Showing : GenomeInfoDb • reset
3
votes
8
replies
353
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 9 hours ago by ★ 3.4k • written 3 days ago by ▴ 20
1
vote
3
replies
796
views
Non-zero exit status error when installing GenomeInfoDbData
DECIPHER GenomeInfoDbData Bioconductor GenomeInfoDb
written 4 months ago by • 0
2
votes
4
replies
843
views
Help with infinite recursion - non-zero exit status in installation of GenomeInfoDbData
Install GenomeInfoDbData GenomeInfoDb
updated 7 months ago by 67k • written 7 months ago by ▴ 20
2
votes
4
replies
1.0k
views
seqlevelsStyle() not working
ensembldb genomei GenomeInfoDb
written 10 months ago by ▴ 70
0
votes
1
reply
1.5k
views
package ‘GenomeInfoDb’ could not be loaded
GenomeInfoDb GenomeInfoDbData
updated 22 months ago by ★ 4.6k • written 22 months ago by • 0
16
votes
10
replies
7.4k
views
Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
GenomeInfoDb
updated 22 months ago by 16k • written 3.2 years ago by ▴ 20
1
vote
3
replies
3.3k
views
Unable to GetGRangesFromEnsDb
single GenomeInfoDb
updated 24 months ago by • 0 • written 2.9 years ago by • 0
1
vote
5
replies
1.7k
views
Unable to load mm10 genome for use with GenomicDistributions package
GenomeInfoDb GenomeInfoDbData GenomicDistributionsData GenomicDistributions
2.5 years ago rashford • 0
0
votes
1
reply
1.6k
views
GenomeInfoDbData cannot install in R and warning had non-zero exit status
GenomeInfoDb
updated 2.8 years ago by 67k • written 2.8 years ago by • 0
1
vote
4
replies
1.4k
views
seqinfo got changed after `library(rtracklayer)`
rtracklayer GenomeInfoDb
3.0 years ago Ge Tan ▴ 20
3
votes
2
replies
1.3k
views
Please allow integers in `numeric` format in `seqlengths`
GenomeInfoDb
updated 3.1 years ago by 16k • written 3.1 years ago by ▴ 180
0
votes
3
replies
1.7k
views
Permanent error in installing GenomeInfoDb
GenomeInfoDb
3.1 years ago AZ ▴ 30
0
votes
2
replies
2.8k
views
GenomeInfoDb fails to install
zip GenomeInfoDb
updated 3.3 years ago by 700 • written 3.3 years ago by • 0
3
votes
2
replies
3.9k
views
Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m31) is not TRUE
GenomeInfoDb
updated 3.5 years ago by ▴ 20 • written 3.5 years ago by ▴ 10
0
votes
0
replies
1.2k
views
motifBreakR error with custom BSgenome
GenomeInfoDb motifbreakR
3.7 years ago • updated 3.6 years ago Chris Seidel ▴ 80
3
votes
4
replies
3.3k
views
R Error: package ‘GenomeInfoDb’ could not be loaded on MacBook
error mac DESeq2 GenomeInfoDb R
4.0 years ago • updated 3.9 years ago Dan ▴ 20
0
votes
2
replies
1.3k
views
Error in GenomeInfoDb:::makeNewSeqnames
GenomeInfoDb ggbio
3.9 years ago Konstantinos Yeles ▴ 80
0
votes
1
reply
719
views
RNA gene expression data retrieval for breast cancer subtypes
RNASeqData GenomeInfoDb
updated 4.1 years ago by ★ 4.0k • written 4.1 years ago by • 0
2
votes
2
replies
1.8k
views
How does one modify a single value of a field in a seqinfo object?
GenomicRanges GenomeInfoDb BSgenome isCircular
updated 4.1 years ago by 16k • written 4.2 years ago by ▴ 80
4
votes
3
replies
1.9k
views
OrganismDbi throws error for Oryza Sativa indica org.db preparation
GenomeInfoDb OrganismDbi biomaRt
updated 4.1 years ago by 67k • written 4.1 years ago by ▴ 20
1
vote
2
replies
1.4k
views
Error in csaw::windowCounts when using readParam
csaw GenomeInfoDb
updated 4.3 years ago by ★ 28k • written 4.3 years ago by ▴ 50
2
votes
3
replies
2.1k
views
Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
genomeinfodb hg19 ucsc seqlevel genomicfeatures
updated 4.7 years ago by 67k • written 4.7 years ago by ▴ 100
3
votes
5
replies
1.3k
views
Information on genomic sequences via Seqinfo failing
GenomeInfoDb
updated 4.7 years ago by 16k • written 4.7 years ago by ★ 4.3k
0
votes
7
replies
3.4k
views
Assembly report error for hg19 in GenomeInfoDb
software error GenomeInfoDb HTGTS Transloc-pipeline TranslocHotspots.R
updated 3.8 years ago by ▴ 130 • written 5.2 years ago by • 0
8
votes
11
replies
3.6k
views
GenomeInfoDb's Seqinfo() error on hg38
genomeinfodb
updated 5.9 years ago by 16k • written 5.9 years ago by 43k
0
votes
1
reply
2.0k
views
Issue using ballgown
software error ballgown genomeinfodbdata genomeinfodb
updated 6.3 years ago by 67k • written 6.3 years ago by • 0
7
votes
5
replies
2.1k
views
Strange error in bsseq when trying to assign seqinfo
bsseq genomeinfodb genomicranges seqinfo
written 6.6 years ago by ▴ 140
1
vote
1
reply
1.3k
views
seqnames versus chrom
BiocGen rtracklayer genomeinfodb
updated 6.9 years ago by ★ 11k • written 6.9 years ago by • 0
0
votes
3
replies
6.3k
views
Trouble installing DESeq / GenomeInfoDb
deseq2 genomeinfodb
updated 7.4 years ago by 67k • written 7.4 years ago by • 0
0
votes
1
reply
1.7k
views
errotr in genome infodb
software error roar bioconductor genomeinfodb
7.5 years ago praveenhcu131 • 0
0
votes
1
reply
1.4k
views
seqlevels/keepSeqLevels should set default pruning.mode by a getOption call
genomeinfodb
updated 7.6 years ago by 16k • written 7.6 years ago by ▴ 10
0
votes
1
reply
1.2k
views
GenomeInfoDb: where are the genome patches?
seqnames genomeinfodb
updated 7.6 years ago by 16k • written 7.6 years ago by ▴ 10
0
votes
2
replies
1.5k
views
seqlevelsStyle for chrY in Drosophila?
genomeinfodb dmel seqlevelsstyle
updated 7.6 years ago by ▴ 50 • written 7.6 years ago by ▴ 140
0
votes
7
replies
2.4k
views
regionMatrix for derfinder crashes with seqnames issue on non-human data
derfinder GenomeInfoDb GenomicRanges
7.6 years ago Wayne • 0
1
vote
3
replies
1.8k
views
GenomeInfoDb::Seqinfo() error 404 on the function
GenomeInfoDb Seqinfo 404 error
7.9 years ago bastien.herve • 0
5
votes
3
replies
3.5k
views
keepSeqlevels for GRangesList: drop elements with multiple seqnames
GenomeInfoDb keepSeqlevels
updated 8.1 years ago by ★ 6.8k • written 8.1 years ago by ▴ 40
4
votes
9
replies
5.0k
views
Is it possible to read bigwig files with rtracklayer over https? Comes down to GenomeInfoDb::seqinfo()
rtracklayer genomeinfodb
8.7 years ago • updated 8.6 years ago Leonardo Collado Torres ★ 1.1k
8
votes
7
replies
3.9k
views
Generating a proper TxDb instance from NCBI GFF Annotations File
ncbi refseq maketxdbfromgff fetchExtendedChromInfoFromUCSC genomeinfodb
updated 8.9 years ago by 16k • written 8.9 years ago by ▴ 10
2
votes
5
replies
1.9k
views
GenomeInfoDb::extractSeqlevelsByGroup() on 'Canis familiaris'
genomeinfodb canis familiaris
updated 9.1 years ago by 16k • written 9.1 years ago by ★ 3.4k
0
votes
0
replies
1.4k
views
'GenomeInfoDb' error in the cn.MOPS Package
cnv genomeinfodb
9.4 years ago voksdvoks • 0
6
votes
2
replies
5.7k
views
Get sequences for GRCh38 genome based on TxDb object locations
bsgenome genomeinfodb transcriptdb
updated 10.0 years ago by 16k • written 10.0 years ago by ▴ 760
0
votes
4
replies
1.9k
views
keepStandardChromosomes doesn't respect ordering
genomeinfodb
updated 10.2 years ago by ▴ 390 • written 10.2 years ago by 67k
0
votes
2
replies
2.0k
views
GenomeinfoDB
Mus musculus GenomeInfoDb Mus musculus GenomeInfoDb
updated 10.5 years ago by ▴ 390 • written 10.5 years ago by ★ 13k
43 results • Page 1 of 1
Recent ...
Replies
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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