k
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How to make OrgPackage (BSgenome data) package available for R Bioconductor users
BSGenome
updated 3.7 years ago by 16k • written 3.7 years ago by • 0
2
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7
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1.9k
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Can I use BSgenome for in-house assemblies?
BSgenome
updated 3.7 years ago by 16k • written 3.7 years ago by • 0
3
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5
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1.5k
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unable to forge custom BSgenome after update
BSgenome
updated 3.8 years ago by 16k • written 3.8 years ago by ▴ 80
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0
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834
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how to construct a SNPlocs-class by myself
BSgenome SNPlocs
3.8 years ago Guandong Shang ▴ 40
2
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4
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2.0k
views
BSGenome Forge for non-model organism
BSGenomeForge BSGenome
updated 3.8 years ago by 16k • written 3.8 years ago by • 0
0
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3
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2.2k
views
Can BSGenome forge from non-UCSC/NCBI assemblies?
BSgenome
updated 4.1 years ago by ▴ 10 • written 4.1 years ago by • 0
3
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2
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2.7k
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Forging a BSGenome
BSgenome microtus forging
updated 4.1 years ago by 16k • written 4.1 years ago by ▴ 20
1
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4
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1.8k
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forging a BSgenome data package - Seed file issue
seedfiles BSgenome
4.2 years ago n.mary • 0
2
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2
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1.8k
views
How does one modify a single value of a field in a seqinfo object?
GenomicRanges GenomeInfoDb BSgenome isCircular
updated 4.2 years ago by 16k • written 4.3 years ago by ▴ 80
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3
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1.7k
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Error in Forge the target package (BSgenome)
software error BSgenome
4.4 years ago • updated 4.2 years ago jiazhou0116 • 0
1
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1
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1.2k
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About generating a seed file (DCF format) for forging a BSgenome
software error BSgenome
updated 4.3 years ago by 16k • written 4.4 years ago by • 0
0
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0
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764
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Error in loading forged BSgenome
BSgenome msgbsR
4.3 years ago jiazhou0116 • 0
0
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1
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1.4k
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How can i get repetitive elements genomic ranges in human genome?
repetitive elements IRanges GenomicRanges BSgenome
updated 4.4 years ago by 67k • written 4.4 years ago by ▴ 50
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1
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1.2k
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error when forging a BSgenome
BSgenome
updated 4.7 years ago by 4.1k • written 4.7 years ago by ▴ 10
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4
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2.3k
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Error in seqlevelsStyle after creating a BSgenome package
bsgenome MutationalPatterns
4.8 years ago sibyl.bertrand • 0
0
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2
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1.2k
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vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
4.8 years ago mb2subi • 0
2
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6
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1.4k
views
Can't find library BSgenome.Mmulatta.UCSC for latest genome (mmul10)
annotation mmul10 BSgenome
updated 5.1 years ago by 16k • written 5.1 years ago by ▴ 40
1
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0
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930
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News: New BSgenome data packages for bosTau9, rheMac10, danRer11, and galGal6
BSgenome News
5.1 years ago Hervé Pagès 16k
2
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1
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736
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Does "exclude" argument break BSgenome::vmatchPattern?
BSgenome
updated 5.2 years ago by 67k • written 5.2 years ago by ▴ 160
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6
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2.6k
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Error while attempting to forge BSgenome data package
bsgenome ggbio
updated 5.2 years ago by • 0 • written 10.3 years ago by • 0
3
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15
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2.5k
views
Error in creating BSGenome package
BSGenome
updated 5.3 years ago by 67k • written 5.3 years ago by • 0
0
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3
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1.6k
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Defining BSgenome -> GRanges S4 coercer without package attaching
BSgenome methods GenomicRanges
5.4 years ago Aditya ▴ 160
2
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3
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1.6k
views
What is the use of a masked BSgenome?
BSgenome BSgenome.Mmusculus.UCSC.mm10::Mmusculus Biostrings
updated 5.4 years ago by 4.1k • written 5.4 years ago by ▴ 160
1
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2
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1.2k
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Is it useful to define and export a setAs('BSgenome', 'GRanges')
BSgenome GenomicRanges
updated 5.4 years ago by ★ 11k • written 5.4 years ago by ▴ 160
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2
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1.2k
views
getBSgenome{Bsgenome}: avoid attaching BiocGenerics (and others)
BSgenome Bsgenome.Mmusculus.UCSC.mm10
5.4 years ago Aditya ▴ 160
1
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6
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3.0k
views
How to subset a BSgenome
BSgenome BSgenome.Mmusculus.UCSC.mm10
updated 5.5 years ago by 4.1k • written 5.5 years ago by ▴ 160
0
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6
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1.4k
views
error when using matchProbePair with BSgenome.Hsapiens.UCSC.hg19
matchProbePair BSgenome Biostrings BSgenome.Hsapiens.UCSC.hg19
updated 5.7 years ago by 67k • written 5.7 years ago by • 0
0
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1
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1.1k
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getSeqSrcpaths (forgeBSgenome) error files not found, but they are right there....
bsgenome forgebsgenome getSeqSrcpaths
5.8 years ago tguerreroa90 • 0
2
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1
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1.1k
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 5.8 years ago by 67k • written 5.8 years ago by ▴ 40
0
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9
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1.8k
views
Unable to generate feature vector with custom genome in cleanUpdTSeq
cleanUpdTSeq BSgenome BSgenomeForge
updated 5.9 years ago by ★ 4.3k • written 5.9 years ago by • 0
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Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by QN ▴ 10
Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…
Comment: EdgeR Biological CVs by ATpoint ★ 4.6k
"Joseph" is a spam bot...
Comment: Problems with oarfish + tximport + swish by Im • 0
Office ta kemon
Answer: How to sort negative log2FC or FC in RNAseq for GSEA? by ATpoint ★ 4.6k
GSEA asks whether there are general shifts in gene expression towards certain terms. Hence, you would not split your results tables but ord…
Comment: EdgeR Biological CVs by James • 0
Thank you Gordon and Joseph. I presume question (1) would be answered by using a prior G0 of 0? For question (2), I was expecting a biolog…
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How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Comment: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
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