Showing : bsgenome • reset
9
votes
5
replies
1.4k
views
karyoploteR genome coverage plotting using BSgenome.TAIR10
BSgenome.Athaliana.TAIR.TAIR10. karyoploteR BSgenome
updated 18 months ago by 65k • written 19 months ago by • 0
7
votes
6
replies
3.4k
views
How to find TF binding sites for particular TF's within +- 1000 bases of gene TSS for all genes in human genome?
bsgenome transcription factor binding site enrichment analysis matchpwm
8.9 years ago duncp92 ▴ 20
6
votes
6
replies
2.5k
views
Memory-efficient method to calculate GC content of millions of GRanges
granges biostrings bsapply BSgenome
updated 7.4 years ago by 16k • written 7.4 years ago by ▴ 70
6
votes
3
replies
2.3k
views
News: New Bioconductor package for dbSNP151
SNPlocs.Hsapiens.dbSNP151.GRCh38 BSgenome News
5.8 years ago Hervé Pagès 16k
6
votes
2
replies
5.2k
views
Get sequences for GRCh38 genome based on TxDb object locations
bsgenome genomeinfodb transcriptdb
updated 9.3 years ago by 16k • written 9.3 years ago by ▴ 760
5
votes
15
replies
3.1k
views
problem with QDNAseq's createBins for new BSgenome package
bsgenome biostrings qdnaseq pfalciparum
updated 8.7 years ago by ▴ 50 • written 8.7 years ago by • 0
5
votes
9
replies
3.8k
views
mm10 phastCons data for use with ATACseqQC
ATACseqQC bsgenome phastcons rtracklayer
updated 6.9 years ago by ★ 1.3k • written 6.9 years ago by ▴ 10
4
votes
3
replies
1.6k
views
Extracting sequences from BSgenomeViews object
sequence bsgenome
updated 6.7 years ago by 25k • written 6.7 years ago by ▴ 10
4
votes
1
reply
1.7k
views
Getting "negative length vectors are not allowed" error in BSgenome::getSeq
BSgenome getSeq
updated 6.7 years ago by 25k • written 6.7 years ago by ▴ 110
4
votes
2
replies
1.6k
views
Ignoring N's on Ends of the Chromosome When Using matchPattern
bsgenome matchPattern
updated 8.9 years ago by 16k • written 8.9 years ago by ▴ 20
4
votes
2
replies
3.0k
views
How to get sequences corresponding to a GRanges?
BSgenome BSgenome BSgenome BSgenome
updated 11.5 years ago by 25k • written 11.5 years ago by ▴ 830
3
votes
5
replies
1.8k
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 5.7 years ago by 16k • written 5.7 years ago by ▴ 830
3
votes
5
replies
1.2k
views
unable to forge custom BSgenome after update
BSgenome
updated 3.0 years ago by 16k • written 3.0 years ago by ▴ 80
3
votes
2
replies
1.1k
views
Match all DNAString Occurences in a BSgenome
bsgenome genomicranges function creation
7.7 years ago ewjwallace ▴ 10
3
votes
6
replies
2.6k
views
Assign genes to CpG islands
annotation genomicranges bsgenome
updated 8.5 years ago by ★ 1.3k • written 8.5 years ago by ▴ 10
3
votes
6
replies
1.8k
views
installing BSgenome and problems with XML and RCurl packages
bsgenome
updated 8.3 years ago by 25k • written 8.3 years ago by ▴ 20
3
votes
15
replies
2.1k
views
Error in creating BSGenome package
BSGenome
updated 4.5 years ago by 65k • written 4.5 years ago by • 0
3
votes
2
replies
1.1k
views
Error in XVector while creating a custome BSgenome package
BSgenome
updated 7.5 years ago by ★ 6.5k • written 7.5 years ago by ▴ 10
3
votes
4
replies
1.2k
views
Limit on number of sequence files for forging a BSgenome
BSgenome BSgenome genomes BSgenome BSgenome genomes
updated 11.1 years ago by ★ 6.5k • written 11.1 years ago by ▴ 220
3
votes
2
replies
2.1k
views
Forging a BSGenome
BSgenome microtus forging
updated 3.4 years ago by 16k • written 3.4 years ago by ▴ 20
2
votes
2
replies
1.3k
views
BSgenome package building
bsgenome
updated 5.5 years ago by 65k • written 5.5 years ago by • 0
2
votes
3
replies
1.2k
views
What is the use of a masked BSgenome?
BSgenome BSgenome.Mmusculus.UCSC.mm10::Mmusculus Biostrings
updated 4.6 years ago by 3.8k • written 4.7 years ago by ▴ 160
2
votes
4
replies
1.1k
views
Subset a BSgenome object (keep standard chomosomes) for applying vmatchPattern or vmatchPDict
BSgenome seqinfo
2.1 years ago alain.corvisier • 0
2
votes
2
replies
1.7k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
18 months ago Mog • 0
2
votes
3
replies
1.8k
views
What's the best way to retrieve the sizes (lengths) of chromosomes for a reference genome assembly?
bsgenome chromosome reference genome
updated 6.1 years ago by 16k • written 6.1 years ago by ▴ 10
2
votes
1
reply
1.1k
views
Using 'BSgenome::export' to write each chromosome of an organism into separate files
bsgenome biocgenerics bsapply export
updated 6.1 years ago by 65k • written 6.2 years ago by • 0
2
votes
3
replies
845
views
Request : Add Chinese Spring Wheat genome to BSgenome
BSgenome
updated 3 months ago by • 0 • written 23 months ago by ▴ 10
2
votes
1
reply
814
views
How to find the BSgenome object that provided the seqinfo of a GRanges object ?
BSgenome
updated 2.2 years ago by 16k • written 2.2 years ago by ▴ 180
2
votes
5
replies
2.3k
views
Forge a BSgenome data package
bsgenome bsgenome forge
7.2 years ago • updated 6.8 years ago jodiera • 0
2
votes
1
reply
877
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 5.1 years ago by 65k • written 5.1 years ago by ▴ 40
2
votes
3
replies
2.9k
views
How to remove aberrant chromosomes from a BSgenome object?
bsgenome r
updated 7.9 years ago by 16k • written 7.9 years ago by • 0
2
votes
3
replies
1.8k
views
How to add chromosomes to a BSgenome ?
bsgenome virus
updated 7.6 years ago by 16k • written 7.7 years ago by ▴ 180
2
votes
4
replies
1.7k
views
BSGenome Forge for non-model organism
BSGenomeForge BSGenome
updated 3.0 years ago by 16k • written 3.0 years ago by • 0
2
votes
7
replies
1.5k
views
Can I use BSgenome for in-house assemblies?
BSgenome
updated 3.0 years ago by 16k • written 3.0 years ago by • 0
2
votes
1
reply
588
views
Does "exclude" argument break BSgenome::vmatchPattern?
BSgenome
updated 4.4 years ago by 65k • written 4.4 years ago by ▴ 160
2
votes
2
replies
1.4k
views
"Wobble" patterns for genome searching using Biostrings
biostrings bsgenome motif RGYW
8.8 years ago fongchunchan ▴ 30
2
votes
2
replies
2.0k
views
Views on BSgenome object
BSgenome
9.5 years ago • updated 9.4 years ago Kasper Daniel Hansen ★ 6.5k
2
votes
6
replies
1.1k
views
Can't find library BSgenome.Mmulatta.UCSC for latest genome (mmul10)
annotation mmul10 BSgenome
updated 4.4 years ago by 16k • written 4.4 years ago by ▴ 40
2
votes
4
replies
2.9k
views
getSeq{BSgenome} error: Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append)
bsgenome rsamtools
8.3 years ago komal.rathi ▴ 120
2
votes
4
replies
7.3k
views
merging GRange objects
Annotation BSgenome BSgenome Annotation BSgenome BSgenome
updated 10.8 years ago by 16k • written 10.8 years ago by ★ 13k
2
votes
5
replies
1.3k
views
obtaining a complete global alignment via pairwiseAlignment
Alignment GO Cancer BSgenome BSgenome Alignment GO Cancer BSgenome BSgenome
updated 10.9 years ago by 25k • written 10.9 years ago by ★ 13k
2
votes
1
reply
2.3k
views
getSeq with GRanges object error: function not found
biostrings bsgenome granges
updated 9.6 years ago by 25k • written 9.6 years ago by ▴ 20
2
votes
6
replies
2.5k
views
Working with Arabidopsis Databases
bsgenome biomart getPromoterSeq txdb
8.7 years ago oliwindram ▴ 10
2
votes
2
replies
1.5k
views
How does one modify a single value of a field in a seqinfo object?
GenomicRanges GenomeInfoDb BSgenome isCircular
updated 3.4 years ago by 16k • written 3.6 years ago by ▴ 80
2
votes
4
replies
501
views
Need help generating BSgenome and orgdb
OrgDb BSgenome
5 months ago • updated 10 weeks ago mat149 ▴ 70
2
votes
1
reply
1.6k
views
export BSgenome directly in gzipped fasta
bsgenome gzip fasta
updated 8.0 years ago by ▴ 90 • written 8.0 years ago by ▴ 80
1
vote
6
replies
2.4k
views
How to subset a BSgenome
BSgenome BSgenome.Mmusculus.UCSC.mm10
updated 4.7 years ago by 3.8k • written 4.7 years ago by ▴ 160
1
vote
6
replies
1.9k
views
MEDIP: Problem with MEDIPS.createSet
medips bsgenome medip-seq
updated 6.1 years ago by ▴ 570 • written 6.1 years ago by • 0
1
vote
3
replies
2.1k
views
BSgenome Sscrofa 11.1
sus scrofa bsgenome
updated 6.7 years ago by 25k • written 6.7 years ago by • 0
1
vote
8
replies
1.7k
views
CRISPRseek with genome not available in BSgenome
bsgenome crisprseek
updated 6.8 years ago by ★ 4.3k • written 7.1 years ago by • 0
50 results • Page 1 of 1
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Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2 by Weiqian ▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
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Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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