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annotate
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0
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Create design matrix for differential methylation analysis
Annotation
annotate
DifferentialMethylation
minfiDataEPIC
updated 6 months ago by
Basti
▴ 750 • written 6 months ago by
titangerd
• 0
0
votes
2
replies
558
views
annotate peaks using a custom genome
ChIPSeq
annotate
ChIPpeakAnno
updated 11 months ago by
Kai Hu
▴ 70 • written 11 months ago by
C T
▴ 140
0
votes
8
replies
1.1k
views
fail to annotate chromosome data to single cell object
error
SingleCell
annotate
updated 4 months ago by
yw24418
• 0 • written 12 months ago by
sandra.garces.19
• 0
4
votes
3
replies
1.4k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran
Clustering
SingleCellExperiment
annotate
cluster
updated 20 months ago by
James W. MacDonald
65k • written 20 months ago by
achoppe
▴ 10
0
votes
0
replies
739
views
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
vote
2
replies
2.5k
views
mapping mouse ENSEMBL ids to human gene symbol
Annotation
AnnotationDbi
annotate
updated 2.7 years ago by
James W. MacDonald
65k • written 2.7 years ago by
cosomol999
• 0
2
votes
1
reply
626
views
The best pacakge to annotate a set of regions
annotate
updated 3.4 years ago by
James W. MacDonald
65k • written 3.4 years ago by
changxu.fan
▴ 20
0
votes
4
replies
1.3k
views
Annotating a sequence, new to bioconductor
annotate
updated 5.5 years ago by
James W. MacDonald
65k • written 5.5 years ago by
Teeps
• 0
0
votes
3
replies
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
votes
1
reply
1.2k
views
RNAseq _generating tx2gene table and using kallisto output to run DEseq
deseq
annotate
updated 6.3 years ago by
Michael Love
41k • written 6.3 years ago by
nupur.dasgupta
• 0
0
votes
4
replies
6.4k
views
How to annotate the Affymetrix Human Genome U133 Plus 2.0 Array chip
oligo
annotate
6.4 years ago
llkxiaolan
▴ 10
0
votes
1
reply
1.7k
views
How many genes are appropriate for GO enrichment analysis
go
annotate
rna-seq
clusterprofiler
updated 6.4 years ago by
k.vitting.seerup
▴ 120 • written 6.4 years ago by
Jack
• 0
0
votes
1
reply
1.3k
views
querying annotation hub for common TF, in common cell line returns no results....
annotate
annotationhub
updated 6.5 years ago by
shepherl
3.8k • written 6.5 years ago by
chrisclarkson100
▴ 50
0
votes
8
replies
1.6k
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 6.6 years ago by
James W. MacDonald
65k • written 6.6 years ago by
felixwertek
• 0
0
votes
3
replies
2.2k
views
Getting Differentially Expressed Genes from GOSeq Categories
goseq
gene ontology
biomart
annotate
category
updated 6.7 years ago by
b.nota
▴ 360 • written 6.8 years ago by
krc3004
▴ 10
0
votes
1
reply
1.1k
views
Annotation of Probe id to Gene
bioconductor
annotate
microarray
arabidopsis thaliana
updated 6.7 years ago by
James W. MacDonald
65k • written 6.7 years ago by
rkp
• 0
0
votes
4
replies
1.3k
views
TimmR error for hgu133a.db
software error
annotate
hgu133a
updated 7.1 years ago by
James W. MacDonald
65k • written 7.1 years ago by
pascalschulthess
• 0
3
votes
6
replies
2.5k
views
RSQLite::dbGetPreparedQuery() is deprecated in AnnotationForge
annotation
microarray
annotate
annotationforge
7.1 years ago
MOD
• 0
6
votes
5
replies
14k
views
Installation of package DESeq2
deseq2
rcurl
annotate
genefilter
geneplotter
updated 7.2 years ago by
Martin Morgan
25k • written 7.2 years ago by
Rémi Willamme
▴ 10
1
vote
2
replies
2.1k
views
blastSequences queries failing due to BLAST switch to https?
annotate
blastSequences
BLAST
https
updated 7.5 years ago by
Martin Morgan
25k • written 7.5 years ago by
ariel.hecht
• 0
0
votes
2
replies
1.5k
views
Problems using intansv...
annotate
annotate
updated 7.8 years ago by
akv22
• 0 • written 10.0 years ago by
Phil Ross
▴ 10
2
votes
1
reply
1.0k
views
Use matchPattern for large DNAStrings
biostrings
annotate
updated 7.8 years ago by
Hervé Pagès
16k • written 7.8 years ago by
Vinicius Henrique da Silva
▴ 40
0
votes
1
reply
1.4k
views
How to identify the microarray annotation library automatically from GEO study ID?
limma
microarray
annotation
bioconductor
annotate
updated 7.9 years ago by
James W. MacDonald
65k • written 7.9 years ago by
lijin.abc
• 0
0
votes
1
reply
1.5k
views
Getting data on the out-of-frame transcripts
annotate
sequencing
genomicfeatures
updated 8.7 years ago by
Hervé Pagès
16k • written 8.7 years ago by
janson.white
• 0
0
votes
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
votes
1
reply
1.2k
views
.getNcbiURL returns old NCBI url ?
annotate
ncbi
url
9.2 years ago
reuma
• 0
0
votes
1
reply
1.7k
views
can't run functions in 'annotate'
annotate
9.3 years ago
boris.steipe
• 0
1
vote
2
replies
1.5k
views
about library(Homo.sapiens) from TxDb.Hsapiens.UCSC.hg18.knownGene
annotate
9.4 years ago
Bogdan
▴ 670
2
votes
2
replies
1.8k
views
BLAST export library 'annotate'
blast
annotate
biostrings
export
fasta
9.4 years ago
b.stielow
• 0
5
votes
2
replies
10k
views
Probe to gene id conversion
annotate
biomart
probe to gene id
updated 9.4 years ago by
James W. MacDonald
65k • written 9.4 years ago by
rafi A
▴ 20
0
votes
6
replies
2.2k
views
Missing as.list generic from AnnotationDbi?
annotate
AnnotationDbi
annotate
AnnotationDbi
updated 9.5 years ago by
Jenny Drnevich
★ 2.0k • written 10.8 years ago by
Ryan C. Thompson
★ 7.9k
0
votes
2
replies
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
Tengfei Yin
▴ 490 • written 9.6 years ago by
Laurent Gatto
1.6k
0
votes
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
Tengfei Yin
▴ 490 • written 9.6 years ago by
Anne Deslattes Mays
▴ 30
0
votes
0
replies
1.4k
views
ChIPpeakAnno
SNP
Annotation
annotate
convert
SNP
Annotation
annotate
convert
9.6 years ago
Julie Zhu
★ 4.3k
0
votes
1
reply
1.2k
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
Lukas Chavez
▴ 570 • written 9.7 years ago by
Guest User
★ 13k
0
votes
1
reply
1.8k
views
annotation for TAqman assay IDs
Annotation
probe
annotate
Annotation
probe
annotate
updated 9.7 years ago by
James W. MacDonald
65k • written 9.7 years ago by
Bernard North
▴ 10
0
votes
2
replies
1.5k
views
Affymetrix mouse 430_2 array - annotation problem
Annotation
mouse4302
annotate
Annotation
mouse4302
annotate
updated 9.7 years ago by
James W. MacDonald
65k • written 9.7 years ago by
Rao,Xiayu
▴ 550
0
votes
5
replies
4.2k
views
annotating microarray data with mogene10stv1
Microarray
Annotation
annotate
limma
ASSIGN
Microarray
Annotation
annotate
limma
ASSIGN
updated 9.7 years ago by
James W. MacDonald
65k • written 9.7 years ago by
Jakub Stanislaw Nowak
▴ 70
0
votes
2
replies
2.9k
views
Biomart annotation
annotate
convert
annotate
convert
updated 9.7 years ago by
John Blischak
▴ 190 • written 9.7 years ago by
jarod_v6@libero.it
▴ 40
0
votes
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
Jason Hackney
▴ 160 • written 9.8 years ago by
James W. MacDonald
65k
1
vote
8
replies
3.6k
views
GRanges apply functions
GO
annotate
GO
annotate
updated 9.8 years ago by
Tim Triche
★ 4.2k • written 9.8 years ago by
Lescai, Francesco
▴ 380
0
votes
1
reply
3.0k
views
ChIPseeker: Error in annotatePeak
Sequencing
GO
annotate
ChIPseeker
Sequencing
GO
annotate
ChIPseeker
9.9 years ago
António Miguel de Jesus Domingues
▴ 490
0
votes
1
reply
1.5k
views
ChIPpeakAnno
annotate
ChIPpeakAnno
annotate
ChIPpeakAnno
updated 9.9 years ago by
Julie Zhu
★ 4.3k • written 9.9 years ago by
Paolo Kunderfranco
▴ 350
0
votes
0
replies
981
views
lumi-package problem: nuID [e.g. nuID2EntrezID()] from vignette example throws an error on my system
annotate
annotate
10.0 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
votes
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
Hervé Pagès
16k • written 10.2 years ago by
Janet Young
▴ 740
0
votes
0
replies
906
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
10.3 years ago
Valerie Obenchain
★ 6.8k
0
votes
5
replies
1.4k
views
multiple annotations with get()?
Biobase
annotate
convert
Biobase
annotate
convert
updated 10.5 years ago by
Sean Davis
21k • written 10.5 years ago by
Ed Siefker
▴ 230
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
Wei Shi
★ 3.6k • written 10.5 years ago by
Kemal Akat
▴ 120
50 results • Page
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Comment: error when using M-values in ChAMP
by
hortenseguillaume96
• 0
Hello Tian, I'd like to get the M-values matrix so that I can carry out a linear regression study. However, when I apply the champ.load fu…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Votes
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
Answer: error in ChAMP loading file
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