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Showing :
GenomeInfoDb
•
reset
2
votes
3
replies
287
views
seqlevelsStyle() not working
ensembldb
genomei
GenomeInfoDb
10 weeks ago
Kai Hu
▴ 70
0
votes
1
reply
693
views
package ‘GenomeInfoDb’ could not be loaded
GenomeInfoDb
GenomeInfoDbData
updated 14 months ago by
ATpoint
★ 4.0k • written 14 months ago by
exferin
• 0
16
votes
10
replies
6.6k
views
Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
GenomeInfoDb
updated 14 months ago by
Hervé Pagès
16k • written 2.5 years ago by
sarah.howles
▴ 20
1
vote
3
replies
2.5k
views
Unable to GetGRangesFromEnsDb
single
GenomeInfoDb
updated 16 months ago by
Yichao
• 0 • written 2.3 years ago by
Francesco Monticolo
• 0
1
vote
5
replies
1.3k
views
Unable to load mm10 genome for use with GenomicDistributions package
GenomeInfoDb
GenomeInfoDbData
GenomicDistributionsData
GenomicDistributions
22 months ago
rashford
• 0
0
votes
1
reply
1.2k
views
GenomeInfoDbData cannot install in R and warning had non-zero exit status
GenomeInfoDb
updated 2.1 years ago by
James W. MacDonald
65k • written 2.1 years ago by
yt_lei1998
• 0
1
vote
4
replies
1.1k
views
seqinfo got changed after `library(rtracklayer)`
rtracklayer
GenomeInfoDb
2.4 years ago
Ge Tan
▴ 20
3
votes
2
replies
1.1k
views
Please allow integers in `numeric` format in `seqlengths`
GenomeInfoDb
updated 2.4 years ago by
Hervé Pagès
16k • written 2.4 years ago by
Charles Plessy
▴ 180
0
votes
3
replies
1.3k
views
Permanent error in installing GenomeInfoDb
GenomeInfoDb
2.4 years ago
AZ
▴ 30
0
votes
2
replies
2.1k
views
GenomeInfoDb fails to install
zip
GenomeInfoDb
updated 2.7 years ago by
Marcel Ramos
690 • written 2.7 years ago by
David
• 0
3
votes
2
replies
3.6k
views
Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m31) is not TRUE
GenomeInfoDb
updated 2.8 years ago by
Rob Syme
▴ 20 • written 2.8 years ago by
jason.ossart
▴ 10
0
votes
0
replies
877
views
motifBreakR error with custom BSgenome
GenomeInfoDb
motifbreakR
3.0 years ago
Chris Seidel
▴ 80
3
votes
4
replies
2.8k
views
R Error: package ‘GenomeInfoDb’ could not be loaded on MacBook
error
mac
DESeq2
GenomeInfoDb
R
3.3 years ago • updated 3.2 years ago
Dan
▴ 20
0
votes
2
replies
1.0k
views
Error in GenomeInfoDb:::makeNewSeqnames
GenomeInfoDb
ggbio
3.3 years ago
Konstantinos Yeles
▴ 80
0
votes
1
reply
581
views
RNA gene expression data retrieval for breast cancer subtypes
RNASeqData
GenomeInfoDb
updated 3.4 years ago by
Kevin Blighe
★ 3.9k • written 3.4 years ago by
G.G.H.T.
• 0
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
Hervé Pagès
16k • written 3.6 years ago by
Chris Seidel
▴ 80
4
votes
3
replies
1.4k
views
OrganismDbi throws error for Oryza Sativa indica org.db preparation
GenomeInfoDb
OrganismDbi
biomaRt
updated 3.5 years ago by
James W. MacDonald
65k • written 3.5 years ago by
rohitsatyam102
▴ 20
1
vote
2
replies
1.1k
views
Error in csaw::windowCounts when using readParam
csaw
GenomeInfoDb
updated 3.6 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
RichardJActon
▴ 50
2
votes
3
replies
1.7k
views
Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
genomeinfodb
hg19
ucsc
seqlevel
genomicfeatures
updated 4.1 years ago by
James W. MacDonald
65k • written 4.1 years ago by
foehn
▴ 100
3
votes
5
replies
1.1k
views
Information on genomic sequences via Seqinfo failing
GenomeInfoDb
updated 4.1 years ago by
Hervé Pagès
16k • written 4.1 years ago by
Benilton Carvalho
★ 4.3k
0
votes
7
replies
2.8k
views
Assembly report error for hg19 in GenomeInfoDb
software error
GenomeInfoDb
HTGTS
Transloc-pipeline
TranslocHotspots.R
updated 3.1 years ago by
markus.riester
▴ 130 • written 4.6 years ago by
roshniroy16
• 0
8
votes
11
replies
3.1k
views
GenomeInfoDb's Seqinfo() error on hg38
genomeinfodb
updated 5.2 years ago by
Hervé Pagès
16k • written 5.2 years ago by
Michael Love
41k
0
votes
1
reply
1.8k
views
Issue using ballgown
software error
ballgown
genomeinfodbdata
genomeinfodb
updated 5.6 years ago by
James W. MacDonald
65k • written 5.6 years ago by
dualeahmed
• 0
7
votes
5
replies
1.8k
views
Strange error in bsseq when trying to assign seqinfo
bsseq
genomeinfodb
genomicranges
seqinfo
written 5.9 years ago by
rcavalca
▴ 140
1
vote
1
reply
1.1k
views
seqnames versus chrom
BiocGen
rtracklayer
genomeinfodb
updated 6.3 years ago by
Michael Lawrence
★ 11k • written 6.3 years ago by
felix.ernst
• 0
0
votes
3
replies
5.9k
views
Trouble installing DESeq / GenomeInfoDb
deseq2
genomeinfodb
updated 6.7 years ago by
James W. MacDonald
65k • written 6.7 years ago by
nathan.medd
• 0
0
votes
1
reply
1.4k
views
errotr in genome infodb
software error
roar
bioconductor
genomeinfodb
6.8 years ago
praveenhcu131
• 0
0
votes
1
reply
1.1k
views
seqlevels/keepSeqLevels should set default pruning.mode by a getOption call
genomeinfodb
updated 6.9 years ago by
Hervé Pagès
16k • written 6.9 years ago by
matt.chambers42
▴ 10
0
votes
1
reply
975
views
GenomeInfoDb: where are the genome patches?
seqnames
genomeinfodb
updated 6.9 years ago by
Hervé Pagès
16k • written 6.9 years ago by
matt.chambers42
▴ 10
0
votes
2
replies
1.2k
views
seqlevelsStyle for chrY in Drosophila?
genomeinfodb
dmel
seqlevelsstyle
updated 6.9 years ago by
daniel.vantwisk
▴ 50 • written 6.9 years ago by
liz.ingsimmons
▴ 140
0
votes
7
replies
2.0k
views
regionMatrix for derfinder crashes with seqnames issue on non-human data
derfinder
GenomeInfoDb
GenomicRanges
7.0 years ago
Wayne
• 0
1
vote
3
replies
1.5k
views
GenomeInfoDb::Seqinfo() error 404 on the function
GenomeInfoDb
Seqinfo
404 error
7.2 years ago
bastien.herve
• 0
5
votes
3
replies
3.0k
views
keepSeqlevels for GRangesList: drop elements with multiple seqnames
GenomeInfoDb
keepSeqlevels
updated 7.4 years ago by
Valerie Obenchain
★ 6.8k • written 7.5 years ago by
Chao-Jen Wong
▴ 40
4
votes
9
replies
4.4k
views
Is it possible to read bigwig files with rtracklayer over https? Comes down to GenomeInfoDb::seqinfo()
rtracklayer
genomeinfodb
8.0 years ago
Leonardo Collado Torres
★ 1.0k
8
votes
7
replies
3.4k
views
Generating a proper TxDb instance from NCBI GFF Annotations File
ncbi
refseq
maketxdbfromgff
fetchExtendedChromInfoFromUCSC
genomeinfodb
updated 8.3 years ago by
Hervé Pagès
16k • written 8.3 years ago by
gokcen.eraslan
▴ 10
2
votes
5
replies
1.6k
views
GenomeInfoDb::extractSeqlevelsByGroup() on 'Canis familiaris'
genomeinfodb
canis familiaris
updated 8.5 years ago by
Hervé Pagès
16k • written 8.5 years ago by
Robert Castelo
★ 3.3k
0
votes
0
replies
1.3k
views
'GenomeInfoDb' error in the cn.MOPS Package
cnv
genomeinfodb
8.8 years ago
voksdvoks
• 0
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
Hervé Pagès
16k • written 9.4 years ago by
Diego Diez
▴ 760
0
votes
4
replies
1.6k
views
keepStandardChromosomes doesn't respect ordering
genomeinfodb
updated 9.5 years ago by
Sonali Arora
▴ 390 • written 9.5 years ago by
James W. MacDonald
65k
0
votes
2
replies
1.8k
views
GenomeinfoDB
Mus musculus
GenomeInfoDb
Mus musculus
GenomeInfoDb
updated 9.8 years ago by
Sonali Arora
▴ 390 • written 9.8 years ago by
Guest User
★ 13k
40 results • Page
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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…
Comment: Different Shrunk Log2FC according with reference
by
andrebolerbarros
▴ 20
Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge
by
ATpoint
★ 4.0k
The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…
Answer: Different Shrunk Log2FC according with reference
by
ATpoint
★ 4.0k
Please see: https://support.bioconductor.org/p/p134551/ I asked basically the same before. In short, reference level might have an influ…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
Gayatri
• 0
What I meant is even after deleting the NCBI.sqlite file, and re-running the script, an empty NCBI.sqlite file (0 kb) is created which is c…
Votes
Subset DEXSeqDataSet In DEXSeq
How to get all possible comparisons in DiffBind
Comment: get BM error
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
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