Showing : annotate • reset
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Create design matrix for differential methylation analysis
Annotation annotate DifferentialMethylation minfiDataEPIC
updated 7 months ago by ▴ 780 • written 7 months ago by • 0
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2
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616
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 12 months ago by ▴ 70 • written 12 months ago by ▴ 140
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1.2k
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fail to annotate chromosome data to single cell object
error SingleCell annotate
updated 5 months ago by • 0 • written 14 months ago by • 0
4
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3
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SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 21 months ago by 65k • written 21 months 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
22 months ago Palmira • 0
1
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2
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2.6k
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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
660
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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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1.4k
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Annotating a sequence, new to bioconductor
annotate
updated 5.6 years ago by 65k • written 5.6 years ago by • 0
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3
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1.2k
views
How to annotate gene ontologies based on Gene Symbols in R
GO.db annotate
6.2 years ago dusan.petrovic • 0
0
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1
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1.3k
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RNAseq _generating tx2gene table and using kallisto output to run DEseq
deseq annotate
updated 6.4 years ago by 42k • written 6.4 years ago by • 0
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4
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6.6k
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How to annotate the Affymetrix Human Genome U133 Plus 2.0 Array chip
oligo annotate
6.5 years ago llkxiaolan ▴ 10
0
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1
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1.8k
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How many genes are appropriate for GO enrichment analysis
go annotate rna-seq clusterprofiler
updated 6.6 years ago by ▴ 120 • written 6.6 years ago by • 0
0
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1
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1.4k
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querying annotation hub for common TF, in common cell line returns no results....
annotate annotationhub
updated 6.7 years ago by 3.9k • written 6.7 years ago by ▴ 50
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8
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1.7k
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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
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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 6.9 years ago by ▴ 10
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1
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1.2k
views
Annotation of Probe id to Gene
bioconductor annotate microarray arabidopsis thaliana
updated 6.9 years ago by 65k • written 6.9 years ago by • 0
0
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4
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1.4k
views
TimmR error for hgu133a.db
software error annotate hgu133a
updated 7.2 years ago by 65k • written 7.2 years ago by • 0
3
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6
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2.6k
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RSQLite::dbGetPreparedQuery() is deprecated in AnnotationForge
annotation microarray annotate annotationforge
7.2 years ago MOD • 0
6
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5
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14k
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Installation of package DESeq2
deseq2 rcurl annotate genefilter geneplotter
updated 7.3 years ago by 25k • written 7.3 years ago by ▴ 10
1
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2
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2.2k
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blastSequences queries failing due to BLAST switch to https?
annotate blastSequences BLAST https
updated 7.6 years ago by 25k • written 7.6 years ago by • 0
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2
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1.5k
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Problems using intansv...
annotate annotate
updated 7.9 years ago by • 0 • written 10.1 years ago by ▴ 10
2
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1
reply
1.1k
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Use matchPattern for large DNAStrings
biostrings annotate
updated 8.0 years ago by 16k • written 8.0 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 8.8 years ago by 16k • written 8.8 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
8.9 years ago adnan.niazi • 0
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1
reply
1.3k
views
.getNcbiURL returns old NCBI url ?
annotate ncbi url
9.4 years ago reuma • 0
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1
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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
9.5 years ago Bogdan ▴ 670
2
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2
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1.8k
views
BLAST export library 'annotate'
blast annotate biostrings export fasta
9.5 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 9.6 years ago by 65k • written 9.6 years ago by ▴ 20
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6
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2.2k
views
Missing as.list generic from AnnotationDbi?
annotate AnnotationDbi annotate AnnotationDbi
updated 9.6 years ago by ★ 2.0k • written 10.9 years ago by ★ 7.9k
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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 9.7 years ago by ▴ 490 • written 9.7 years ago by 1.6k
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1
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1.5k
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Positional Details with Features through UniProt.ws Ultimately to display as tracks in ggbio
annotate ggbio annotate ggbio
updated 9.7 years ago by ▴ 490 • written 9.7 years ago by ▴ 30
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1.4k
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ChIPpeakAnno
SNP Annotation annotate convert SNP Annotation annotate convert
9.7 years ago Julie Zhu ★ 4.3k
0
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1
reply
1.3k
views
non-CpG methylated regions and strand information in MEDIPS output
BSgenome annotate biomaRt BSgenome MEDIPS BSgenome annotate biomaRt BSgenome MEDIPS
updated 9.8 years ago by ▴ 570 • written 9.8 years ago by ★ 13k
0
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1
reply
1.9k
views
annotation for TAqman assay IDs
Annotation probe annotate Annotation probe annotate
updated 9.8 years ago by 65k • written 9.8 years ago by ▴ 10
0
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2
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1.6k
views
Affymetrix mouse 430_2 array - annotation problem
Annotation mouse4302 annotate Annotation mouse4302 annotate
updated 9.8 years ago by 65k • written 9.8 years ago by ▴ 550
0
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5
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4.3k
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annotating microarray data with mogene10stv1
Microarray Annotation annotate limma ASSIGN Microarray Annotation annotate limma ASSIGN
updated 9.8 years ago by 65k • written 9.8 years ago by ▴ 70
0
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2
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2.9k
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Biomart annotation
annotate convert annotate convert
updated 9.8 years ago by ▴ 190 • written 9.8 years ago by ▴ 40
0
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5
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2.6k
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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 9.9 years ago by ▴ 160 • written 9.9 years ago by 65k
1
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8
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3.7k
views
GRanges apply functions
GO annotate GO annotate
updated 9.9 years ago by ★ 4.2k • written 9.9 years ago by ▴ 380
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 ▴ 510
0
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1
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1.6k
views
ChIPpeakAnno
annotate ChIPpeakAnno annotate ChIPpeakAnno
updated 10.1 years ago by ★ 4.3k • written 10.1 years ago by ▴ 350
0
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0
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1.0k
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
10.2 years ago Cornwell, Adam ▴ 110
0
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9
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2.0k
views
variantAnnotation: alternative GENETIC_CODE, and circular chromosomes?
VariantAnnotation Cancer Yeast annotate Biostrings VariantAnnotation VariantAnnotation
updated 10.3 years ago by 16k • written 10.3 years ago by ▴ 740
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0
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931
views
Ontology
Annotation GO annotate GOstats Annotation GO annotate GOstats
10.3 years ago Marc Carlson ★ 7.2k
0
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0
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1.3k
views
zero-row result breaks select() on PolyPhen.Hsapiens.* and SIFT.Hsapiens.*
VariantAnnotation Annotation PolyPhen SIFT annotate VariantAnnotation ensemblVEP Annotation
10.5 years ago Valerie Obenchain ★ 6.8k
0
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5
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1.5k
views
multiple annotations with get()?
Biobase annotate convert Biobase annotate convert
updated 10.6 years ago by 21k • written 10.6 years ago by ▴ 230
0
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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 10.6 years ago by ★ 3.6k • written 10.6 years ago by ▴ 120
50 results • Page 1 of 1
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Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Dylan.Sheerin • 0
Thank you very much, Gordon. I'll give voomLmFit a go! And for comparisons between the cohorts I presume duplicateCorrelation with standar…
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Gordon Smyth 50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Comment: Log-cpm values from limma by Gordon Smyth 50k
No, it does not mean that. `voom()` uses the design matrix, including the W covariates, to compute precision weights but not to adjust the …
Comment: Extremely small p-values using Limma for proteomic data by Abbey • 0
This is the code. The only part I changed was adding the contrasts.fit as you suggested. Thanks for taking a look! ``` # Load necessary …
Comment: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
Probably. I would not expect such large fold changes. But without seeing your code, who knows?
Votes
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
Bioconductor 3.19 is Released!
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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