Showing : annotate • reset
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Create design matrix for differential methylation analysis
Annotation annotate DifferentialMethylation minfiDataEPIC
updated 23 months ago by ▴ 780 • written 23 months ago by • 0
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 2.4 years ago by ▴ 70 • written 2.4 years ago by ▴ 140
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fail to annotate chromosome data to single cell object
error SingleCell annotate
updated 21 months ago by • 0 • written 2.5 years 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 3.1 years ago by 68k • written 3.1 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
3.2 years ago Palmira • 0
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mapping mouse ENSEMBL ids to human gene symbol
Annotation AnnotationDbi annotate
updated 4.1 years ago by 68k • written 4.1 years ago by • 0
2
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1
reply
910
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The best pacakge to annotate a set of regions
annotate
updated 4.9 years ago by 68k • written 4.9 years ago by ▴ 20
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Annotating a sequence, new to bioconductor
annotate
updated 6.9 years ago by 68k • written 6.9 years ago by • 0
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3
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1.5k
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How to annotate gene ontologies based on Gene Symbols in R
GO.db annotate
7.5 years ago dusan.petrovic • 0
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1
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RNAseq _generating tx2gene table and using kallisto output to run DEseq
deseq annotate
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
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4
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How to annotate the Affymetrix Human Genome U133 Plus 2.0 Array chip
oligo annotate
7.8 years ago llkxiaolan ▴ 10
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1
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3.4k
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How many genes are appropriate for GO enrichment analysis
go annotate rna-seq clusterprofiler
updated 7.9 years ago by ▴ 120 • written 7.9 years ago by ▴ 20
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1.8k
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querying annotation hub for common TF, in common cell line returns no results....
annotate annotationhub
updated 8.0 years ago by 4.2k • written 8.0 years ago by ▴ 50
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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 8.0 years ago by 68k • written 8.0 years ago by • 0
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Getting Differentially Expressed Genes from GOSeq Categories
goseq gene ontology biomart annotate category
updated 8.1 years ago by ▴ 370 • written 8.2 years ago by ▴ 10
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1.6k
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Annotation of Probe id to Gene
bioconductor annotate microarray arabidopsis thaliana
updated 8.2 years ago by 68k • written 8.2 years ago by • 0
0
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4
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1.8k
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TimmR error for hgu133a.db
software error annotate hgu133a
updated 8.5 years ago by 68k • written 8.5 years ago by • 0
3
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6
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RSQLite::dbGetPreparedQuery() is deprecated in AnnotationForge
annotation microarray annotate annotationforge
8.6 years ago MOD • 0
6
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5
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Installation of package DESeq2
deseq2 rcurl annotate genefilter geneplotter
updated 8.6 years ago by 25k • written 8.6 years ago by ▴ 10
1
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2
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blastSequences queries failing due to BLAST switch to https?
annotate blastSequences BLAST https
updated 8.9 years ago by 25k • written 8.9 years ago by • 0
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Problems using intansv...
annotate annotate
updated 9.2 years ago by • 0 • written 11.4 years ago by ▴ 10
2
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1
reply
1.4k
views
Use matchPattern for large DNAStrings
biostrings annotate
updated 9.3 years ago by 16k • written 9.3 years ago by ▴ 40
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1
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1.8k
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How to identify the microarray annotation library automatically from GEO study ID?
limma microarray annotation bioconductor annotate
updated 9.3 years ago by 68k • written 9.3 years ago by • 0
0
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1
reply
1.9k
views
Getting data on the out-of-frame transcripts
annotate sequencing genomicfeatures
updated 10.1 years ago by 16k • written 10.1 years ago by • 0
0
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1
reply
2.4k
views
Difference in TxDb.Hsapiens.UCSC.hg19.knownGene and UCSC knownGene
annotate exons txdb.hsapiens.ucsc.hg19.knowngene
10.2 years ago adnan.niazi • 0
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reply
1.5k
views
.getNcbiURL returns old NCBI url ?
annotate ncbi url
10.7 years ago reuma • 0
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1
reply
2.0k
views
can't run functions in 'annotate'
annotate
10.8 years ago boris.steipe • 0
1
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1.9k
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about library(Homo.sapiens) from TxDb.Hsapiens.UCSC.hg18.knownGene
annotate
10.8 years ago Bogdan ▴ 670
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2
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2.3k
views
BLAST export library 'annotate'
blast annotate biostrings export fasta
10.8 years ago b.stielow • 0
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12k
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Probe to gene id conversion
annotate biomart probe to gene id
updated 10.9 years ago by 68k • written 10.9 years ago by ▴ 20
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6
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2.7k
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Missing as.list generic from AnnotationDbi?
annotate AnnotationDbi annotate AnnotationDbi
updated 11.0 years ago by ★ 2.0k • written 12.2 years ago by ★ 7.9k
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2
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Bioconductor Digest, Vol 138, Issue 27
annotate biovizBase ggbio UniProt.ws Pbase annotate biovizBase ggbio UniProt.ws Pbase
updated 11.0 years ago by ▴ 490 • written 11.0 years ago by 1.6k
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1
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1.8k
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Positional Details with Features through UniProt.ws Ultimately to display as tracks in ggbio
annotate ggbio annotate ggbio
updated 11.0 years ago by ▴ 490 • written 11.1 years ago by ▴ 30
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ChIPpeakAnno
SNP Annotation annotate convert SNP Annotation annotate convert
11.0 years ago Julie Zhu ★ 4.3k
0
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1
reply
1.6k
views
non-CpG methylated regions and strand information in MEDIPS output
BSgenome annotate biomaRt BSgenome MEDIPS BSgenome annotate biomaRt BSgenome MEDIPS
updated 11.1 years ago by ▴ 570 • written 11.1 years ago by ★ 13k
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2.2k
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annotation for TAqman assay IDs
Annotation probe annotate Annotation probe annotate
updated 11.1 years ago by 68k • written 11.1 years ago by ▴ 10
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Affymetrix mouse 430_2 array - annotation problem
Annotation mouse4302 annotate Annotation mouse4302 annotate
updated 11.1 years ago by 68k • written 11.1 years ago by ▴ 550
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annotating microarray data with mogene10stv1
Microarray Annotation annotate limma ASSIGN Microarray Annotation annotate limma ASSIGN
updated 11.1 years ago by 68k • written 11.1 years ago by ▴ 70
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Biomart annotation
annotate convert annotate convert
updated 11.1 years ago by ▴ 190 • written 11.1 years ago by ▴ 40
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5
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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 11.2 years ago by ▴ 160 • written 11.2 years ago by 68k
1
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4.4k
views
GRanges apply functions
GO annotate GO annotate
updated 11.2 years ago by ★ 4.2k • written 11.2 years ago by ▴ 380
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1
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4.2k
views
ChIPseeker: Error in annotatePeak
Sequencing GO annotate ChIPseeker Sequencing GO annotate ChIPseeker
11.3 years ago António Miguel de Jesus Domingues ▴ 510
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1.9k
views
ChIPpeakAnno
annotate ChIPpeakAnno annotate ChIPpeakAnno
updated 11.4 years ago by ★ 4.3k • written 11.4 years ago by ▴ 350
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lumi-package problem: nuID [e.g. nuID2EntrezID()] from vignette example throws an error on my system
annotate annotate
11.4 years ago Guest User ★ 13k
2
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1
reply
1.6k
views
HTqPCR- gene names not maintained in limmaCtData
annotate ddCt HTqPCR annotate ddCt HTqPCR
11.5 years ago Cornwell, Adam ▴ 110
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9
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2.5k
views
variantAnnotation: alternative GENETIC_CODE, and circular chromosomes?
VariantAnnotation Cancer Yeast annotate Biostrings VariantAnnotation VariantAnnotation
updated 11.6 years ago by 16k • written 11.6 years ago by ▴ 740
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Ontology
Annotation GO annotate GOstats Annotation GO annotate GOstats
11.6 years ago Marc Carlson ★ 7.2k
0
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1.5k
views
zero-row result breaks select() on PolyPhen.Hsapiens.* and SIFT.Hsapiens.*
VariantAnnotation Annotation PolyPhen SIFT annotate VariantAnnotation ensemblVEP Annotation
11.8 years ago Valerie Obenchain ★ 6.8k
0
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5
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1.9k
views
multiple annotations with get()?
Biobase annotate convert Biobase annotate convert
updated 11.9 years ago by 21k • written 11.9 years ago by ▴ 230
0
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2
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1.8k
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 11.9 years ago by ★ 3.6k • written 11.9 years ago by ▴ 120
346 results • Page 1 of 7
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Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …
Answer: A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::sel by James W. MacDonald 68k
Apparently it's been over-ridden by a different UniProtKB ID ``` > select(org.Ss.eg.db, "MYH11", "UNIPROT", "SYMBOL") 'select()' retu…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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