Showing : BSGenome • reset
0
votes
5
replies
8.9k
views
how to operate on a DNAStringSet object
BSgenome BSgenome BSgenome BSgenome
11.1 years ago Chris Seidel ▴ 80
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
0
votes
5
replies
6.3k
views
Problem in BSgenome.Hsapiens.UCSC.hg19 Installation
bsgenome installation software error
updated 8.9 years ago by 25k • written 8.9 years ago by • 0
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
0
votes
2
replies
5.0k
views
Any tools to convert .gff to .gtf format
AnnotationData CrispRdesignR BSgenome
updated 19 months ago by ★ 1.6k • written 19 months ago by • 0
0
votes
5
replies
4.6k
views
Finding mismatches between reads and reference sequence
Infrastructure Cancer BSgenome BSgenome Infrastructure Cancer BSgenome BSgenome
updated 11.0 years ago by ▴ 30 • written 11.0 years ago by 16k
1
vote
12
replies
4.1k
views
error in loadFun(x,seqname,ranges). BSgenome.Hsapiens.UCSC.hg19
bsgenome
updated 5.9 years ago by 65k • written 5.9 years ago by ▴ 10
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
0
votes
1
reply
3.6k
views
org.Hs.eg.db
BSgenome BSgenome BSgenome BSgenome
updated 10.5 years ago by 65k • written 10.6 years ago by ★ 13k
0
votes
1
reply
3.5k
views
GRanges Constructor With seqlengths
BSgenome BSgenome BSgenome BSgenome
11.9 years ago Dario Strbenac ★ 1.5k
0
votes
3
replies
3.4k
views
Working with ensembl 73 & BSGenome
Annotation BSgenome TranscriptDb biomaRt BSgenome Annotation BSgenome TranscriptDb biomaRt
updated 10.5 years ago by 16k • written 10.5 years ago by ★ 13k
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
0
votes
8
replies
3.1k
views
QuasR: how to use an indexed reference genome?
BSgenome BSgenome genomes QuasR BSgenome BSgenome genomes QuasR
updated 10.9 years ago by ▴ 350 • written 10.9 years ago by ▴ 750
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
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
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
0
votes
5
replies
2.9k
views
Biostrings::matchPattern,extract sequences
GO BSgenome BSgenome GO BSgenome BSgenome
updated 10.6 years ago by 16k • written 10.6 years ago by ★ 4.3k
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
0
votes
3
replies
2.8k
views
MEDIPS, GRanges, IRanges error processing BAM file
Alignment BSgenome PROcess BSgenome IRanges MEDIPS Alignment BSgenome PROcess BSgenome
updated 10.7 years ago by ▴ 570 • written 10.7 years ago by ▴ 40
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
0
votes
17
replies
2.6k
views
problems with strand in predictCoding
VariantAnnotation Annotation BSgenome BSgenome VariantAnnotation VariantAnnotation BSgenome
updated 12.0 years ago by ▴ 20 • written 12.0 years ago by ▴ 50
0
votes
7
replies
2.6k
views
GTF file error when using easyRNAseq�
Annotation Organism BSgenome BSgenome DESeq easyRNASeq Annotation Organism BSgenome DESeq
updated 10.4 years ago by ★ 1.2k • written 10.4 years ago by ★ 13k
0
votes
7
replies
2.6k
views
QuasR on Linux Cluster
BSgenome BSgenome QuasR BSgenome BSgenome QuasR
updated 10.5 years ago by ▴ 350 • written 10.5 years ago by ▴ 340
0
votes
1
reply
2.6k
views
biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene") fails
BSgenome hexbin BSgenome IRanges genomeIntervals GenomicRanges girafe Rsamtools HiTC HiTC
updated 11.1 years ago by ★ 8.2k • written 11.1 years ago by ▴ 100
0
votes
2
replies
2.6k
views
BSgenome forging -- not valid BSgenomeDataPkgSeed slots
bsgenome
9.3 years ago qiwang1993 • 0
1
vote
7
replies
2.5k
views
Mapping Probes to a Genome
BSgenome biostrings probe mapping
updated 7.0 years ago by ▴ 10 • written 7.6 years ago by ★ 1.5k
0
votes
13
replies
2.5k
views
forge BSgenome data package
BSgenome Biostrings BSgenome BSgenome Biostrings BSgenome
updated 13.2 years ago by 16k • written 13.2 years ago by ▴ 330
2
votes
6
replies
2.5k
views
Working with Arabidopsis Databases
bsgenome biomart getPromoterSeq txdb
8.7 years ago oliwindram ▴ 10
0
votes
5
replies
2.5k
views
Motif enrichment analysis: Error in transfac format and background frequencies from BSGenome
BSgenome convert BSgenome PWMEnrich MotifDb
updated 9.6 years ago by ▴ 80 • written 9.6 years ago by ▴ 50
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
0
votes
3
replies
2.4k
views
featureCounts segfault
Annotation BSgenome BSgenome Rsubread Annotation BSgenome BSgenome Rsubread
updated 9.9 years ago by ★ 3.6k • written 9.9 years ago by ★ 7.9k
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
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
0
votes
6
replies
2.3k
views
Error while attempting to forge BSgenome data package
bsgenome ggbio
updated 4.5 years ago by • 0 • written 9.5 years ago by • 0
0
votes
13
replies
2.3k
views
How to plot NGS data?
GO BSgenome geneplotter PROcess BSgenome genomes GO BSgenome geneplotter PROcess genomes
updated 12.2 years ago by 25k • written 12.2 years ago by ▴ 30
0
votes
2
replies
2.3k
views
Coverage vs GC bias - how to?
Coverage BSgenome BSgenome IRanges Coverage BSgenome BSgenome IRanges
updated 13.6 years ago by ▴ 590 • written 13.6 years ago by ▴ 100
0
votes
3
replies
2.3k
views
seqlevels in VCF objects
BSgenome BSgenome genomes BSgenome BSgenome genomes
updated 11.3 years ago by ★ 6.8k • written 11.3 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
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
0
votes
2
replies
2.3k
views
Biobase use problem
BSgenome BSgenome BSgenome BSgenome
updated 12.6 years ago by 21k • written 12.6 years ago by ▴ 30
0
votes
9
replies
2.2k
views
Restriction enzyme digestion
BSgenome BSgenome BSgenome BSgenome
updated 15.9 years ago by 16k • written 15.9 years ago by ▴ 90
0
votes
2
replies
2.2k
views
BSGenome::getSeq gives error: Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append)
bsgenome getseq
updated 8.4 years ago by 25k • written 8.4 years ago by • 0
0
votes
8
replies
2.2k
views
vmatchPDict?
BSgenome probe BSgenome BSgenome probe BSgenome
updated 11.3 years ago by 16k • written 11.3 years ago by ▴ 130
0
votes
2
replies
2.2k
views
MT reference differences between hg19/GRCH37
BSgenome BSgenome BSgenome BSgenome
11.1 years ago Julian Gehring ★ 1.3k
0
votes
5
replies
2.1k
views
yieldSize and paired end data in SummarizeOverlaps error?
BSgenome PROcess BSgenome ASSIGN BSgenome PROcess BSgenome ASSIGN
updated 11.1 years ago by ★ 6.8k • written 11.1 years ago by ▴ 10
0
votes
4
replies
2.1k
views
BSgenomes vs ENSEMBL
Transcription Annotation BSgenome annotate Biostrings BSgenome Transcription Annotation
updated 15.5 years ago by 16k • written 15.5 years ago by ★ 3.9k
0
votes
2
replies
2.1k
views
PWM matching using matchPWM in Biostrings
Transcription BSgenome Biostrings BSgenome Transcription BSgenome Biostrings BSgenome
updated 14.9 years ago by ★ 1.6k • written 14.9 years ago by ▴ 10
0
votes
5
replies
2.1k
views
MEDIPS.createSet error
Alignment BSgenome BSgenome MEDIPS Alignment BSgenome BSgenome MEDIPS
updated 10.1 years ago by ▴ 570 • written 10.1 years ago by ▴ 220
1
vote
2
replies
2.1k
views
Finding mismatches between reads and reference sequence
bsgenome cigar alignment
updated 9.4 years ago by 16k • written 9.4 years ago by ▴ 40
1
vote
1
reply
2.1k
views
package ‘BSgenome.Hsapiens.UCSC.hg38’ is not available (for R version 3.1.2)
bsgenome hg38 r version 3.1.2
updated 8.6 years ago by 65k • written 8.6 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Differentially expressed genes in monocle pseudotime by Gordon Smyth 50k
You might try the methods in this paper: Cheng J, Smyth GK*, Chen Y* (2023). Unraveling the timeline of gene expression: A pseudotempora…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Thank you Michael for your attention to my question. I am truly grateful. I subsetted the data using lines of codes to include only the g…
Comment: [DiffBind] Obtaining normalization factors by Henry ▴ 10
I see, thank you for your suggestion! I managed to use a separate RLE normalization to obtain the size factors.
Answer: Memory errors using read.bismark? by Peter Hickey ▴ 690
Thanks for sharing an example file. This is a very large non-CpG methylation dataset, which are tricky to work with for a number of reason…
Comment: Reading huge bismark coverage files using bbseq::read.bismark by Peter Hickey ▴ 690
Superficially, your issue is similar to [https://github.com/hansenlab/bsseq/issues/136](https://github.com/hansenlab/bsseq/issues/136). You…
Votes
Comment: [DiffBind] Obtaining normalization factors
Answer: ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with var
Comment: Not fully paired differential gene expression analysis
Answer: GSVA error
Comment: DESeq2 - Plot Nr. Genes vs Variance explained in PCA
Awards • All
Popular Question to paria.alipour • 0
Popular Question to Eman • 0
Popular Question to James W. MacDonald 65k
Scholar to nhaus ▴ 30
Popular Question to shepherl 3.8k
Locations • All
Spain, 6 minutes ago
WEHI, Melbourne, Australia, 8 minutes ago
France, 9 minutes ago
United Kingdom, 10 minutes ago
France, 13 minutes ago
Traffic: 706 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6