Showing : annotation • reset
0
votes
6
replies
307
views
unable to access Annotationhub latest record
DNAMethylation AnnotationHub EPICv2manifest annotation
updated 14 days ago by ▴ 170 • written 23 days ago by • 0
2
votes
1
reply
188
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 4 weeks ago by ★ 3.9k • written 4 weeks ago by ▴ 10
0
votes
0
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150
views
Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
11 weeks ago nilanjanamani88 • 0
0
votes
1
reply
441
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
368
views
News: Bioconductor 3.18 db0s, OrgDbs, and TxDbs now available
db0 release Annotation
7 months ago kayla.interdonato ▴ 160
0
votes
1
reply
3.4k
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
654
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
votes
4
replies
914
views
Use with_go along with other filters in getBM function
Annotation biomaRt
11 months ago • updated 10 months ago RuBBiT0 ▴ 10
0
votes
2
replies
695
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
votes
4
replies
1.1k
views
BioCann repository index warning on Apple Silicon (Bioc 3.17 / R 4.3)
Annotation
11 months ago Michael Steinbaugh ▴ 90
0
votes
0
replies
507
views
AnnotationDbi Error: PROSITE is defunct.
ChipDb AnnotationDbi Annotation
13 months ago • updated 12 months ago ahiser • 0
0
votes
3
replies
709
views
Annotated dendogram (tree) from tbl_graph
dendogram ggtreeExtra ggtree annotation Annotation
13 months ago christian.dina • 0
0
votes
0
replies
633
views
News: Bioconductor 3.17 db0s, OrgDbs, and TxDbs now available
release db0 Annotation
13 months ago kayla.interdonato ▴ 160
2
votes
1
reply
521
views
Doubts about manipulation and annotation of microarray files deposited at GEO
MicroarrayData Annotation GEOdata
updated 14 months ago by 65k • written 14 months ago by • 0
0
votes
1
reply
805
views
Create an Annotation DB file for a non-model organism
AnnotationDbi annotation ChIPseeker
updated 14 months ago by 65k • written 14 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 14 months ago by ★ 3.9k • written 14 months ago by ▴ 10
0
votes
1
reply
529
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
replies
881
views
A look inside annotation packages
Annotation
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 18 months ago by ▴ 30
0
votes
0
replies
624
views
News: Bioconductor 3.16 db0s, OrgDbs and TxDbs now available
release db0 annotation
19 months ago kayla.interdonato ▴ 160
0
votes
1
reply
592
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
792
views
News: Bioconductor 3.15 db0s, OrgDbs and TxDbs now available
annotation release db0
2.0 years ago kayla.interdonato ▴ 160
0
votes
0
replies
605
views
low mapping between annotated genome and transcriptome
transcriptome Annotation mapping
2.1 years ago Ava • 0
0
votes
1
reply
787
views
peak annotation
ChIPpeakAnno Annotation
updated 2.0 years ago by ▴ 70 • written 2.1 years ago by ▴ 670
0
votes
0
replies
670
views
using annotation data of an organism(eg. Oryza sativa) from AnnotationHub for mgoSim
AnnotationHubSoftware GOSemSim annotation
2.2 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 3.8k • written 2.3 years ago by ▴ 20
0
votes
0
replies
696
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
953
views
How to get Cytogenetic band for muscles gene by using Biomart or other tools in R
Annotation biomaRt ensembldb
written 2.4 years ago by • 0
0
votes
0
replies
775
views
Error with getBM: 'The query to the BioMart webservice returned an invalid result.'
process annotationTools AnnotationFilter Annotation biomaRt
2.4 years ago Shane • 0
0
votes
1
reply
827
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
697
views
anotacion para Anopheles Albimanus
anopheles_albimanus Annotation
updated 2.6 years ago by 3.8k • written 2.6 years ago by • 0
3
votes
1
reply
2.1k
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 2.6 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
2.0k
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
5.1k
views
LOC gene IDs for characterised genes in annotation files
Annotation RNAseq
updated 2.2 years ago by • 0 • written 3.0 years ago by • 0
1
vote
0
replies
817
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 ★ 4.0k • 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
917
views
Geno Ontology Analysis using gene symbol
GO.db Annotation Clusterprofile GeneOntology
updated 3.1 years ago by ▴ 780 • written 3.1 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
3.4 years ago • updated 3.2 years ago Mar Mar ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by SamGG ▴ 350
Is useless the assumption that the majority of genes have no variation in expression (bearing in mind that they are distributed over the en…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Votes
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
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