Showing : Annotation • reset
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Bioconductor version cannot be validated
Bioconductor Annotation Ann
written 2.2 years ago by • 0
0
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5
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2.4k
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Aclust package: IlluminaHumanMethylation450kCHR37 not found
illuminahumanmethylation450k.db aclust methylation annotation illumina
written 9.3 years ago by • 0
1
vote
2
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1.1k
views
Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
annotation geneIDs flatheadmullet
updated 8 months ago by 68k • written 8 months ago by • 0
1
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1
reply
433
views
Merging annotation with differential expression output
annotation RNASeqData
updated 8 months ago by 68k • written 8 months ago by • 0
0
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2
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642
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Annotation package for Manduca sexta
annotation Manducasexta AnnotationData
8 months ago GA ▴ 10
1
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2
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1.9k
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help documentation for keytypes in annotationdbi packages
annotation
updated 9 months ago by ▴ 10 • written 5.1 years ago by • 0
0
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0
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409
views
Help with mouse cell type annotation
annotation SingleR mouse SingleCellData scRNAseq
9 months ago Muhammad • 0
0
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1
reply
456
views
affymetrix
genomes Annotation
updated 10 months ago by 68k • written 10 months ago by • 0
5
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13
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2.4k
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Installing annotation package in locally
AnnotationDbi AnnotationHub Annotation AnnotationForge
13 months ago KABILAN • 0
0
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1
reply
566
views
how do I convert an Ilumn IDREF to a CPG loci
AnnotationDbi Annotation annotation BiologicalQuestion
updated 14 months ago by 68k • written 14 months ago by • 0
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0
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666
views
Job: Ensembl Job Vacancies
genomes Annotation GenomicVariation ensembldb
15 months ago Aleena_Ensembl ▴ 30
1
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2
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1.2k
views
Struggling to convert a large list of non-model genes into human orthologs, any suggestions?
annotation
17 months ago ronin • 0
2
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2
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1.3k
views
Get gene symbols for a set of hg19 coordinates
annotation hg19
18 months ago pcantalupo ▴ 10
1
vote
6
replies
1.8k
views
unable to access Annotationhub latest record
DNAMethylation AnnotationHub EPICv2manifest annotation
updated 20 months ago by ▴ 230 • written 20 months ago by • 0
2
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2
replies
1.4k
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
written 20 months ago by ▴ 10
0
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0
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816
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
22 months ago nilanjanamani88 • 0
0
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5
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2.7k
views
Normalizing Affy Almac Xcel Array Data from CEL files
Annotation affy oligo ffpe Annotation affy oligo ffpe
written 11.9 years ago by ★ 13k
5
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11
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5.3k
views
How to annotate gene names for genomic coordinates?
annotation
written 10.5 years ago by • 0
0
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1
reply
1.1k
views
Create design matrix for differential methylation analysis
Annotation annotate DifferentialMethylation minfiDataEPIC
updated 2.2 years ago by ▴ 780 • written 2.2 years ago by • 0
1
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0
replies
1.6k
views
News: Bioconductor 3.18 db0s, OrgDbs, and TxDbs now available
db0 release Annotation
2.2 years ago kayla.interdonato ▴ 160
3
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4
replies
1.3k
views
Questions Trying to Re-create MicroArray Data (GSE97562) (Fig. 2)
MicroRNAArrayData GSE97562 pd.hugene.1.0.st.v1 Annotation
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
2
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4
replies
1.9k
views
Use with_go along with other filters in getBM function
Annotation biomaRt
2.5 years ago RuBBiT0 ▴ 10
0
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2
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1.7k
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How to find probe enhancer annotation for Illumina EPIC array?
IlluminaHumanMethylationEPICmanifest ChAMP annotation
updated 2.6 years ago by 68k • written 2.6 years ago by • 0
0
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4
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2.0k
views
BioCann repository index warning on Apple Silicon (Bioc 3.17 / R 4.3)
Annotation
2.6 years ago Michael Steinbaugh ▴ 90
0
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0
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1.2k
views
AnnotationDbi Error: PROSITE is defunct.
ChipDb AnnotationDbi Annotation
2.7 years ago ahiser • 0
0
votes
3
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1.4k
views
Annotated dendogram (tree) from tbl_graph
dendogram ggtreeExtra ggtree annotation Annotation
2.7 years ago christian.dina • 0
0
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0
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1.3k
views
News: Bioconductor 3.17 db0s, OrgDbs, and TxDbs now available
release db0 Annotation
2.7 years ago kayla.interdonato ▴ 160
2
votes
1
reply
1.0k
views
Doubts about manipulation and annotation of microarray files deposited at GEO
MicroarrayData Annotation GEOdata
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
0
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1
reply
1.6k
views
Create an Annotation DB file for a non-model organism
AnnotationDbi annotation ChIPseeker
updated 2.8 years ago by 68k • written 2.8 years ago by ▴ 50
3
votes
3
replies
2.2k
views
Is ther an annotation package for sheep (Ovis aries)
sheep database_package Annotation
updated 2.8 years ago by ★ 4.1k • written 2.9 years ago by ▴ 10
0
votes
1
reply
960
views
Bioconductor tool for curating annotations?
Annotation
updated 2.9 years ago by ▴ 760 • written 2.9 years ago by ▴ 180
3
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2
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3.6k
views
I cannot install annotables package in Rstudio (macOS)
DESeq2 PackageTypeData package Annotation
2.9 years ago m-bihie ▴ 10
1
vote
9
replies
2.3k
views
Is it possible to annotate a GRanges Object that has scaffolding names and not chromosome numbers?
Annotation
updated 2.9 years ago by 68k • written 2.9 years ago by • 0
0
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3
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1.5k
views
A look inside annotation packages
Annotation
3.0 years ago Ed Siefker ▴ 230
3
votes
2
replies
8.9k
views
How to convert Illumina HT_12_v4 annotation
convert R annotation microarray illumina human ht-12 v4
updated 3.0 years ago by ▴ 200 • written 8.0 years ago by • 0
2
votes
3
replies
3.1k
views
Packages dependent on rtracklayer fail: ERROR: lazy loading failed, unable to load shared object rtracklayer.so
SingleCellMultiModal ensembldb rtracklayer Annotation
updated 2.9 years ago by • 0 • written 3.0 years ago by ▴ 10
0
votes
5
replies
3.5k
views
Error when annotating ENSEMBLE transcript IDs from chicken annotation DB
R ensembldb Annotation
updated 3.2 years ago by ★ 4.1k • written 3.2 years ago by ▴ 30
0
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0
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1.3k
views
News: Bioconductor 3.16 db0s, OrgDbs and TxDbs now available
release db0 annotation
3.2 years ago kayla.interdonato ▴ 160
0
votes
1
reply
956
views
Annotation data packages for plant parasitic nematodes
AnnotationData Annotation
updated 3.2 years ago by 68k • written 3.2 years ago by • 0
1
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3
replies
3.3k
views
Trouble importing my own Gene Ontology Annotation into topGO
Annotation GeneOntology topGO GO
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 60
0
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1
reply
1.5k
views
News: Bioconductor 3.15 db0s, OrgDbs and TxDbs now available
annotation release db0
3.7 years ago • updated 3.6 years ago kayla.interdonato ▴ 160
0
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0
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1.0k
views
low mapping between annotated genome and transcriptome
transcriptome Annotation mapping
3.7 years ago Ava • 0
0
votes
1
reply
1.4k
views
peak annotation
ChIPpeakAnno Annotation
updated 3.6 years ago by ▴ 70 • written 3.7 years ago by ▴ 670
0
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0
replies
1.2k
views
using annotation data of an organism(eg. Oryza sativa) from AnnotationHub for mgoSim
AnnotationHubSoftware GOSemSim annotation
3.9 years ago Amandeep • 0
0
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1
reply
1.9k
views
SNP annotation
SNPRelate SNP GWASTools Annotation GWASdata
updated 3.9 years ago by ▴ 890 • written 4.0 years ago by • 0
0
votes
1
reply
2.1k
views
How to download annotation package for oryza sativa Japonica and Oryza sativa indica for pathway analysis?
reactomePA package annotation
updated 3.9 years ago by 4.2k • written 3.9 years ago by ▴ 20
0
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0
replies
1.1k
views
Is it possible to output ensembl id for annotatr build_annotations basicgenes?
Annotation annotatr
4.0 years ago Ahdee ▴ 60
0
votes
2
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3.4k
views
getBM error in the biomaRt R package
Annotation
updated 3.3 years ago by • 0 • written 4.0 years ago by • 0
0
votes
1
reply
1.5k
views
How to get Cytogenetic band for muscles gene by using Biomart or other tools in R
Annotation biomaRt ensembldb
written 4.1 years ago by • 0
0
votes
0
replies
1.4k
views
Error with getBM: 'The query to the BioMart webservice returned an invalid result.'
process annotationTools AnnotationFilter Annotation biomaRt
4.1 years ago Shane • 0
1,978 results • Page 1 of 40
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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…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
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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