Showing : genomeinfodb • reset
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
16
votes
10
replies
6.7k
views
Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
GenomeInfoDb
updated 15 months ago by 16k • written 2.5 years ago by ▴ 20
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
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
8
votes
7
replies
3.5k
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
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
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
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
2
votes
5
replies
1.7k
views
GenomeInfoDb::extractSeqlevelsByGroup() on 'Canis familiaris'
genomeinfodb canis familiaris
updated 8.5 years ago by 16k • written 8.5 years ago by ★ 3.3k
7
votes
5
replies
1.8k
views
Strange error in bsseq when trying to assign seqinfo
bsseq genomeinfodb genomicranges seqinfo
written 6.0 years ago by ▴ 140
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
3
votes
4
replies
2.9k
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
1
vote
4
replies
1.1k
views
seqinfo got changed after `library(rtracklayer)`
rtracklayer GenomeInfoDb
2.4 years ago Ge Tan ▴ 20
2
votes
3
replies
312
views
seqlevelsStyle() not working
ensembldb genomei GenomeInfoDb
12 weeks ago Kai Hu ▴ 70
5
votes
3
replies
3.0k
views
keepSeqlevels for GRangesList: drop elements with multiple seqnames
GenomeInfoDb keepSeqlevels
updated 7.5 years ago by ★ 6.8k • written 7.5 years ago by ▴ 40
1
vote
3
replies
1.5k
views
GenomeInfoDb::Seqinfo() error 404 on the function
GenomeInfoDb Seqinfo 404 error
7.3 years ago • updated 7.2 years ago bastien.herve • 0
0
votes
3
replies
5.9k
views
Trouble installing DESeq / GenomeInfoDb
deseq2 genomeinfodb
updated 6.8 years ago by 65k • written 6.8 years ago by • 0
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
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
0
votes
3
replies
1.3k
views
Permanent error in installing GenomeInfoDb
GenomeInfoDb
2.5 years ago • updated 2.4 years ago AZ ▴ 30
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
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 3.5 years ago by 16k • written 3.6 years ago by ▴ 80
1
vote
2
replies
1.2k
views
Error in csaw::windowCounts when using readParam
csaw GenomeInfoDb
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 50
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
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
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
2
replies
1.0k
views
Error in GenomeInfoDb:::makeNewSeqnames
GenomeInfoDb ggbio
3.3 years ago Konstantinos Yeles ▴ 80
0
votes
2
replies
2.2k
views
GenomeInfoDb fails to install
zip GenomeInfoDb
updated 2.7 years ago by 690 • written 2.7 years ago by • 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 16k • written 9.4 years ago by ▴ 760
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
1
reply
588
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
1.2k
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
1
reply
717
views
package ‘GenomeInfoDb’ could not be loaded
GenomeInfoDb GenomeInfoDbData
updated 14 months ago by ★ 4.1k • written 14 months 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
0
votes
1
reply
980
views
GenomeInfoDb: where are the genome patches?
seqnames genomeinfodb
updated 6.9 years ago by 16k • written 6.9 years ago by ▴ 10
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
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
0
votes
0
replies
1.3k
views
'GenomeInfoDb' error in the cn.MOPS Package
cnv genomeinfodb
8.8 years ago voksdvoks • 0
0
votes
0
replies
888
views
motifBreakR error with custom BSgenome
GenomeInfoDb motifbreakR
3.0 years ago Chris Seidel ▴ 80
40 results • Page 1 of 1
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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 by Gordon Smyth 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? by James W. MacDonald 65k
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!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
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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