Showing : annotate • reset
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708
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Create design matrix for differential methylation analysis
Annotation annotate DifferentialMethylation minfiDataEPIC
updated 12 months ago by ▴ 780 • written 12 months ago by • 0
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2
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823
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 17 months ago by ▴ 70 • written 17 months ago by ▴ 140
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8
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1.4k
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fail to annotate chromosome data to single cell object
error SingleCell annotate
updated 10 months ago by • 0 • written 19 months ago by • 0
4
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3
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1.9k
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SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 2.2 years ago by 67k • written 2.2 years ago by ▴ 10
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Problem with "TxDb.Mmusculus.UCSC.mm39.refGene" to annotate genes with ChIPseeker
TxDb.Mmusculus.UCSC.mm39.refGene ChIPseeker annotate
2.3 years ago Palmira • 0
1
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2
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3.1k
views
mapping mouse ENSEMBL ids to human gene symbol
Annotation AnnotationDbi annotate
updated 3.2 years ago by 67k • written 3.2 years ago by • 0
2
votes
1
reply
758
views
The best pacakge to annotate a set of regions
annotate
updated 4.0 years ago by 67k • written 4.0 years ago by ▴ 20
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4
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1.6k
views
Annotating a sequence, new to bioconductor
annotate
updated 6.0 years ago by 67k • written 6.0 years ago by • 0
0
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3
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1.3k
views
How to annotate gene ontologies based on Gene Symbols in R
GO.db annotate
6.6 years ago dusan.petrovic • 0
0
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1
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1.4k
views
RNAseq _generating tx2gene table and using kallisto output to run DEseq
deseq annotate
updated 6.8 years ago by 42k • written 6.8 years ago by • 0
0
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4
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7.1k
views
How to annotate the Affymetrix Human Genome U133 Plus 2.0 Array chip
oligo annotate
6.9 years ago llkxiaolan ▴ 10
0
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1
reply
2.3k
views
How many genes are appropriate for GO enrichment analysis
go annotate rna-seq clusterprofiler
updated 7.0 years ago by ▴ 120 • written 7.0 years ago by ▴ 20
0
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1
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1.5k
views
querying annotation hub for common TF, in common cell line returns no results....
annotate annotationhub
updated 7.1 years ago by 4.0k • written 7.1 years ago by ▴ 50
0
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8
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1.9k
views
Can't find Ly76 on my Affymetrix MoGene 2.0ST array annotated with pd.mogene.2.0.st package
pd.mogene.2.0.st mogene20sttranscriptcluster.db annotate
updated 7.1 years ago by 67k • written 7.1 years ago by • 0
0
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3
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2.4k
views
Getting Differentially Expressed Genes from GOSeq Categories
goseq gene ontology biomart annotate category
updated 7.2 years ago by ▴ 370 • written 7.3 years ago by ▴ 10
0
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1
reply
1.4k
views
Annotation of Probe id to Gene
bioconductor annotate microarray arabidopsis thaliana
updated 7.3 years ago by 67k • written 7.3 years ago by • 0
0
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4
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1.5k
views
TimmR error for hgu133a.db
software error annotate hgu133a
updated 7.6 years ago by 67k • written 7.6 years ago by • 0
3
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6
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2.8k
views
RSQLite::dbGetPreparedQuery() is deprecated in AnnotationForge
annotation microarray annotate annotationforge
7.7 years ago MOD • 0
6
votes
5
replies
14k
views
Installation of package DESeq2
deseq2 rcurl annotate genefilter geneplotter
updated 7.7 years ago by 25k • written 7.7 years ago by ▴ 10
1
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2
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2.3k
views
blastSequences queries failing due to BLAST switch to https?
annotate blastSequences BLAST https
updated 8.0 years ago by 25k • written 8.0 years ago by • 0
0
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2
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1.7k
views
Problems using intansv...
annotate annotate
updated 8.3 years ago by • 0 • written 10.5 years ago by ▴ 10
2
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1
reply
1.2k
views
Use matchPattern for large DNAStrings
biostrings annotate
updated 8.4 years ago by 16k • written 8.4 years ago by ▴ 40
0
votes
1
reply
1.6k
views
How to identify the microarray annotation library automatically from GEO study ID?
limma microarray annotation bioconductor annotate
updated 8.4 years ago by 67k • written 8.4 years ago by • 0
0
votes
1
reply
1.6k
views
Getting data on the out-of-frame transcripts
annotate sequencing genomicfeatures
updated 9.2 years ago by 16k • written 9.2 years ago by • 0
0
votes
1
reply
2.1k
views
Difference in TxDb.Hsapiens.UCSC.hg19.knownGene and UCSC knownGene
annotate exons txdb.hsapiens.ucsc.hg19.knowngene
9.3 years ago adnan.niazi • 0
0
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1
reply
1.4k
views
.getNcbiURL returns old NCBI url ?
annotate ncbi url
9.8 years ago reuma • 0
0
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1
reply
1.8k
views
can't run functions in 'annotate'
annotate
9.9 years ago boris.steipe • 0
1
vote
2
replies
1.7k
views
about library(Homo.sapiens) from TxDb.Hsapiens.UCSC.hg18.knownGene
annotate
9.9 years ago Bogdan ▴ 670
2
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2
replies
2.0k
views
BLAST export library 'annotate'
blast annotate biostrings export fasta
9.9 years ago b.stielow • 0
5
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2
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11k
views
Probe to gene id conversion
annotate biomart probe to gene id
updated 10.0 years ago by 67k • written 10.0 years ago by ▴ 20
0
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6
replies
2.4k
views
Missing as.list generic from AnnotationDbi?
annotate AnnotationDbi annotate AnnotationDbi
updated 10.1 years ago by ★ 2.0k • written 11.3 years ago by ★ 7.9k
0
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2
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2.0k
views
Bioconductor Digest, Vol 138, Issue 27
annotate biovizBase ggbio UniProt.ws Pbase annotate biovizBase ggbio UniProt.ws Pbase
updated 10.1 years ago by ▴ 490 • written 10.1 years ago by 1.6k
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1
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1.6k
views
Positional Details with Features through UniProt.ws Ultimately to display as tracks in ggbio
annotate ggbio annotate ggbio
updated 10.1 years ago by ▴ 490 • written 10.2 years ago by ▴ 30
0
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0
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1.5k
views
ChIPpeakAnno
SNP Annotation annotate convert SNP Annotation annotate convert
10.1 years ago Julie Zhu ★ 4.3k
0
votes
1
reply
1.4k
views
non-CpG methylated regions and strand information in MEDIPS output
BSgenome annotate biomaRt BSgenome MEDIPS BSgenome annotate biomaRt BSgenome MEDIPS
updated 10.2 years ago by ▴ 570 • written 10.2 years ago by ★ 13k
0
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1
reply
2.0k
views
annotation for TAqman assay IDs
Annotation probe annotate Annotation probe annotate
updated 10.2 years ago by 67k • written 10.2 years ago by ▴ 10
0
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2
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1.7k
views
Affymetrix mouse 430_2 array - annotation problem
Annotation mouse4302 annotate Annotation mouse4302 annotate
updated 10.2 years ago by 67k • written 10.2 years ago by ▴ 550
0
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5
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4.5k
views
annotating microarray data with mogene10stv1
Microarray Annotation annotate limma ASSIGN Microarray Annotation annotate limma ASSIGN
updated 10.2 years ago by 67k • written 10.2 years ago by ▴ 70
0
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2
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3.0k
views
Biomart annotation
annotate convert annotate convert
updated 10.2 years ago by ▴ 190 • written 10.2 years ago by ▴ 40
0
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5
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2.8k
views
Issues about how to filter and annotate the MoGene-2_0-st and MoEx-1_0-st-v1 array probe sets
Annotation probe annotate annaffy oligo ReportingTools Annotation probe annotate annaffy
updated 10.3 years ago by ▴ 160 • written 10.3 years ago by 67k
1
vote
8
replies
4.0k
views
GRanges apply functions
GO annotate GO annotate
updated 10.3 years ago by ★ 4.2k • written 10.3 years ago by ▴ 380
0
votes
1
reply
3.5k
views
ChIPseeker: Error in annotatePeak
Sequencing GO annotate ChIPseeker Sequencing GO annotate ChIPseeker
10.4 years ago António Miguel de Jesus Domingues ▴ 510
0
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1
reply
1.7k
views
ChIPpeakAnno
annotate ChIPpeakAnno annotate ChIPpeakAnno
updated 10.5 years ago by ★ 4.3k • written 10.5 years ago by ▴ 350
0
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0
replies
1.1k
views
lumi-package problem: nuID [e.g. nuID2EntrezID()] from vignette example throws an error on my system
annotate annotate
10.5 years ago Guest User ★ 13k
2
votes
1
reply
1.4k
views
HTqPCR- gene names not maintained in limmaCtData
annotate ddCt HTqPCR annotate ddCt HTqPCR
10.6 years ago Cornwell, Adam ▴ 110
0
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9
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2.1k
views
variantAnnotation: alternative GENETIC_CODE, and circular chromosomes?
VariantAnnotation Cancer Yeast annotate Biostrings VariantAnnotation VariantAnnotation
updated 10.7 years ago by 16k • written 10.7 years ago by ▴ 740
0
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0
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1.0k
views
Ontology
Annotation GO annotate GOstats Annotation GO annotate GOstats
10.7 years ago Marc Carlson ★ 7.2k
0
votes
0
replies
1.4k
views
zero-row result breaks select() on PolyPhen.Hsapiens.* and SIFT.Hsapiens.*
VariantAnnotation Annotation PolyPhen SIFT annotate VariantAnnotation ensemblVEP Annotation
10.9 years ago Valerie Obenchain ★ 6.8k
0
votes
5
replies
1.6k
views
multiple annotations with get()?
Biobase annotate convert Biobase annotate convert
updated 11.0 years ago by 21k • written 11.0 years ago by ▴ 230
0
votes
2
replies
1.6k
views
limma_3.17.23 - missing ILMN identifiers in EList objects after read.ilmn
Annotation Normalization GO probe annotate Annotation Normalization GO probe annotate
updated 11.0 years ago by ★ 3.6k • written 11.0 years ago by ▴ 120
50 results • Page 1 of 1
Recent ...
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Answer: Annotation for EPICv2 by James W. MacDonald 67k
The CpG you point out is in the intronic region of SHANK2, so will not be in any of the locations you have in your barplot. ![enter ima…
Comment: WGCNA by Lluís Revilla Sancho ▴ 750
This is a question of a package outside Bioconductor, it would be best to ask to the maintainer. But i think he moved to industry and the w…
Comment: dmpFinder for other objects by James W. MacDonald 67k
Yes, but you should probably use M-values instead of betas (convert using `logit2`). However, `dmpFinder` is just a way to allow people to…
Comment: Highly DE genes but small count difference within conditions by Michael Love 42k
This last problem, I don't know how to help with, I think there's high variability here and not many degrees of freedom to overcome that
Answer: [DESeq2] Introduce a bias in DESeq2 by Michael Love 42k
This is often called an offset in statistical modeling. We have some support site posts about how to do this in DESeq2. Search for posts me…
Votes
Answer: Highly DE genes but small count difference within conditions
Answer: edgeR 4.2.1 compression bug: a minimally reproducible snippet
Trying to use enrichGO
Answer: edgeR 4.2.1 compression bug: a minimally reproducible snippet
Answer: dmpFinder for other objects
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