Showing : Annotation • reset
0
votes
6
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332
views
unable to access Annotationhub latest record
DNAMethylation AnnotationHub EPICv2manifest annotation
updated 22 days ago by ▴ 180 • written 4 weeks ago by • 0
2
votes
1
reply
211
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 5 weeks ago by ★ 3.9k • written 6 weeks ago by ▴ 10
0
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0
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169
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
12 weeks ago nilanjanamani88 • 0
0
votes
1
reply
460
views
Create design matrix for differential methylation analysis
Annotation annotate DifferentialMethylation minfiDataEPIC
updated 7 months ago by ▴ 780 • written 7 months ago by • 0
1
vote
0
replies
396
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News: Bioconductor 3.18 db0s, OrgDbs, and TxDbs now available
db0 release Annotation
7 months ago kayla.interdonato ▴ 160
0
votes
1
reply
3.5k
views
Bioconductor version cannot be validated
Bioconductor Annotation Ann
updated 7 months ago by 65k • written 7 months ago by • 0
3
votes
4
replies
673
views
Questions Trying to Re-create MicroArray Data (GSE97562) (Fig. 2)
MicroRNAArrayData GSE97562 pd.hugene.1.0.st.v1 Annotation
updated 9 months ago by 65k • written 9 months ago by • 0
2
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4
replies
934
views
Use with_go along with other filters in getBM function
Annotation biomaRt
11 months ago RuBBiT0 ▴ 10
0
votes
2
replies
710
views
How to find probe enhancer annotation for Illumina EPIC array?
IlluminaHumanMethylationEPICmanifest ChAMP annotation
updated 11 months ago by 65k • written 11 months ago by • 0
0
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4
replies
1.2k
views
BioCann repository index warning on Apple Silicon (Bioc 3.17 / R 4.3)
Annotation
11 months ago Michael Steinbaugh ▴ 90
0
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0
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516
views
AnnotationDbi Error: PROSITE is defunct.
ChipDb AnnotationDbi Annotation
13 months ago ahiser • 0
0
votes
3
replies
722
views
Annotated dendogram (tree) from tbl_graph
dendogram ggtreeExtra ggtree annotation Annotation
13 months ago christian.dina • 0
0
votes
0
replies
653
views
News: Bioconductor 3.17 db0s, OrgDbs, and TxDbs now available
release db0 Annotation
13 months ago kayla.interdonato ▴ 160
2
votes
1
reply
535
views
Doubts about manipulation and annotation of microarray files deposited at GEO
MicroarrayData Annotation GEOdata
updated 15 months ago by 65k • written 15 months ago by • 0
0
votes
1
reply
818
views
Create an Annotation DB file for a non-model organism
AnnotationDbi annotation ChIPseeker
updated 15 months ago by 65k • written 15 months ago by ▴ 50
3
votes
3
replies
1.1k
views
Is ther an annotation package for sheep (Ovis aries)
sheep database_package Annotation
updated 15 months ago by ★ 3.9k • written 15 months ago by ▴ 10
0
votes
1
reply
536
views
Bioconductor tool for curating annotations?
Annotation
updated 15 months ago by ▴ 730 • written 15 months ago by ▴ 180
3
votes
2
replies
2.1k
views
I cannot install annotables package in Rstudio (macOS)
DESeq2 PackageTypeData package Annotation
15 months ago m-bihie ▴ 10
1
vote
9
replies
1.3k
views
Is it possible to annotate a GRanges Object that has scaffolding names and not chromosome numbers?
Annotation
updated 15 months ago by 65k • written 15 months ago by • 0
0
votes
3
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890
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A look inside annotation packages
Annotation
17 months ago • updated 16 months ago Ed Siefker ▴ 230
2
votes
3
replies
1.7k
views
Packages dependent on rtracklayer fail: ERROR: lazy loading failed, unable to load shared object rtracklayer.so
SingleCellMultiModal ensembldb rtracklayer Annotation
updated 15 months ago by • 0 • written 17 months ago by ▴ 10
0
votes
5
replies
2.0k
views
Error when annotating ENSEMBLE transcript IDs from chicken annotation DB
R ensembldb Annotation
updated 18 months ago by ★ 3.9k • written 19 months ago by ▴ 30
0
votes
0
replies
632
views
News: Bioconductor 3.16 db0s, OrgDbs and TxDbs now available
release db0 annotation
19 months ago kayla.interdonato ▴ 160
0
votes
1
reply
601
views
Annotation data packages for plant parasitic nematodes
AnnotationData Annotation
updated 19 months ago by 65k • written 19 months ago by • 0
1
vote
3
replies
1.6k
views
Trouble importing my own Gene Ontology Annotation into topGO
Annotation GeneOntology topGO GO
updated 22 months ago by 65k • written 22 months ago by ▴ 60
0
votes
1
reply
804
views
News: Bioconductor 3.15 db0s, OrgDbs and TxDbs now available
annotation release db0
2.1 years ago • updated 2.0 years ago kayla.interdonato ▴ 160
0
votes
0
replies
613
views
low mapping between annotated genome and transcriptome
transcriptome Annotation mapping
2.1 years ago Ava • 0
0
votes
1
reply
796
views
peak annotation
ChIPpeakAnno Annotation
updated 2.0 years ago by ▴ 70 • written 2.1 years ago by ▴ 670
0
votes
0
replies
680
views
using annotation data of an organism(eg. Oryza sativa) from AnnotationHub for mgoSim
AnnotationHubSoftware GOSemSim annotation
2.3 years ago Amandeep • 0
0
votes
1
reply
1.3k
views
How to download annotation package for oryza sativa Japonica and Oryza sativa indica for pathway analysis?
reactomePA package annotation
updated 2.3 years ago by 3.9k • written 2.3 years ago by ▴ 20
0
votes
0
replies
708
views
Is it possible to output ensembl id for annotatr build_annotations basicgenes?
Annotation annotatr
2.4 years ago Ahdee ▴ 50
0
votes
1
reply
1.1k
views
SNP annotation
SNPRelate SNP GWASTools Annotation GWASdata
updated 2.3 years ago by ▴ 870 • written 2.4 years ago by • 0
0
votes
2
replies
1.8k
views
getBM error in the biomaRt R package
Annotation
updated 20 months ago by • 0 • written 2.4 years ago by • 0
0
votes
1
reply
962
views
How to get Cytogenetic band for muscles gene by using Biomart or other tools in R
Annotation biomaRt ensembldb
written 2.5 years ago by • 0
0
votes
0
replies
791
views
Error with getBM: 'The query to the BioMart webservice returned an invalid result.'
process annotationTools AnnotationFilter Annotation biomaRt
2.5 years ago Shane • 0
0
votes
1
reply
846
views
Issue with annotation package mouse4302.db
mouse4302.db annotation
updated 2.5 years ago by 65k • written 2.5 years ago by • 0
0
votes
1
reply
705
views
anotacion para Anopheles Albimanus
anopheles_albimanus Annotation
updated 2.6 years ago by 3.9k • written 2.6 years ago by • 0
3
votes
1
reply
2.2k
views
Converting between UCSC id and gene symbol with bioconductor annotation resources
AnnotationData AnnotationDbi annotation
updated 2.6 years ago by 65k • written 2.6 years ago by • 0
1
vote
1
reply
2.0k
views
ComplexHeatmap: Not able to change the annotations size of the heatmap
ComplexHeatmap Anno Annotation
updated 2.7 years ago by ▴ 260 • written 2.7 years ago by ▴ 10
1
vote
2
replies
2.6k
views
mapping mouse ENSEMBL ids to human gene symbol
Annotation AnnotationDbi annotate
updated 2.8 years ago by 65k • written 2.8 years ago by • 0
5
votes
10
replies
2.1k
views
How to do annotation with Limma
annotation limma
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by • 0
1
vote
2
replies
1.5k
views
trouble with ENSEMBL ids for Org.Ss.eg.db
Annotation org.Ss.eg.db AnnotationDbi
2.9 years ago carine.genet • 0
3
votes
9
replies
5.2k
views
LOC gene IDs for characterised genes in annotation files
Annotation RNAseq
updated 2.3 years ago by • 0 • written 3.0 years ago by • 0
1
vote
0
replies
828
views
News: Bioconductor 3.13 db0s, OrgDbs and TxDbs now available
annotation release db0
3.0 years ago kayla.interdonato ▴ 160
8
votes
2
replies
1.6k
views
how can I annotate my scRNAseq clusters from a Rat experiment?
scRNAseq Rattus_norvegicus_Data annotation
updated 3.0 years ago by ★ 4.1k • written 3.0 years ago by ▴ 10
0
votes
9
replies
1.8k
views
The GO annotation of fugal species outside of 20 model organisms is outdated
GO biomartr annotation ensemble fungi
updated 3.0 years ago by 65k • written 3.0 years ago by • 0
2
votes
1
reply
922
views
Geno Ontology Analysis using gene symbol
GO.db Annotation Clusterprofile GeneOntology
updated 3.2 years ago by ▴ 780 • written 3.2 years ago by • 0
0
votes
2
replies
1.8k
views
Annotation for Macaca fascicularis
Macaca_fascicularis annotation
updated 3.2 years ago by 65k • written 3.2 years ago by • 0
2
votes
2
replies
2.6k
views
mapping gene type or biotype to ENSEMBL ID
ensembldb biomaRt org.Hs.eg.db Annotation
updated 3.3 years ago by ★ 2.0k • written 3.3 years ago by • 0
2
votes
2
replies
2.4k
views
ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
3.5 years ago • updated 3.2 years ago Mar Mar ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
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…
Answer: Too many significant genes when integrating gtex and tcga by James W. MacDonald 65k
See `?results`, in particular the lfcThreshold argument.
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Votes
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
stuck on unimplemented type 'list' in 'EncodeElement'
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