Showing : GenomeInfoDb • reset
0
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GenomeInfoDbData cannot install in R and warning had non-zero exit status
GenomeInfoDb
updated 10 months ago by • 0 • written 3.8 years ago by • 0
4
votes
9
replies
3.0k
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 10 months ago by ★ 3.4k • written 12 months ago by ▴ 20
1
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3
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1.6k
views
Non-zero exit status error when installing GenomeInfoDbData
DECIPHER GenomeInfoDbData Bioconductor GenomeInfoDb
written 16 months ago by • 0
2
votes
4
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1.6k
views
Help with infinite recursion - non-zero exit status in installation of GenomeInfoDbData
Install GenomeInfoDbData GenomeInfoDb
updated 19 months ago by 68k • written 19 months ago by ▴ 20
2
votes
4
replies
1.7k
views
seqlevelsStyle() not working
ensembldb genomei GenomeInfoDb
written 22 months ago by ▴ 70
0
votes
1
reply
2.5k
views
package ‘GenomeInfoDb’ could not be loaded
GenomeInfoDb GenomeInfoDbData
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by • 0
16
votes
10
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8.2k
views
Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
GenomeInfoDb
updated 2.9 years ago by 16k • written 4.2 years ago by ▴ 20
1
vote
3
replies
4.2k
views
Unable to GetGRangesFromEnsDb
single GenomeInfoDb
updated 3.0 years ago by • 0 • written 3.9 years ago by • 0
1
vote
5
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2.2k
views
Unable to load mm10 genome for use with GenomicDistributions package
GenomeInfoDb GenomeInfoDbData GenomicDistributionsData GenomicDistributions
3.5 years ago rashford • 0
1
vote
4
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1.8k
views
seqinfo got changed after `library(rtracklayer)`
rtracklayer GenomeInfoDb
4.0 years ago Ge Tan ▴ 20
3
votes
2
replies
1.7k
views
Please allow integers in `numeric` format in `seqlengths`
GenomeInfoDb
updated 4.0 years ago by 16k • written 4.1 years ago by ▴ 180
0
votes
3
replies
2.2k
views
Permanent error in installing GenomeInfoDb
GenomeInfoDb
4.1 years ago AZ ▴ 30
0
votes
2
replies
3.4k
views
GenomeInfoDb fails to install
zip GenomeInfoDb
updated 4.3 years ago by 700 • written 4.3 years ago by • 0
3
votes
2
replies
4.2k
views
Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m31) is not TRUE
GenomeInfoDb
updated 4.4 years ago by ▴ 20 • written 4.5 years ago by ▴ 10
7
votes
5
replies
2.6k
views
Strange error in bsseq when trying to assign seqinfo
bsseq genomeinfodb genomicranges seqinfo
written 7.6 years ago by ▴ 140
0
votes
0
replies
1.5k
views
motifBreakR error with custom BSgenome
GenomeInfoDb motifbreakR
4.7 years ago • updated 4.6 years ago Chris Seidel ▴ 80
0
votes
7
replies
4.1k
views
Assembly report error for hg19 in GenomeInfoDb
software error GenomeInfoDb HTGTS Transloc-pipeline TranslocHotspots.R
updated 4.7 years ago by ▴ 130 • written 6.2 years ago by • 0
3
votes
4
replies
3.8k
views
R Error: package ‘GenomeInfoDb’ could not be loaded on MacBook
error mac DESeq2 GenomeInfoDb R
5.0 years ago • updated 4.9 years ago Dan ▴ 20
0
votes
2
replies
1.7k
views
Error in GenomeInfoDb:::makeNewSeqnames
GenomeInfoDb ggbio
4.9 years ago Konstantinos Yeles ▴ 90
0
votes
1
reply
907
views
RNA gene expression data retrieval for breast cancer subtypes
RNASeqData GenomeInfoDb
updated 5.1 years ago by ★ 4.0k • written 5.1 years ago by • 0
2
votes
2
replies
2.2k
views
How does one modify a single value of a field in a seqinfo object?
GenomicRanges GenomeInfoDb BSgenome isCircular
updated 5.1 years ago by 16k • written 5.2 years ago by ▴ 80
4
votes
3
replies
2.3k
views
OrganismDbi throws error for Oryza Sativa indica org.db preparation
GenomeInfoDb OrganismDbi biomaRt
updated 5.1 years ago by 68k • written 5.1 years ago by ▴ 20
1
vote
2
replies
1.7k
views
Error in csaw::windowCounts when using readParam
csaw GenomeInfoDb
updated 5.3 years ago by ★ 29k • written 5.3 years ago by ▴ 50
2
votes
3
replies
2.5k
views
Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
genomeinfodb hg19 ucsc seqlevel genomicfeatures
updated 5.7 years ago by 68k • written 5.7 years ago by ▴ 100
3
votes
5
replies
1.7k
views
Information on genomic sequences via Seqinfo failing
GenomeInfoDb
updated 5.7 years ago by 16k • written 5.7 years ago by ★ 4.3k
8
votes
11
replies
4.2k
views
GenomeInfoDb's Seqinfo() error on hg38
genomeinfodb
updated 6.8 years ago by 16k • written 6.8 years ago by 43k
0
votes
1
reply
2.3k
views
Issue using ballgown
software error ballgown genomeinfodbdata genomeinfodb
updated 7.2 years ago by 68k • written 7.2 years ago by • 0
1
vote
1
reply
1.5k
views
seqnames versus chrom
BiocGen rtracklayer genomeinfodb
updated 7.9 years ago by ★ 11k • written 7.9 years ago by • 0
0
votes
3
replies
6.6k
views
Trouble installing DESeq / GenomeInfoDb
deseq2 genomeinfodb
updated 8.4 years ago by 68k • written 8.4 years ago by • 0
0
votes
1
reply
2.0k
views
errotr in genome infodb
software error roar bioconductor genomeinfodb
8.4 years ago praveenhcu131 • 0
0
votes
1
reply
1.7k
views
seqlevels/keepSeqLevels should set default pruning.mode by a getOption call
genomeinfodb
updated 8.5 years ago by 16k • written 8.5 years ago by ▴ 10
0
votes
1
reply
1.4k
views
GenomeInfoDb: where are the genome patches?
seqnames genomeinfodb
updated 8.6 years ago by 16k • written 8.6 years ago by ▴ 10
0
votes
2
replies
1.7k
views
seqlevelsStyle for chrY in Drosophila?
genomeinfodb dmel seqlevelsstyle
updated 8.6 years ago by ▴ 50 • written 8.6 years ago by ▴ 140
0
votes
7
replies
3.0k
views
regionMatrix for derfinder crashes with seqnames issue on non-human data
derfinder GenomeInfoDb GenomicRanges
8.6 years ago Wayne • 0
1
vote
3
replies
2.0k
views
GenomeInfoDb::Seqinfo() error 404 on the function
GenomeInfoDb Seqinfo 404 error
8.9 years ago bastien.herve • 0
5
votes
3
replies
4.0k
views
keepSeqlevels for GRangesList: drop elements with multiple seqnames
GenomeInfoDb keepSeqlevels
updated 9.1 years ago by ★ 6.8k • written 9.1 years ago by ▴ 40
4
votes
9
replies
5.7k
views
Is it possible to read bigwig files with rtracklayer over https? Comes down to GenomeInfoDb::seqinfo()
rtracklayer genomeinfodb
9.6 years ago Leonardo Collado Torres ★ 1.1k
8
votes
7
replies
4.7k
views
Generating a proper TxDb instance from NCBI GFF Annotations File
ncbi refseq maketxdbfromgff fetchExtendedChromInfoFromUCSC genomeinfodb
updated 9.9 years ago by 16k • written 9.9 years ago by ▴ 10
2
votes
5
replies
2.2k
views
GenomeInfoDb::extractSeqlevelsByGroup() on 'Canis familiaris'
genomeinfodb canis familiaris
updated 10.1 years ago by 16k • written 10.1 years ago by ★ 3.4k
0
votes
0
replies
1.6k
views
'GenomeInfoDb' error in the cn.MOPS Package
cnv genomeinfodb
10.4 years ago voksdvoks • 0
6
votes
2
replies
6.4k
views
Get sequences for GRCh38 genome based on TxDb object locations
bsgenome genomeinfodb transcriptdb
updated 11.0 years ago by 16k • written 11.0 years ago by ▴ 760
0
votes
4
replies
2.2k
views
keepStandardChromosomes doesn't respect ordering
genomeinfodb
updated 11.2 years ago by ▴ 390 • written 11.2 years ago by 68k
0
votes
2
replies
2.3k
views
GenomeinfoDB
Mus musculus GenomeInfoDb Mus musculus GenomeInfoDb
updated 11.5 years ago by ▴ 390 • written 11.5 years ago by ★ 13k
43 results • Page 1 of 1
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Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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