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BSgenome
•
reset
0
votes
5
replies
9.0k
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 10.9 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 8.9 years ago by
Martin Morgan
25k • written 8.9 years ago by
nabaneeta85
• 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
2
replies
5.1k
views
Any tools to convert .gff to .gtf format
AnnotationData
CrispRdesignR
BSgenome
updated 20 months ago by
Malcolm Cook
★ 1.6k • written 20 months ago by
Manoj Kumar R
• 0
0
votes
5
replies
4.6k
views
Finding mismatches between reads and reference sequence
Infrastructure
Cancer
BSgenome
BSgenome
Infrastructure
Cancer
BSgenome
BSgenome
updated 11.1 years ago by
David Greber
▴ 30 • written 11.1 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 5.9 years ago by
James W. MacDonald
65k • written 5.9 years ago by
sophialovechan
▴ 10
5
votes
9
replies
3.8k
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 10.6 years ago by
James W. MacDonald
65k • written 10.6 years ago by
Guest User
★ 13k
0
votes
1
reply
3.5k
views
GRanges Constructor With seqlengths
BSgenome
BSgenome
BSgenome
BSgenome
11.9 years ago
Dario Strbenac
★ 1.5k
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
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
Hervé Pagès
16k • written 10.5 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 8.7 years ago by
ilari.scheinin
▴ 50 • written 8.7 years ago by
penington.j
• 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
Martin Morgan
25k • written 11.5 years ago by
Cei Abreu-Goodger
▴ 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
Hervé Pagès
16k • written 7.9 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
8.3 years ago
komal.rathi
▴ 120
0
votes
5
replies
2.9k
views
Biostrings::matchPattern,extract sequences
GO
BSgenome
BSgenome
GO
BSgenome
BSgenome
updated 10.6 years ago by
Hervé Pagès
16k • written 10.6 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 10.7 years ago by
Lukas Chavez
▴ 570 • written 10.7 years ago by
Jonathan Ellis
▴ 40
3
votes
6
replies
2.6k
views
Assign genes to CpG islands
annotation
genomicranges
bsgenome
updated 8.5 years ago by
Ou, Jianhong
★ 1.3k • written 8.5 years ago by
José Luis Lavín
▴ 10
0
votes
7
replies
2.6k
views
GTF file error when using easyRNAseq�
Annotation
Organism
BSgenome
BSgenome
DESeq
easyRNASeq
Annotation
Organism
BSgenome
DESeq
updated 10.5 years ago by
delhomme@embl.de
★ 1.2k • written 10.5 years ago by
Guest User
★ 13k
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
bnorthoff@web.de
▴ 20 • written 12.0 years ago by
Jeremiah Degenhardt
▴ 50
0
votes
7
replies
2.6k
views
QuasR on Linux Cluster
BSgenome
BSgenome
QuasR
BSgenome
BSgenome
QuasR
updated 10.5 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 11.1 years ago by
Dan Tenenbaum
★ 8.2k • written 11.1 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
2.5k
views
Mapping Probes to a Genome
BSgenome
biostrings
probe mapping
updated 7.0 years ago by
holgerbrandl
▴ 10 • written 7.7 years ago by
Dario Strbenac
★ 1.5k
0
votes
13
replies
2.5k
views
forge BSgenome data package
BSgenome
Biostrings
BSgenome
BSgenome
Biostrings
BSgenome
updated 13.3 years ago by
Hervé Pagès
16k • written 13.3 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
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 10.0 years ago by
Ryan C. Thompson
★ 7.9k
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
6
replies
2.4k
views
Error while attempting to forge BSgenome data package
bsgenome
ggbio
updated 4.5 years ago by
serfraz.saad
• 0 • written 9.5 years ago by
pterry
• 0
2
votes
1
reply
2.4k
views
getSeq with GRanges object error: function not found
biostrings
bsgenome
granges
updated 9.6 years ago by
Martin Morgan
25k • written 9.6 years ago by
Miskey, Csaba
▴ 20
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
Martin Morgan
25k • written 12.2 years ago by
Bernd Jagla
▴ 30
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
0
votes
3
replies
2.3k
views
seqlevels in VCF objects
BSgenome
BSgenome
genomes
BSgenome
BSgenome
genomes
updated 11.3 years ago by
Valerie Obenchain
★ 6.8k • written 11.3 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 13.6 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
7.2 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
Sean Davis
21k • written 12.6 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 11.4 years ago by
Hervé Pagès
16k • written 11.4 years ago by
David Iles
▴ 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
2.2k
views
yieldSize and paired end data in SummarizeOverlaps error?
BSgenome
PROcess
BSgenome
ASSIGN
BSgenome
PROcess
BSgenome
ASSIGN
updated 11.1 years ago by
Valerie Obenchain
★ 6.8k • written 11.2 years ago by
Thomas Whisenant
▴ 10
0
votes
4
replies
2.1k
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
★ 3.9k
0
votes
5
replies
2.1k
views
MEDIPS.createSet error
Alignment
BSgenome
BSgenome
MEDIPS
Alignment
BSgenome
BSgenome
MEDIPS
updated 10.1 years ago by
Lukas Chavez
▴ 570 • written 10.1 years ago by
Vining, Kelly
▴ 220
3
votes
2
replies
2.1k
views
Forging a BSGenome
BSgenome
microtus
forging
updated 3.4 years ago by
Hervé Pagès
16k • written 3.4 years ago by
A.J.
▴ 20
0
votes
2
replies
2.1k
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
1
vote
2
replies
2.1k
views
Finding mismatches between reads and reference sequence
bsgenome
cigar
alignment
updated 9.4 years ago by
Hervé Pagès
16k • written 9.4 years ago by
Stefanie Tauber
▴ 40
50 results • Page
1 of 1
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Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
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50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
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This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
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Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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