Showing : GenomeInfoDb • reset
0
votes
4
replies
1.6k
views
keepStandardChromosomes doesn't respect ordering
genomeinfodb
updated 9.5 years ago by ▴ 390 • written 9.5 years ago by 65k
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
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
1
vote
3
replies
2.5k
views
Unable to GetGRangesFromEnsDb
single GenomeInfoDb
updated 16 months ago by • 0 • written 2.3 years ago by • 0
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
3
replies
1.3k
views
Permanent error in installing GenomeInfoDb
GenomeInfoDb
2.4 years ago AZ ▴ 30
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 16k • written 8.3 years ago by ▴ 10
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 16k • written 2.5 years ago by ▴ 20
2
votes
3
replies
286
views
seqlevelsStyle() not working
ensembldb genomei GenomeInfoDb
10 weeks ago Kai Hu ▴ 70
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 16k • written 6.9 years ago by ▴ 10
0
votes
3
replies
5.9k
views
Trouble installing DESeq / GenomeInfoDb
deseq2 genomeinfodb
updated 6.7 years ago by 65k • written 6.7 years ago by • 0
1
vote
1
reply
1.1k
views
seqnames versus chrom
BiocGen rtracklayer genomeinfodb
updated 6.3 years ago by ★ 11k • written 6.3 years ago by • 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 ▴ 140
0
votes
1
reply
1.8k
views
Issue using ballgown
software error ballgown genomeinfodbdata genomeinfodb
updated 5.6 years ago by 65k • written 5.6 years ago by • 0
8
votes
11
replies
3.1k
views
GenomeInfoDb's Seqinfo() error on hg38
genomeinfodb
updated 5.2 years ago by 16k • written 5.2 years ago by 41k
1
vote
2
replies
1.1k
views
Error in csaw::windowCounts when using readParam
csaw GenomeInfoDb
updated 3.6 years ago by ★ 28k • written 3.7 years ago by ▴ 50
3
votes
5
replies
1.1k
views
Information on genomic sequences via Seqinfo failing
GenomeInfoDb
updated 4.1 years ago by 16k • written 4.1 years ago by ★ 4.3k
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 65k • written 4.1 years ago by ▴ 100
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 65k • written 3.5 years ago by ▴ 20
0
votes
2
replies
1.0k
views
Error in GenomeInfoDb:::makeNewSeqnames
GenomeInfoDb ggbio
3.3 years ago Konstantinos Yeles ▴ 80
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 16k • written 2.4 years ago by ▴ 180
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 ▴ 130 • written 4.6 years ago by • 0
0
votes
2
replies
1.8k
views
GenomeinfoDB
Mus musculus GenomeInfoDb Mus musculus GenomeInfoDb
updated 9.8 years ago by ▴ 390 • written 9.8 years ago by ★ 13k
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
2
votes
5
replies
1.6k
views
GenomeInfoDb::extractSeqlevelsByGroup() on 'Canis familiaris'
genomeinfodb canis familiaris
updated 8.5 years ago by 16k • written 8.5 years ago by ★ 3.3k
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
5
votes
3
replies
3.0k
views
keepSeqlevels for GRangesList: drop elements with multiple seqnames
GenomeInfoDb keepSeqlevels
updated 7.4 years ago by ★ 6.8k • written 7.5 years ago by ▴ 40
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
0
votes
2
replies
1.2k
views
seqlevelsStyle for chrY in Drosophila?
genomeinfodb dmel seqlevelsstyle
updated 6.9 years ago by ▴ 50 • written 6.9 years ago by ▴ 140
0
votes
1
reply
973
views
GenomeInfoDb: where are the genome patches?
seqnames genomeinfodb
updated 6.9 years ago by 16k • written 6.9 years ago by ▴ 10
0
votes
1
reply
691
views
package ‘GenomeInfoDb’ could not be loaded
GenomeInfoDb GenomeInfoDbData
updated 14 months ago by ★ 4.0k • written 14 months ago by • 0
0
votes
2
replies
2.1k
views
GenomeInfoDb fails to install
zip GenomeInfoDb
updated 2.7 years ago by 690 • written 2.7 years ago by • 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 ▴ 20 • written 2.8 years ago by ▴ 10
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 65k • written 2.1 years ago by • 0
0
votes
0
replies
877
views
motifBreakR error with custom BSgenome
GenomeInfoDb motifbreakR
3.0 years ago Chris Seidel ▴ 80
0
votes
0
replies
1.3k
views
'GenomeInfoDb' error in the cn.MOPS Package
cnv genomeinfodb
8.8 years ago voksdvoks • 0
0
votes
1
reply
581
views
RNA gene expression data retrieval for breast cancer subtypes
RNASeqData GenomeInfoDb
updated 3.4 years ago by ★ 3.9k • written 3.4 years ago by • 0
0
votes
1
reply
1.4k
views
errotr in genome infodb
software error roar bioconductor genomeinfodb
6.8 years ago praveenhcu131 • 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
40 results • Page 1 of 1
Recent ...
Replies
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq by Michael Love 41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Answer: Citation for edgeR user guide by Gordon Smyth 50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class? by James W. MacDonald 65k
What do you mean by 'the information'? Do you have things in particular that you want?
Comment: minfi::read.metharray.exp by clacarion • 0
I think its work with `read.metharray.sheet` ```r > sheet <- read.metharray.sheet("/Users/clarachretienneau/Desktop/clock_epigenetic/PJ120…
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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