Showing : annotation • reset
14
votes
19
replies
19k
views
DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2 annotation granges
updated 2.2 years ago by ▴ 60 • written 9.5 years ago by ▴ 120
11
votes
15
replies
4.1k
views
Annotation for Affymetrix GeneChip PrimeView.
annotation
updated 4.0 years ago by ★ 3.9k • written 4.0 years ago by • 0
11
votes
23
replies
2.6k
views
crlmm support for Illumina arrays with no annotation package?
crlmm QCarray annotation
updated 4.3 years ago by • 0 • written 4.5 years ago by ▴ 30
11
votes
0
replies
5.7k
views
Tutorial: Introduction to Bioconductor for high-throughput sequence analysis
GenomicRanges Annotation RNAseq visualization Tutorial
8.8 years ago Martin Morgan 25k
9
votes
2
replies
2.4k
views
How to deal with Affymetrix GeneChip probeids that map to multiple genes
hta20sttranscriptcluster.db probe mapping annotation pd.hta.2.0 annotationdbi
updated 7.6 years ago by 65k • written 7.6 years ago by ▴ 20
9
votes
10
replies
1.4k
views
Mapping of GENE symbols into ENTREZ
limma annotation Gene
4.6 years ago • updated 4.2 years ago omarrafiqued ▴ 50
8
votes
4
replies
4.7k
views
how to extract "Gene type" from org.Mm.eg.db?
annotation org.Mm.eg.db
9.4 years ago • updated 9.3 years ago Guido Hooiveld ★ 3.9k
8
votes
2
replies
1.6k
views
how can I annotate my scRNAseq clusters from a Rat experiment?
scRNAseq Rattus_norvegicus_Data annotation
updated 2.9 years ago by ★ 4.0k • written 3.0 years ago by ▴ 10
7
votes
6
replies
1.7k
views
SNP location annotation problem in "VariantAnnotation" package
annotation variantannotation
updated 6.6 years ago by ★ 6.8k • written 6.6 years ago by ▴ 20
7
votes
8
replies
2.0k
views
Microarray analysis using RMA method using affy, limma
microarray annotation aureus affy
6.2 years ago neranjan007 • 0
7
votes
10
replies
6.2k
views
annotating gene for transcript type/biotype
annotation homo.sapiens
updated 3.4 years ago by 65k • written 8.5 years ago by ▴ 40
7
votes
11
replies
2.3k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 4.0 years ago by ★ 3.2k • written 4.0 years ago by ▴ 60
7
votes
0
replies
3.7k
views
Tutorial: New edX "Data analysis for Life Sciences" module: High performance computing for reproducible genomics
annotation genomicranges visualization docker shiny Tutorial
8.1 years ago Vincent J. Carey, Jr. 6.7k
7
votes
4
replies
3.5k
views
PDCD1 missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
txdb txdb.hsapiens.ucsc.hg19.knowngene txdb.hsapiens.ucsc.hg38.knowngene org.hs.eg.db annotation
8.0 years ago enricoferrero ▴ 660
6
votes
4
replies
1.2k
views
Missing KRAS in locateVariants or TxDb.Hsapiens.UCSC.hg19.knownGene?
software error annotation
updated 9.5 years ago by ★ 6.8k • written 9.5 years ago by ▴ 10
6
votes
5
replies
1.6k
views
Bug: mappedkeys(ath1121501ACCNUM) returns character(0)
annotation arabidopsis thaliana
8.8 years ago knishida ▴ 20
6
votes
11
replies
1.7k
views
"associated_gene" attribute from biomaRt returns too few values - SNP(rsID dataset)
r biomart SNP annotation HUGO
updated 3.7 years ago by ★ 6.5k • written 3.7 years ago by • 0
6
votes
5
replies
999
views
PTEN missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
TxDb annotation TxDb.Hsapiens.UCSC.hg38.knownGene
updated 4.2 years ago by 3.8k • written 4.2 years ago by ▴ 150
6
votes
4
replies
3.1k
views
AnnotationData Packages for Agilent microarrays
microarray annotation limma .db Agilent
updated 4.6 years ago by 65k • written 4.6 years ago by ▴ 30
6
votes
6
replies
3.4k
views
Error in .checkKeys(value, Lkeys(x), x@ifnotfound)
Gostats go term annotation drosophila melanogaster error
updated 7.2 years ago by ▴ 10 • written 7.9 years ago by ▴ 300
6
votes
2
replies
2.2k
views
How to add my own Entrez Gene IDs rather than using the ones from a default package?
annotation entrez gene ids software error
updated 5.0 years ago by 50k • written 5.0 years ago by ▴ 60
6
votes
1
reply
3.0k
views
[ReportingTools] HTMLReport of DESeq2 results using Ensembl Gene Ids
Sequencing Annotation convert biomaRt ReportingTools DESeq2 Sequencing Annotation convert
updated 9.3 years ago by ▴ 370 • written 10.4 years ago by ▴ 160
5
votes
10
replies
1.4k
views
tximport and stevia, how to build tx2gene without any reference genome
deseq2 annotation
updated 4.1 years ago by 41k • written 4.1 years ago by ▴ 60
5
votes
11
replies
4.1k
views
How to annotate gene names for genomic coordinates?
annotation
written 8.8 years ago by • 0
5
votes
7
replies
8.3k
views
Creating an Expression Set with a csv file
eset annotation
updated 8.8 years ago by ▴ 760 • written 8.8 years ago by ▴ 20
5
votes
1
reply
2.8k
views
finding overlapping regions within 2 different bed files with different features
R annotation
updated 7.4 years ago by 25k • written 7.4 years ago by ▴ 50
5
votes
2
replies
1.1k
views
Codelink annotation error in Ubuntu 16.04
codelink annotation ubuntu
updated 7.4 years ago by 25k • written 7.4 years ago by ▴ 260
5
votes
2
replies
13k
views
Complex Heatmap - hide one legend, show 2 - out off three annotations
complexheatmap bioconductor annotation heatmap legend
7.9 years ago • updated 7.8 years ago annkatrin.goepfert ▴ 10
5
votes
22
replies
5.5k
views
sqliteSendQuery error in AnnotationForge bioconductor package
bioconductor annotationforge annotationdbi annotation r
updated 7.8 years ago by ★ 1.0k • written 9.2 years ago by • 0
5
votes
0
replies
2.1k
views
News: edX online course introducing Bioconductor now up and running
annotation bioconductor News
updated 6.3 years ago by 25k • written 6.3 years ago by 6.7k
5
votes
10
replies
2.0k
views
How to do annotation with Limma
annotation limma
updated 2.8 years ago by ★ 3.9k • written 2.9 years ago by • 0
5
votes
8
replies
2.4k
views
how to annotate arrays
affy annotation microarray oligo
updated 3.4 years ago by 65k • written 8.7 years ago by • 0
5
votes
4
replies
1000
views
How can I create ChipDb for Solanum lycopersicum?
annotation
updated 8.6 years ago by 65k • written 8.6 years ago by ▴ 20
4
votes
3
replies
1.1k
views
How to set custom Brainarray annotation for Biobase ExpressionSet object?
affymetrix microarrays expressionset biobase annotation brainarray
updated 6.8 years ago by 65k • written 6.8 years ago by • 0
4
votes
3
replies
4.8k
views
Use R/Bioconductor to match BLAST hits to GO terms?
GO BLAST annotation
updated 9.5 years ago by ★ 7.2k • written 9.5 years ago by ▴ 250
4
votes
8
replies
1.8k
views
Designing a model matrix and further process?
limma annotation R process
6.7 years ago Biotechuos4 • 0
4
votes
10
replies
2.5k
views
how to analyze WGCNA results?
cancer probe deseq2 annotation normalization
updated 3.9 years ago by ★ 3.9k • written 3.9 years ago by ▴ 10
4
votes
13
replies
4.3k
views
How to create an output file with sequence ID's from multiple BLAST result using blastSequences in "Biostrings"
annotation blast biostrings
updated 8.8 years ago by 25k • written 8.8 years ago by • 0
4
votes
8
replies
6.0k
views
gene ID conversion
annotation
updated 14 months ago by ★ 3.9k • written 4.0 years ago by ▴ 20
4
votes
0
replies
1.5k
views
News: Hands-on Bioconductor course, 7 Sept 2015, Tokyo
sequencing transcription variantfiltering annotation News
8.8 years ago Matthew Ritchie ▴ 1000
4
votes
5
replies
1.4k
views
Analyzing gene expression data( not celfiles) in limma and annotating results
limma annotation
updated 9.1 years ago by ★ 13k • written 9.1 years ago by ▴ 10
4
votes
4
replies
2.6k
views
Retrieve canonical transcript for each gene via ensembldb R package
annotation ensembldb
updated 21 months ago by ▴ 40 • written 5.2 years ago by • 0
4
votes
4
replies
2.0k
views
Why does Homo.sapiens import TxDb.Hsapiens.UCSC.hg19.knownGene instead of TxDb.Hsapiens.UCSC.hg38.knownGene?
homo.sapiens txdb annotation
updated 8.0 years ago by ★ 6.8k • written 8.0 years ago by ▴ 660
4
votes
6
replies
1.9k
views
Gene set Testing with Limma for Agilent IDs probes?
limma agilent microarrays gene set testing annotation
7.2 years ago Bouzid.a ▴ 20
4
votes
4
replies
6.3k
views
What is NCBI Gene ID, where to find it and how to convert to entrez ID?
annotation
updated 4.5 years ago by 65k • written 4.5 years ago by • 0
4
votes
9
replies
2.5k
views
Common workflow to build an microarray annatation package, like hgu133a.db
annotation
updated 8.3 years ago by 65k • written 8.3 years ago by • 0
4
votes
2
replies
1.1k
views
Microarray data annotation
Microarray Annotation Microarray Annotation
updated 19.8 years ago by 21k • written 19.8 years ago by ▴ 60
4
votes
0
replies
761
views
News: Map between protein and genome coordinates using ensembldb
ensembdb annotation News
6.4 years ago Johannes Rainer ★ 2.0k
4
votes
4
replies
2.4k
views
Annotation package for Codelink 55K Human Array
r annotation codelink
updated 8.8 years ago by ▴ 760 • written 8.8 years ago by ▴ 260
4
votes
2
replies
2.2k
views
TCGA-biolink: GRCH38 RNA-seq, normalized counts matrix, Converting ensemble gene name into common gene name
tcgabiolinks grch38 annotation
updated 6.5 years ago by ▴ 270 • written 6.5 years ago by • 0
50 results • Page 1 of 1
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Comment: Error in champ.load(): The following specified files do not exist by Basti ▴ 760
The error stems from the Basename column, please see solution here : https://support.bioconductor.org/p/p132482/
Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma by Gordon Smyth 50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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