Showing : annotate • reset
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Create design matrix for differential methylation analysis
Annotation annotate DifferentialMethylation minfiDataEPIC
updated 6 months ago by ▴ 770 • written 6 months ago by • 0
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2
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587
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 11 months ago by ▴ 70 • written 12 months ago by ▴ 140
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8
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1.1k
views
fail to annotate chromosome data to single cell object
error SingleCell annotate
updated 5 months ago by • 0 • written 13 months ago by • 0
4
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3
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1.4k
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SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 20 months ago by 65k • written 20 months ago by ▴ 10
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0
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765
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Problem with "TxDb.Mmusculus.UCSC.mm39.refGene" to annotate genes with ChIPseeker
TxDb.Mmusculus.UCSC.mm39.refGene ChIPseeker annotate
21 months ago Palmira • 0
1
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2
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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
2
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1
reply
642
views
The best pacakge to annotate a set of regions
annotate
updated 3.5 years ago by 65k • written 3.5 years ago by ▴ 20
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4
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1.3k
views
Annotating a sequence, new to bioconductor
annotate
updated 5.6 years ago by 65k • written 5.6 years ago by • 0
0
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3
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1.1k
views
How to annotate gene ontologies based on Gene Symbols in R
GO.db annotate
6.1 years ago dusan.petrovic • 0
0
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1
reply
1.2k
views
RNAseq _generating tx2gene table and using kallisto output to run DEseq
deseq annotate
updated 6.4 years ago by 41k • written 6.4 years ago by • 0
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4
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6.5k
views
How to annotate the Affymetrix Human Genome U133 Plus 2.0 Array chip
oligo annotate
6.4 years ago llkxiaolan ▴ 10
0
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1
reply
1.8k
views
How many genes are appropriate for GO enrichment analysis
go annotate rna-seq clusterprofiler
updated 6.5 years ago by ▴ 120 • written 6.5 years ago by • 0
0
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1
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1.4k
views
querying annotation hub for common TF, in common cell line returns no results....
annotate annotationhub
updated 6.6 years ago by 3.8k • written 6.6 years ago by ▴ 50
0
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8
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1.7k
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 6.7 years ago by 65k • written 6.7 years ago by • 0
0
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1
reply
1.2k
views
Annotation of Probe id to Gene
bioconductor annotate microarray arabidopsis thaliana
updated 6.8 years ago by 65k • written 6.8 years ago by • 0
0
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3
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2.2k
views
Getting Differentially Expressed Genes from GOSeq Categories
goseq gene ontology biomart annotate category
updated 6.8 years ago by ▴ 360 • written 6.8 years ago by ▴ 10
0
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4
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1.3k
views
TimmR error for hgu133a.db
software error annotate hgu133a
updated 7.1 years ago by 65k • written 7.1 years ago by • 0
3
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6
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2.6k
views
RSQLite::dbGetPreparedQuery() is deprecated in AnnotationForge
annotation microarray annotate annotationforge
7.2 years ago MOD • 0
6
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5
replies
14k
views
Installation of package DESeq2
deseq2 rcurl annotate genefilter geneplotter
updated 7.3 years ago by 25k • written 7.3 years ago by ▴ 10
1
vote
2
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2.2k
views
blastSequences queries failing due to BLAST switch to https?
annotate blastSequences BLAST https
updated 7.5 years ago by 25k • written 7.5 years ago by • 0
2
votes
1
reply
1.0k
views
Use matchPattern for large DNAStrings
biostrings annotate
updated 7.9 years ago by 16k • written 7.9 years ago by ▴ 40
0
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1
reply
1.5k
views
How to identify the microarray annotation library automatically from GEO study ID?
limma microarray annotation bioconductor annotate
updated 8.0 years ago by 65k • written 8.0 years ago by • 0
0
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1
reply
1.5k
views
Getting data on the out-of-frame transcripts
annotate sequencing genomicfeatures
updated 8.7 years ago by 16k • written 8.7 years ago by • 0
0
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1
reply
2.0k
views
Difference in TxDb.Hsapiens.UCSC.hg19.knownGene and UCSC knownGene
annotate exons txdb.hsapiens.ucsc.hg19.knowngene
8.8 years ago adnan.niazi • 0
0
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1
reply
1.2k
views
.getNcbiURL returns old NCBI url ?
annotate ncbi url
9.3 years ago reuma • 0
0
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1
reply
1.7k
views
can't run functions in 'annotate'
annotate
9.4 years ago boris.steipe • 0
1
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2
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1.6k
views
about library(Homo.sapiens) from TxDb.Hsapiens.UCSC.hg18.knownGene
annotate
9.4 years ago Bogdan ▴ 670
2
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2
replies
1.8k
views
BLAST export library 'annotate'
blast annotate biostrings export fasta
9.4 years ago b.stielow • 0
5
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2
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10k
views
Probe to gene id conversion
annotate biomart probe to gene id
updated 9.5 years ago by 65k • written 9.5 years ago by ▴ 20
0
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2
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1.8k
views
Bioconductor Digest, Vol 138, Issue 27
annotate biovizBase ggbio UniProt.ws Pbase annotate biovizBase ggbio UniProt.ws Pbase
updated 9.6 years ago by ▴ 490 • written 9.6 years ago by 1.6k
0
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0
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1.4k
views
ChIPpeakAnno
SNP Annotation annotate convert SNP Annotation annotate convert
9.7 years ago Julie Zhu ★ 4.3k
0
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1
reply
1.4k
views
Positional Details with Features through UniProt.ws Ultimately to display as tracks in ggbio
annotate ggbio annotate ggbio
updated 9.6 years ago by ▴ 490 • written 9.7 years ago by ▴ 30
0
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1
reply
1.3k
views
non-CpG methylated regions and strand information in MEDIPS output
BSgenome annotate biomaRt BSgenome MEDIPS BSgenome annotate biomaRt BSgenome MEDIPS
updated 9.7 years ago by ▴ 570 • written 9.7 years ago by ★ 13k
0
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1
reply
1.8k
views
annotation for TAqman assay IDs
Annotation probe annotate Annotation probe annotate
updated 9.7 years ago by 65k • written 9.7 years ago by ▴ 10
0
votes
2
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1.5k
views
Affymetrix mouse 430_2 array - annotation problem
Annotation mouse4302 annotate Annotation mouse4302 annotate
updated 9.7 years ago by 65k • written 9.7 years ago by ▴ 550
0
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5
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4.3k
views
annotating microarray data with mogene10stv1
Microarray Annotation annotate limma ASSIGN Microarray Annotation annotate limma ASSIGN
updated 9.7 years ago by 65k • written 9.8 years ago by ▴ 70
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2
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2.9k
views
Biomart annotation
annotate convert annotate convert
updated 9.8 years ago by ▴ 190 • written 9.8 years ago by ▴ 40
1
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8
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3.7k
views
GRanges apply functions
GO annotate GO annotate
updated 9.8 years ago by ★ 4.2k • written 9.8 years ago by ▴ 380
0
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5
replies
2.6k
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 9.8 years ago by ▴ 160 • written 9.9 years ago by 65k
0
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1
reply
3.1k
views
ChIPseeker: Error in annotatePeak
Sequencing GO annotate ChIPseeker Sequencing GO annotate ChIPseeker
10.0 years ago António Miguel de Jesus Domingues ▴ 490
0
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1
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1.5k
views
ChIPpeakAnno
annotate ChIPpeakAnno annotate ChIPpeakAnno
updated 10.0 years ago by ★ 4.3k • written 10.0 years ago by ▴ 350
0
votes
2
replies
1.5k
views
Problems using intansv...
annotate annotate
updated 7.8 years ago by • 0 • written 10.0 years ago by ▴ 10
0
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0
replies
991
views
lumi-package problem: nuID [e.g. nuID2EntrezID()] from vignette example throws an error on my system
annotate annotate
10.1 years ago Guest User ★ 13k
2
votes
1
reply
1.3k
views
HTqPCR- gene names not maintained in limmaCtData
annotate ddCt HTqPCR annotate ddCt HTqPCR
10.1 years ago Cornwell, Adam ▴ 110
0
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9
replies
1.9k
views
variantAnnotation: alternative GENETIC_CODE, and circular chromosomes?
VariantAnnotation Cancer Yeast annotate Biostrings VariantAnnotation VariantAnnotation
updated 10.2 years ago by 16k • written 10.2 years ago by ▴ 740
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0
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918
views
Ontology
Annotation GO annotate GOstats Annotation GO annotate GOstats
10.2 years ago Marc Carlson ★ 7.2k
0
votes
0
replies
1.2k
views
zero-row result breaks select() on PolyPhen.Hsapiens.* and SIFT.Hsapiens.*
VariantAnnotation Annotation PolyPhen SIFT annotate VariantAnnotation ensemblVEP Annotation
10.4 years ago Valerie Obenchain ★ 6.8k
0
votes
5
replies
1.5k
views
multiple annotations with get()?
Biobase annotate convert Biobase annotate convert
updated 10.5 years ago by 21k • written 10.5 years ago by ▴ 230
0
votes
0
replies
1.0k
views
ChIPpeakAnno Question, regarding BED scores
Annotation annotate ChIPpeakAnno Annotation annotate ChIPpeakAnno
10.5 years ago Julie Zhu ★ 4.3k
0
votes
2
replies
1.5k
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 10.5 years ago by ★ 3.6k • written 10.5 years ago by ▴ 120
50 results • Page 1 of 1
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Answer: rlog transformation by Michael Love 41k
It is dependent on the other samples in the dataset.
Answer: ONT long-read RNA sequencing - data analysis options by Michael Love 41k
*"This worked really well for brain but has not work as well for lung as I get #N/A for many padj"* See the vignette for the cause of th…
Answer: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by Michael Love 41k
Starting from the very top, do you understand the error? You need to provide sample info that matches 1-to-1 the columns of the counts matr…
Answer: covariate with negative and positive values by Michael Love 41k
Not a problem. However, if the values are very large (eg 1e6) or very small (eg 1e-6), it's a good idea to center and scale the variable…
Comment: FilterByExpr low counts with small sample size by Jonathan ▴ 10
Usually I run `voomLmFit`, although in order to create the mean-variance trend plots for this particular post, I ran `voom`; I've checked -…
Votes
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
Comment: Reading huge bismark coverage files using bbseq::read.bismark
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