Showing : BSGenome • reset
9
votes
5
replies
1.4k
views
karyoploteR genome coverage plotting using BSgenome.TAIR10
BSgenome.Athaliana.TAIR.TAIR10. karyoploteR BSgenome
updated 19 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 9.4 years ago by 16k • written 9.4 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
19 months ago • updated 18 months ago Mog • 0
2
votes
3
replies
1.9k
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 6.2 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 6.2 years ago by 65k • written 6.2 years ago by • 0
2
votes
3
replies
850
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
816
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
879
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
589
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 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
511
views
Need help generating BSgenome and orgdb
OrgDb BSgenome
6 months ago • updated 11 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: get BM error by James W. MacDonald 65k
The genes you present are orthologous mappings from D. rerio to other teleost fishes, so it is probably going to be difficult to map to NCB…
Answer: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
You can also use a combination of the `org.Hs.eg.db` and `GO.db` packages. ``` > library(GO.db) > library(org.Hs.eg.db) > go <- m…
Comment: Different Shrunk Log2FC according with reference by Michael Love 41k
I took a look and the posterior width for these (fairly rare) examples overlaps zero. So the posterior when it disagrees is not narrow. An…
Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs by Guangchuang Yu ★ 1.2k
an example is also presented in <https://pubmed.ncbi.nlm.nih.gov/34557778/>.
Comment: Trying to use enrichGO by Guido Hooiveld ★ 3.9k
Nothing would prevent you from using the `enrichGO` function (or any other function for over-representation analysis [ORA]) with only 14 ge…
Votes
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds
Subset DEXSeqDataSet In DEXSeq
How to get all possible comparisons in DiffBind
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