Showing : GenomeInfoDb • reset
16
votes
10
replies
6.6k
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
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
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
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
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
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
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
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
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
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
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
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
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
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
2
votes
3
replies
296
views
seqlevelsStyle() not working
ensembldb genomei GenomeInfoDb
11 weeks ago Kai Hu ▴ 70
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
1
vote
2
replies
1.1k
views
Error in csaw::windowCounts when using readParam
csaw GenomeInfoDb
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 50
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
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
1
vote
4
replies
1.1k
views
seqinfo got changed after `library(rtracklayer)`
rtracklayer GenomeInfoDb
2.4 years ago Ge Tan ▴ 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
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
1.4k
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 16k • written 6.9 years ago by ▴ 10
0
votes
1
reply
976
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
584
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
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
3
replies
1.3k
views
Permanent error in installing GenomeInfoDb
GenomeInfoDb
2.4 years ago AZ ▴ 30
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
0
replies
1.3k
views
'GenomeInfoDb' error in the cn.MOPS Package
cnv genomeinfodb
8.8 years ago voksdvoks • 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
701
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
1.8k
views
GenomeinfoDB
Mus musculus GenomeInfoDb Mus musculus GenomeInfoDb
updated 9.8 years ago by ▴ 390 • written 9.8 years ago by ★ 13k
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
0
votes
0
replies
881
views
motifBreakR error with custom BSgenome
GenomeInfoDb motifbreakR
3.0 years ago Chris Seidel ▴ 80
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
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
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
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
40 results • Page 1 of 1
Recent ...
Replies
Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123 by Gordon Smyth 50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Votes
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
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