Showing : BSgenome • reset
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Package needs internet access
BSgenome BSgenome.Hsapiens.UCSC.hg38 Offline
updated 5 months ago by 68k • written 5 months ago by ▴ 20
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Any tools to convert .gff to .gtf format
AnnotationData CrispRdesignR BSgenome
updated 3 months ago by • 0 • written 2.7 years ago by • 0
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6
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1.4k
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Help creating BSgenome object for new canine and feline genomes?
BSgenome
updated 14 months ago by 68k • written 14 months ago by • 0
2
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4
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1.1k
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Need help generating BSgenome and orgdb
OrgDb BSgenome
18 months ago • updated 14 months ago mat149 ▴ 80
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3
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1.1k
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Using injectSNPs with a custom set of SNPs
SNPlocs BSgenome
written 18 months ago by • 0
0
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3
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1.2k
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Get Intron Seq
intron BSgenome.Hsapiens.UCSC.hg38 BSgenome
updated 22 months ago by ★ 4.8k • written 22 months ago by • 0
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4
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2.5k
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BSgenome for ensembl mm10
BSgenomeForge BSgenome
updated 22 months ago by 68k • written 22 months ago by • 0
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4
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1.2k
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Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 23 months ago by 16k • written 23 months ago by • 0
1
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1
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769
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add genome to BSgenome
bsgenome
updated 2.4 years ago by 4.1k • written 2.4 years ago by ▴ 10
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2
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2.9k
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getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
2.6 years ago Mog • 0
9
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5
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2.0k
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karyoploteR genome coverage plotting using BSgenome.TAIR10
BSgenome.Athaliana.TAIR.TAIR10. karyoploteR BSgenome
updated 2.6 years ago by 68k • written 2.6 years ago by • 0
2
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3
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1.3k
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Request : Add Chinese Spring Wheat genome to BSgenome
BSgenome
updated 15 months ago by • 0 • written 3.0 years ago by ▴ 10
1
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1
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1.0k
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Request: Add Marmoset (calJac4) genome to BSgenome
BSgenome
updated 3.0 years ago by 16k • written 3.0 years ago by • 0
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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
3.0 years ago Hervé Pagès 16k
1
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1
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1.3k
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Fail to install BSgenome and library
BSgenome Celegans
updated 3.0 years ago by 16k • written 3.0 years ago by • 0
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0
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1.1k
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How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
3.0 years ago Charles Plessy ▴ 180
2
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4
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1.8k
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Subset a BSgenome object (keep standard chomosomes) for applying vmatchPattern or vmatchPDict
BSgenome seqinfo
3.1 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 3.2 years ago by 16k • written 3.2 years ago by ▴ 180
1
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5
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1.7k
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submitting a BSgenome package
BSgenome
4.5 years ago • updated 3.3 years ago deisianyufg • 0
1
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2
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1.3k
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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
3.5 years ago geo.vogler ▴ 10
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2
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1.2k
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How to make OrgPackage (BSgenome data) package available for R Bioconductor users
BSGenome
updated 4.0 years ago by 16k • written 4.0 years ago by • 0
2
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7
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2.1k
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Can I use BSgenome for in-house assemblies?
BSgenome
updated 4.0 years ago by 16k • written 4.0 years ago by • 0
3
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5
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1.7k
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unable to forge custom BSgenome after update
BSgenome
updated 4.0 years ago by 16k • written 4.0 years ago by ▴ 80
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0
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880
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how to construct a SNPlocs-class by myself
BSgenome SNPlocs
4.0 years ago Guandong Shang ▴ 40
2
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4
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2.2k
views
BSGenome Forge for non-model organism
BSGenomeForge BSGenome
updated 4.0 years ago by 16k • written 4.1 years ago by • 0
0
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3
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2.5k
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Can BSGenome forge from non-UCSC/NCBI assemblies?
BSgenome
updated 4.3 years ago by ▴ 10 • written 4.4 years ago by • 0
3
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2
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3.0k
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Forging a BSGenome
BSgenome microtus forging
updated 4.4 years ago by 16k • written 4.4 years ago by ▴ 20
1
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4
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2.0k
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forging a BSgenome data package - Seed file issue
seedfiles BSgenome
4.5 years ago • updated 4.4 years ago n.mary • 0
2
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2
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2.0k
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How does one modify a single value of a field in a seqinfo object?
GenomicRanges GenomeInfoDb BSgenome isCircular
updated 4.5 years ago by 16k • written 4.6 years ago by ▴ 80
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3
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1.8k
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Error in Forge the target package (BSgenome)
software error BSgenome
4.6 years ago • updated 4.5 years ago jiazhou0116 • 0
1
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1
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1.3k
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About generating a seed file (DCF format) for forging a BSgenome
software error BSgenome
updated 4.6 years ago by 16k • written 4.6 years ago by • 0
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0
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805
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Error in loading forged BSgenome
BSgenome msgbsR
4.6 years ago jiazhou0116 • 0
0
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1
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1.7k
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How can i get repetitive elements genomic ranges in human genome?
repetitive elements IRanges GenomicRanges BSgenome
updated 4.7 years ago by 68k • written 4.7 years ago by ▴ 50
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1
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1.3k
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error when forging a BSgenome
BSgenome
updated 4.9 years ago by 4.1k • written 4.9 years ago by ▴ 10
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4
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2.5k
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Error in seqlevelsStyle after creating a BSgenome package
bsgenome MutationalPatterns
5.1 years ago • updated 5.0 years ago sibyl.bertrand • 0
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2
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1.3k
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vmatchPattern error using a DNA string and BSgenome
Biostrings vmatchPattern BSgenome
5.1 years ago mb2subi • 0
2
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6
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1.5k
views
Can't find library BSgenome.Mmulatta.UCSC for latest genome (mmul10)
annotation mmul10 BSgenome
updated 5.4 years ago by 16k • written 5.4 years ago by ▴ 40
1
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0
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988
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News: New BSgenome data packages for bosTau9, rheMac10, danRer11, and galGal6
BSgenome News
5.4 years ago Hervé Pagès 16k
2
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1
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792
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Does "exclude" argument break BSgenome::vmatchPattern?
BSgenome
updated 5.4 years ago by 68k • written 5.4 years ago by ▴ 160
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6
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2.8k
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Error while attempting to forge BSgenome data package
bsgenome ggbio
updated 5.5 years ago by • 0 • written 10.5 years ago by • 0
3
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15
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2.7k
views
Error in creating BSGenome package
BSGenome
updated 5.5 years ago by 68k • written 5.5 years ago by • 0
0
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3
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1.7k
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Defining BSgenome -> GRanges S4 coercer without package attaching
BSgenome methods GenomicRanges
5.6 years ago Aditya ▴ 160
2
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3
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1.7k
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What is the use of a masked BSgenome?
BSgenome BSgenome.Mmusculus.UCSC.mm10::Mmusculus Biostrings
updated 5.6 years ago by 4.1k • written 5.7 years ago by ▴ 160
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2
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1.3k
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Is it useful to define and export a setAs('BSgenome', 'GRanges')
BSgenome GenomicRanges
updated 5.6 years ago by ★ 11k • written 5.6 years ago by ▴ 160
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2
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1.3k
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getBSgenome{Bsgenome}: avoid attaching BiocGenerics (and others)
BSgenome Bsgenome.Mmusculus.UCSC.mm10
5.7 years ago Aditya ▴ 160
1
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6
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3.2k
views
How to subset a BSgenome
BSgenome BSgenome.Mmusculus.UCSC.mm10
updated 5.7 years ago by 4.1k • written 5.7 years ago by ▴ 160
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6
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1.5k
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error when using matchProbePair with BSgenome.Hsapiens.UCSC.hg19
matchProbePair BSgenome Biostrings BSgenome.Hsapiens.UCSC.hg19
updated 5.9 years ago by 68k • written 5.9 years ago by • 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
6.1 years ago tguerreroa90 • 0
2
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1
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1.2k
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Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 6.1 years ago by 68k • written 6.1 years ago by ▴ 40
0
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9
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2.0k
views
Unable to generate feature vector with custom genome in cleanUpdTSeq
cleanUpdTSeq BSgenome BSgenomeForge
updated 6.1 years ago by ★ 4.3k • written 6.1 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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