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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 7 months ago by
Basti
▴ 780 • written 7 months ago by
titangerd
• 0
0
votes
2
replies
617
views
annotate peaks using a custom genome
ChIPSeq
annotate
ChIPpeakAnno
updated 12 months ago by
Kai Hu
▴ 70 • written 12 months ago by
C T
▴ 140
0
votes
8
replies
1.2k
views
fail to annotate chromosome data to single cell object
error
SingleCell
annotate
updated 5 months ago by
yw24418
• 0 • written 14 months ago by
sandra.garces.19
• 0
4
votes
3
replies
1.5k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran
Clustering
SingleCellExperiment
annotate
cluster
updated 21 months ago by
James W. MacDonald
65k • written 21 months ago by
achoppe
▴ 10
0
votes
0
replies
798
views
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
vote
2
replies
2.6k
views
mapping mouse ENSEMBL ids to human gene symbol
Annotation
AnnotationDbi
annotate
updated 2.8 years ago by
James W. MacDonald
65k • written 2.8 years ago by
cosomol999
• 0
2
votes
1
reply
662
views
The best pacakge to annotate a set of regions
annotate
updated 3.5 years ago by
James W. MacDonald
65k • written 3.5 years ago by
changxu.fan
▴ 20
0
votes
4
replies
1.4k
views
Annotating a sequence, new to bioconductor
annotate
updated 5.6 years ago by
James W. MacDonald
65k • written 5.6 years ago by
Teeps
• 0
0
votes
3
replies
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
votes
1
reply
1.3k
views
RNAseq _generating tx2gene table and using kallisto output to run DEseq
deseq
annotate
updated 6.4 years ago by
Michael Love
42k • written 6.4 years ago by
nupur.dasgupta
• 0
0
votes
4
replies
6.6k
views
How to annotate the Affymetrix Human Genome U133 Plus 2.0 Array chip
oligo
annotate
6.5 years ago
llkxiaolan
▴ 10
0
votes
1
reply
1.8k
views
How many genes are appropriate for GO enrichment analysis
go
annotate
rna-seq
clusterprofiler
updated 6.6 years ago by
k.vitting.seerup
▴ 120 • written 6.6 years ago by
Jack
• 0
0
votes
1
reply
1.4k
views
querying annotation hub for common TF, in common cell line returns no results....
annotate
annotationhub
updated 6.7 years ago by
shepherl
3.9k • written 6.7 years ago by
chrisclarkson100
▴ 50
0
votes
8
replies
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
James W. MacDonald
65k • written 6.7 years ago by
felixwertek
• 0
0
votes
3
replies
2.3k
views
Getting Differentially Expressed Genes from GOSeq Categories
goseq
gene ontology
biomart
annotate
category
updated 6.8 years ago by
b.nota
▴ 360 • written 6.9 years ago by
krc3004
▴ 10
0
votes
1
reply
1.2k
views
Annotation of Probe id to Gene
bioconductor
annotate
microarray
arabidopsis thaliana
updated 6.9 years ago by
James W. MacDonald
65k • written 6.9 years ago by
rkp
• 0
0
votes
4
replies
1.4k
views
TimmR error for hgu133a.db
software error
annotate
hgu133a
updated 7.2 years ago by
James W. MacDonald
65k • written 7.2 years ago by
pascalschulthess
• 0
3
votes
6
replies
2.6k
views
RSQLite::dbGetPreparedQuery() is deprecated in AnnotationForge
annotation
microarray
annotate
annotationforge
7.2 years ago
MOD
• 0
6
votes
5
replies
14k
views
Installation of package DESeq2
deseq2
rcurl
annotate
genefilter
geneplotter
updated 7.3 years ago by
Martin Morgan
25k • written 7.3 years ago by
Rémi Willamme
▴ 10
1
vote
2
replies
2.2k
views
blastSequences queries failing due to BLAST switch to https?
annotate
blastSequences
BLAST
https
updated 7.6 years ago by
Martin Morgan
25k • written 7.6 years ago by
ariel.hecht
• 0
0
votes
2
replies
1.5k
views
Problems using intansv...
annotate
annotate
updated 7.9 years ago by
akv22
• 0 • written 10.1 years ago by
Phil Ross
▴ 10
2
votes
1
reply
1.1k
views
Use matchPattern for large DNAStrings
biostrings
annotate
updated 8.0 years ago by
Hervé Pagès
16k • written 8.0 years ago by
Vinicius Henrique da Silva
▴ 40
0
votes
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
James W. MacDonald
65k • written 8.0 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 8.8 years ago by
Hervé Pagès
16k • written 8.8 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
8.9 years ago
adnan.niazi
• 0
0
votes
1
reply
1.3k
views
.getNcbiURL returns old NCBI url ?
annotate
ncbi
url
9.4 years ago
reuma
• 0
0
votes
1
reply
1.7k
views
can't run functions in 'annotate'
annotate
9.4 years ago
boris.steipe
• 0
1
vote
2
replies
1.6k
views
about library(Homo.sapiens) from TxDb.Hsapiens.UCSC.hg18.knownGene
annotate
9.5 years ago
Bogdan
▴ 670
2
votes
2
replies
1.8k
views
BLAST export library 'annotate'
blast
annotate
biostrings
export
fasta
9.5 years ago
b.stielow
• 0
5
votes
2
replies
10k
views
Probe to gene id conversion
annotate
biomart
probe to gene id
updated 9.6 years ago by
James W. MacDonald
65k • written 9.6 years ago by
rafi A
▴ 20
0
votes
6
replies
2.2k
views
Missing as.list generic from AnnotationDbi?
annotate
AnnotationDbi
annotate
AnnotationDbi
updated 9.6 years ago by
Jenny Drnevich
★ 2.0k • written 10.9 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 9.7 years ago by
Tengfei Yin
▴ 490 • written 9.7 years ago by
Laurent Gatto
1.6k
0
votes
1
reply
1.5k
views
Positional Details with Features through UniProt.ws Ultimately to display as tracks in ggbio
annotate
ggbio
annotate
ggbio
updated 9.7 years ago by
Tengfei Yin
▴ 490 • written 9.7 years ago by
Anne Deslattes Mays
▴ 30
0
votes
0
replies
1.4k
views
ChIPpeakAnno
SNP
Annotation
annotate
convert
SNP
Annotation
annotate
convert
9.7 years ago
Julie Zhu
★ 4.3k
0
votes
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
Lukas Chavez
▴ 570 • written 9.8 years ago by
Guest User
★ 13k
0
votes
1
reply
1.9k
views
annotation for TAqman assay IDs
Annotation
probe
annotate
Annotation
probe
annotate
updated 9.8 years ago by
James W. MacDonald
65k • written 9.8 years ago by
Bernard North
▴ 10
0
votes
2
replies
1.6k
views
Affymetrix mouse 430_2 array - annotation problem
Annotation
mouse4302
annotate
Annotation
mouse4302
annotate
updated 9.8 years ago by
James W. MacDonald
65k • written 9.8 years ago by
Rao,Xiayu
▴ 550
0
votes
5
replies
4.3k
views
annotating microarray data with mogene10stv1
Microarray
Annotation
annotate
limma
ASSIGN
Microarray
Annotation
annotate
limma
ASSIGN
updated 9.8 years ago by
James W. MacDonald
65k • written 9.8 years ago by
Jakub Stanislaw Nowak
▴ 70
0
votes
2
replies
2.9k
views
Biomart annotation
annotate
convert
annotate
convert
updated 9.8 years ago by
John Blischak
▴ 190 • written 9.8 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 9.9 years ago by
Jason Hackney
▴ 160 • written 9.9 years ago by
James W. MacDonald
65k
1
vote
8
replies
3.7k
views
GRanges apply functions
GO
annotate
GO
annotate
updated 9.9 years ago by
Tim Triche
★ 4.2k • written 9.9 years ago by
Lescai, Francesco
▴ 380
0
votes
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
votes
1
reply
1.6k
views
ChIPpeakAnno
annotate
ChIPpeakAnno
annotate
ChIPpeakAnno
updated 10.1 years ago by
Julie Zhu
★ 4.3k • written 10.1 years ago by
Paolo Kunderfranco
▴ 350
0
votes
0
replies
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
votes
9
replies
2.0k
views
variantAnnotation: alternative GENETIC_CODE, and circular chromosomes?
VariantAnnotation
Cancer
Yeast
annotate
Biostrings
VariantAnnotation
VariantAnnotation
updated 10.3 years ago by
Hervé Pagès
16k • written 10.3 years ago by
Janet Young
▴ 740
0
votes
0
replies
932
views
Ontology
Annotation
GO
annotate
GOstats
Annotation
GO
annotate
GOstats
10.3 years ago
Marc Carlson
★ 7.2k
0
votes
0
replies
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
votes
5
replies
1.5k
views
multiple annotations with get()?
Biobase
annotate
convert
Biobase
annotate
convert
updated 10.6 years ago by
Sean Davis
21k • written 10.6 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 10.6 years ago by
Wei Shi
★ 3.6k • written 10.6 years ago by
Kemal Akat
▴ 120
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Comment: deseq2 results
by
sajadahmad41454
• 0
thank you so much and sorry for bothering you again and again, it is urgent because it is my project deadline. i have removed that sample a…
Comment: deseq2 results
by
swbarnes2
★ 1.4k
Ask the people who made the libraires if there was anything unusual in the QC of the outlier sample. Try to figure out what biologically …
Comment: Can't post a question containing code?
by
NATASHA
• 0
did you find a solution? I´m having the same problem
Comment: error
by
NATASHA
• 0
Please ignore, i didnt copy all the scrip
Comment: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
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