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Showing :
BSGenome
•
reset
0
votes
5
replies
9.0k
views
how to operate on a DNAStringSet object
BSgenome
BSgenome
BSgenome
BSgenome
11.2 years ago
Chris Seidel
▴ 80
2
votes
4
replies
7.4k
views
merging GRange objects
Annotation
BSgenome
BSgenome
Annotation
BSgenome
BSgenome
updated 10.9 years ago by
Hervé Pagès
16k • written 10.9 years ago by
Guest User
★ 13k
0
votes
5
replies
6.3k
views
Problem in BSgenome.Hsapiens.UCSC.hg19 Installation
bsgenome
installation
software error
updated 9.0 years ago by
Martin Morgan
25k • written 9.0 years ago by
nabaneeta85
• 0
0
votes
2
replies
5.3k
views
Any tools to convert .gff to .gtf format
AnnotationData
CrispRdesignR
BSgenome
updated 21 months ago by
Malcolm Cook
★ 1.6k • written 21 months ago by
Manoj Kumar R
• 0
6
votes
2
replies
5.3k
views
Get sequences for GRCh38 genome based on TxDb object locations
bsgenome
genomeinfodb
transcriptdb
updated 9.4 years ago by
Hervé Pagès
16k • written 9.4 years ago by
Diego Diez
▴ 760
0
votes
5
replies
4.7k
views
Finding mismatches between reads and reference sequence
Infrastructure
Cancer
BSgenome
BSgenome
Infrastructure
Cancer
BSgenome
BSgenome
updated 11.1 years ago by
David Greber
▴ 30 • written 11.2 years ago by
Hervé Pagès
16k
1
vote
12
replies
4.2k
views
error in loadFun(x,seqname,ranges). BSgenome.Hsapiens.UCSC.hg19
bsgenome
updated 6.0 years ago by
James W. MacDonald
66k • written 6.0 years ago by
sophialovechan
▴ 10
5
votes
9
replies
3.9k
views
mm10 phastCons data for use with ATACseqQC
ATACseqQC
bsgenome
phastcons
rtracklayer
updated 7.0 years ago by
Ou, Jianhong
★ 1.3k • written 7.0 years ago by
crysis405
▴ 10
0
votes
1
reply
3.6k
views
org.Hs.eg.db
BSgenome
BSgenome
BSgenome
BSgenome
updated 10.7 years ago by
James W. MacDonald
66k • written 10.7 years ago by
Guest User
★ 13k
0
votes
1
reply
3.6k
views
GRanges Constructor With seqlengths
BSgenome
BSgenome
BSgenome
BSgenome
12.0 years ago
Dario Strbenac
★ 1.5k
7
votes
6
replies
3.5k
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
9.0 years ago
duncp92
▴ 20
0
votes
3
replies
3.4k
views
Working with ensembl 73 & BSGenome
Annotation
BSgenome
TranscriptDb
biomaRt
BSgenome
Annotation
BSgenome
TranscriptDb
biomaRt
updated 10.6 years ago by
Hervé Pagès
16k • written 10.6 years ago by
Guest User
★ 13k
0
votes
8
replies
3.2k
views
QuasR: how to use an indexed reference genome?
BSgenome
BSgenome
genomes
QuasR
BSgenome
BSgenome
genomes
QuasR
updated 11.0 years ago by
Michael Stadler
▴ 350 • written 11.0 years ago by
Paul Shannon
▴ 750
5
votes
15
replies
3.2k
views
problem with QDNAseq's createBins for new BSgenome package
bsgenome
biostrings
qdnaseq
pfalciparum
updated 8.8 years ago by
ilari.scheinin
▴ 50 • written 8.8 years ago by
penington.j
• 0
4
votes
2
replies
3.1k
views
How to get sequences corresponding to a GRanges?
BSgenome
BSgenome
BSgenome
BSgenome
updated 11.6 years ago by
Martin Morgan
25k • written 11.6 years ago by
Cei Abreu-Goodger
▴ 830
2
votes
3
replies
3.0k
views
How to remove aberrant chromosomes from a BSgenome object?
bsgenome
r
updated 8.0 years ago by
Hervé Pagès
16k • written 8.0 years ago by
tlgolan
• 0
2
votes
4
replies
2.9k
views
getSeq{BSgenome} error: Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append)
bsgenome
rsamtools
8.4 years ago
komal.rathi
▴ 120
0
votes
5
replies
2.9k
views
Biostrings::matchPattern,extract sequences
GO
BSgenome
BSgenome
GO
BSgenome
BSgenome
updated 10.7 years ago by
Hervé Pagès
16k • written 10.7 years ago by
Julie Zhu
★ 4.3k
0
votes
3
replies
2.9k
views
MEDIPS, GRanges, IRanges error processing BAM file
Alignment
BSgenome
PROcess
BSgenome
IRanges
MEDIPS
Alignment
BSgenome
PROcess
BSgenome
updated 10.8 years ago by
Lukas Chavez
▴ 570 • written 10.8 years ago by
Jonathan Ellis
▴ 40
0
votes
7
replies
2.7k
views
GTF file error when using easyRNAseq�
Annotation
Organism
BSgenome
BSgenome
DESeq
easyRNASeq
Annotation
Organism
BSgenome
DESeq
updated 10.5 years ago by
delhomme@embl.de
★ 1.2k • written 10.5 years ago by
Guest User
★ 13k
3
votes
6
replies
2.6k
views
Assign genes to CpG islands
annotation
genomicranges
bsgenome
updated 8.6 years ago by
Ou, Jianhong
★ 1.3k • written 8.6 years ago by
José Luis Lavín
▴ 10
0
votes
17
replies
2.6k
views
problems with strand in predictCoding
VariantAnnotation
Annotation
BSgenome
BSgenome
VariantAnnotation
VariantAnnotation
BSgenome
updated 12.1 years ago by
bnorthoff@web.de
▴ 20 • written 12.1 years ago by
Jeremiah Degenhardt
▴ 50
0
votes
7
replies
2.6k
views
QuasR on Linux Cluster
BSgenome
BSgenome
QuasR
BSgenome
BSgenome
QuasR
updated 10.6 years ago by
Michael Stadler
▴ 350 • written 10.6 years ago by
Ugo Borello
▴ 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 11.2 years ago by
Dan Tenenbaum
★ 8.2k • written 11.2 years ago by
Wim Kreinen
▴ 100
0
votes
2
replies
2.6k
views
BSgenome forging -- not valid BSgenomeDataPkgSeed slots
bsgenome
9.4 years ago
qiwang1993
• 0
1
vote
7
replies
2.6k
views
Mapping Probes to a Genome
BSgenome
biostrings
probe mapping
updated 7.1 years ago by
holgerbrandl
▴ 10 • written 7.7 years ago by
Dario Strbenac
★ 1.5k
0
votes
13
replies
2.6k
views
forge BSgenome data package
BSgenome
Biostrings
BSgenome
BSgenome
Biostrings
BSgenome
updated 13.3 years ago by
Hervé Pagès
16k • written 13.4 years ago by
Steve Shen
▴ 330
2
votes
6
replies
2.5k
views
Working with Arabidopsis Databases
bsgenome
biomart
getPromoterSeq
txdb
8.8 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 9.7 years ago by
Robert Stojnic
▴ 80 • written 9.7 years ago by
deepti anand
▴ 50
6
votes
6
replies
2.5k
views
Memory-efficient method to calculate GC content of millions of GRanges
granges
biostrings
bsapply
BSgenome
updated 7.5 years ago by
Hervé Pagès
16k • written 7.5 years ago by
jma1991
▴ 70
1
vote
6
replies
2.4k
views
How to subset a BSgenome
BSgenome
BSgenome.Mmusculus.UCSC.mm10
updated 4.8 years ago by
shepherl
3.9k • written 4.8 years ago by
Aditya
▴ 160
0
votes
3
replies
2.4k
views
featureCounts segfault
Annotation
BSgenome
BSgenome
Rsubread
Annotation
BSgenome
BSgenome
Rsubread
updated 10.0 years ago by
Wei Shi
★ 3.6k • written 10.1 years ago by
Ryan C. Thompson
★ 7.9k
0
votes
6
replies
2.4k
views
Error while attempting to forge BSgenome data package
bsgenome
ggbio
updated 4.6 years ago by
serfraz.saad
• 0 • written 9.6 years ago by
pterry
• 0
0
votes
13
replies
2.4k
views
How to plot NGS data?
GO
BSgenome
geneplotter
PROcess
BSgenome
genomes
GO
BSgenome
geneplotter
PROcess
genomes
updated 12.3 years ago by
Martin Morgan
25k • written 12.3 years ago by
Bernd Jagla
▴ 30
2
votes
1
reply
2.4k
views
getSeq with GRanges object error: function not found
biostrings
bsgenome
granges
updated 9.7 years ago by
Martin Morgan
25k • written 9.7 years ago by
Miskey, Csaba
▴ 20
6
votes
3
replies
2.4k
views
News:
New Bioconductor package for dbSNP151
SNPlocs.Hsapiens.dbSNP151.GRCh38
BSgenome
News
5.9 years ago
Hervé Pagès
16k
0
votes
3
replies
2.3k
views
seqlevels in VCF objects
BSgenome
BSgenome
genomes
BSgenome
BSgenome
genomes
updated 11.4 years ago by
Valerie Obenchain
★ 6.8k • written 11.4 years ago by
Murat Tasan
▴ 70
0
votes
2
replies
2.3k
views
Coverage vs GC bias - how to?
Coverage
BSgenome
BSgenome
IRanges
Coverage
BSgenome
BSgenome
IRanges
updated 13.7 years ago by
Harris A. Jaffee
▴ 590 • written 13.7 years ago by
Marc Noguera
▴ 100
2
votes
5
replies
2.3k
views
Forge a BSgenome data package
bsgenome
bsgenome forge
7.3 years ago • updated 6.9 years ago
jodiera
• 0
0
votes
2
replies
2.3k
views
Biobase use problem
BSgenome
BSgenome
BSgenome
BSgenome
updated 12.7 years ago by
Sean Davis
21k • written 12.7 years ago by
Ram H. Sharma
▴ 30
0
votes
9
replies
2.3k
views
Restriction enzyme digestion
BSgenome
BSgenome
BSgenome
BSgenome
updated 16.0 years ago by
Hervé Pagès
16k • written 16.0 years ago by
Anh Tran
▴ 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 8.5 years ago by
Martin Morgan
25k • written 8.5 years ago by
dborgesrmit
• 0
0
votes
8
replies
2.2k
views
vmatchPDict?
BSgenome
probe
BSgenome
BSgenome
probe
BSgenome
updated 11.5 years ago by
Hervé Pagès
16k • written 11.5 years ago by
David Iles
▴ 130
0
votes
2
replies
2.2k
views
MT reference differences between hg19/GRCH37
BSgenome
BSgenome
BSgenome
BSgenome
11.2 years ago
Julian Gehring
★ 1.3k
3
votes
2
replies
2.2k
views
Forging a BSGenome
BSgenome
microtus
forging
updated 3.5 years ago by
Hervé Pagès
16k • written 3.5 years ago by
A.J.
▴ 20
0
votes
5
replies
2.2k
views
yieldSize and paired end data in SummarizeOverlaps error?
BSgenome
PROcess
BSgenome
ASSIGN
BSgenome
PROcess
BSgenome
ASSIGN
updated 11.2 years ago by
Valerie Obenchain
★ 6.8k • written 11.2 years ago by
Thomas Whisenant
▴ 10
0
votes
4
replies
2.2k
views
BSgenomes vs ENSEMBL
Transcription
Annotation
BSgenome
annotate
Biostrings
BSgenome
Transcription
Annotation
updated 15.6 years ago by
Hervé Pagès
16k • written 15.6 years ago by
Guido Hooiveld
★ 4.0k
0
votes
2
replies
2.2k
views
PWM matching using matchPWM in Biostrings
Transcription
BSgenome
Biostrings
BSgenome
Transcription
BSgenome
Biostrings
BSgenome
updated 15.0 years ago by
Patrick Aboyoun
★ 1.6k • written 15.0 years ago by
Kristoffer Rigbolt
▴ 10
0
votes
5
replies
2.1k
views
MEDIPS.createSet error
Alignment
BSgenome
BSgenome
MEDIPS
Alignment
BSgenome
BSgenome
MEDIPS
updated 10.2 years ago by
Lukas Chavez
▴ 570 • written 10.2 years ago by
Vining, Kelly
▴ 220
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 8.7 years ago by
James W. MacDonald
66k • written 8.7 years ago by
kylvalda
• 0
50 results • Page
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Recent ...
Replies
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2
by
BioinfGuru
▴ 30
I would use biomaRt. This is what happens when annotation occurs to early. If possible I would run the DEG analysis on the original output…
Comment: Volcano plot of scRNA-seq data not "centered"
by
ATpoint
★ 4.2k
My comment was generic. If your experiment causes drastic shifts then the situation might be different. The advise is the same: Try to use …
Comment: conumee with Infinium MethylationEPIC v2.0
by
Maximus
• 0
Hi Sole, If there is a combined mixture of MSet of 450K, EPIC and EPICv2, how should I create an annotation object? I tried to create anno…
Comment: Volcano plot of scRNA-seq data not "centered"
by
tjl
• 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Comment: Cannot install oligo on Fedora
by
James W. MacDonald
66k
Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…
Votes
A: Analyzing data without replicates using DiffBind
A: Analyzing data without replicates using DiffBind
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
DESeq2 swap ensembl gene id rownames with gene symbol column
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
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