Showing : annotation • reset
2
votes
27
replies
2.1k
views
Applying NetAffx biological annotation to Affymetrix gene expression dataset
microarray annotation
updated 5.1 years ago by 65k • written 5.1 years ago by ▴ 10
11
votes
23
replies
2.6k
views
crlmm support for Illumina arrays with no annotation package?
crlmm QCarray annotation
updated 4.3 years ago by • 0 • written 4.5 years ago by ▴ 30
5
votes
22
replies
5.5k
views
sqliteSendQuery error in AnnotationForge bioconductor package
bioconductor annotationforge annotationdbi annotation r
updated 7.8 years ago by ★ 1.0k • written 9.2 years ago by • 0
0
votes
19
replies
3.4k
views
Analysis and annotation (full) of Affymetrix Mouse Exon 1.0 ST arrays
Annotation cdf Annotation cdf
updated 11.9 years ago by 65k • written 11.9 years ago by ▴ 340
14
votes
19
replies
19k
views
DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2 annotation granges
updated 2.2 years ago by ▴ 60 • written 9.5 years ago by ▴ 120
3
votes
18
replies
2.8k
views
Annotating codelink data file
r codelink annotation annotationdbi
updated 9.0 years ago by ▴ 760 • written 9.0 years ago by ▴ 260
0
votes
17
replies
8.2k
views
Analysis of Affymetrix Mouse Gene 2.0 ST arrays
Annotation Normalization GO PROcess oligo Annotation Normalization GO PROcess oligo
updated 11.1 years ago by 65k • written 11.1 years ago by ▴ 100
4
votes
17
replies
2.4k
views
annotation conversion from old microarray to latest Entrez and Ensembl ID
biomaRt annotation Ensembl annotationHub
updated 3.6 years ago by ★ 3.9k • written 3.6 years ago by ▴ 10
3
votes
17
replies
4.3k
views
filtering probes in affymetrix data
Annotation limma Annotation limma
updated 10.2 years ago by 65k • written 10.2 years ago by ▴ 180
0
votes
17
replies
2.6k
views
problems with strand in predictCoding
VariantAnnotation Annotation BSgenome BSgenome VariantAnnotation VariantAnnotation BSgenome
updated 12.0 years ago by ▴ 20 • written 12.0 years ago by ▴ 50
2
votes
16
replies
1.6k
views
DESeq2 annotation file
annotation
4.0 years ago zen • 0
2
votes
16
replies
4.1k
views
TxDb annotations for human chrM
GenomicFeatures TxDb.Hsapiens.UCSC.hg19.knownGene annotation
9.2 years ago Robert Castelo ★ 3.2k
11
votes
15
replies
4.1k
views
Annotation for Affymetrix GeneChip PrimeView.
annotation
updated 4.0 years ago by ★ 3.9k • written 4.0 years ago by • 0
1
vote
15
replies
3.4k
views
reactome.db: reactome IDs not mapped to pathway names
annotation pathways
updated 9.0 years ago by ▴ 150 • written 9.5 years ago by ★ 2.0k
2
votes
14
replies
3.5k
views
Annotation of Affy Porcine Gene 1.0 ST array data
limma oligo annotation
updated 9.1 years ago by ▴ 130 • written 9.3 years ago by • 0
3
votes
13
replies
2.9k
views
Rsubread- feature counts
annotation Rsubread featureCounts
updated 5.2 years ago by 50k • written 5.2 years ago by • 0
4
votes
13
replies
4.3k
views
How to create an output file with sequence ID's from multiple BLAST result using blastSequences in "Biostrings"
annotation blast biostrings
updated 8.8 years ago by 25k • written 8.8 years ago by • 0
2
votes
12
replies
2.3k
views
ann_objs$MAPCOUNTS <- AnnotationDbi:::createMAPCOUNTS(dbconn, prefix) does not work well
annotation orgdb
8.2 years ago knishida ▴ 20
0
votes
12
replies
1.9k
views
Annotation.db: how automatically call a mapping?
Annotation moe430a Annotation moe430a
updated 14.8 years ago by 25k • written 14.8 years ago by ★ 3.9k
0
votes
11
replies
1.5k
views
Problem with "ragene10stprobeset.db" package
Annotation annotate Annotation annotate
updated 12.0 years ago by 65k • written 12.0 years ago by ▴ 20
7
votes
11
replies
2.3k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 4.0 years ago by ★ 3.2k • written 4.0 years ago by ▴ 60
0
votes
11
replies
2.7k
views
Clariom D Assays, annotation
annotation
updated 6.4 years ago by 65k • written 6.4 years ago by • 0
0
votes
11
replies
1.9k
views
Complete variant toolbox: gmapR/VariantTools/VariantAnnotation
VariantAnnotation Annotation VariantAnnotation VariantTools VariantAnnotation Annotation
updated 10.4 years ago by ★ 6.8k • written 10.4 years ago by ★ 1.7k
1
vote
11
replies
3.8k
views
oligo package requires the annotation package pd.ht.mg.430.pm - where is it?
oligo microarray annotation
updated 8.6 years ago by 65k • written 8.6 years ago by • 0
5
votes
11
replies
4.1k
views
How to annotate gene names for genomic coordinates?
annotation
written 8.8 years ago by • 0
0
votes
11
replies
1.5k
views
breastCancerNKI patients question
Annotation Annotation
12.5 years ago Xavier Robin ▴ 30
6
votes
11
replies
1.7k
views
"associated_gene" attribute from biomaRt returns too few values - SNP(rsID dataset)
r biomart SNP annotation HUGO
updated 3.7 years ago by ★ 6.5k • written 3.7 years ago by • 0
0
votes
10
replies
2.1k
views
Retrieve Entrez IDs for enriched GO terms
Microarray Annotation GO limma GOstats biomaRt Microarray Annotation GO limma GOstats
updated 14.6 years ago by ★ 2.0k • written 14.6 years ago by ▴ 90
0
votes
10
replies
1.9k
views
package pair "hugene10stv1cdf"/"hugene10stprobeset.db"
Annotation cdf Annotation cdf
updated 14.0 years ago by 65k • written 14.0 years ago by ★ 2.3k
0
votes
10
replies
1.5k
views
how to build a GOstats-compatible annotation package for plasmodium falciparum?
Annotation Yeast GOstats Annotation Yeast GOstats
updated 16.5 years ago by ▴ 30 • written 16.5 years ago by ★ 1.1k
5
votes
10
replies
1.4k
views
tximport and stevia, how to build tx2gene without any reference genome
deseq2 annotation
updated 4.1 years ago by 41k • written 4.1 years ago by ▴ 60
0
votes
10
replies
1.9k
views
comparing GO lists
Annotation GO Cancer graph GOstats Annotation GO Cancer graph GOstats
updated 16.7 years ago by ▴ 130 • written 16.7 years ago by ★ 5.5k
7
votes
10
replies
6.2k
views
annotating gene for transcript type/biotype
annotation homo.sapiens
updated 3.4 years ago by 65k • written 8.5 years ago by ▴ 40
5
votes
10
replies
2.0k
views
How to do annotation with Limma
annotation limma
updated 2.8 years ago by ★ 3.9k • written 2.9 years ago by • 0
9
votes
10
replies
1.4k
views
Mapping of GENE symbols into ENTREZ
limma annotation Gene
4.6 years ago • updated 4.2 years ago omarrafiqued ▴ 50
0
votes
10
replies
2.8k
views
MakeTranscriptDbFromGFF
Annotation TranscriptDb Annotation TranscriptDb
updated 11.0 years ago by ★ 7.2k • written 11.0 years ago by ▴ 340
0
votes
10
replies
3.0k
views
PAIR files -- feature set table
Microarray Annotation Organism annotate pdInfoBuilder Microarray Annotation Organism
updated 10.9 years ago by ★ 4.3k • written 10.9 years ago by ★ 13k
0
votes
10
replies
2.8k
views
gene set enrichment
Annotation Organism Annotation Organism
updated 2.1 years ago by 50k • written 11.4 years ago by ▴ 220
0
votes
10
replies
2.4k
views
assignChromosomeRegion in 2.6.0 ChIPpeakAnno
Microarray Annotation GO Network Regression Survival Infrastructure Escherichia coli ROC
11.1 years ago Julie Zhu ★ 4.3k
2
votes
10
replies
3.5k
views
Extract three types of intergenic regions
granges views annotation iranges
updated 8.5 years ago by ★ 1.7k • written 8.5 years ago by ▴ 50
0
votes
10
replies
1.7k
views
AnnBuilder doesn't work on gene information ("GENENAME", "SYMBOL", etc)
Microarray Annotation probe annotate affy AnnBuilder Microarray Annotation probe annotate
updated 17.8 years ago by ★ 2.9k • written 17.8 years ago by ★ 1.6k
4
votes
10
replies
2.5k
views
how to analyze WGCNA results?
cancer probe deseq2 annotation normalization
updated 3.9 years ago by ★ 3.9k • written 3.9 years ago by ▴ 10
0
votes
9
replies
1.3k
views
SQLForge and probes that map to multiple genes
Annotation Annotation
15.8 years ago Cei Abreu-Goodger ▴ 830
0
votes
9
replies
1.7k
views
GO over representation analysis
Annotation GO maanova Annotation GO maanova
updated 15.7 years ago by ★ 7.2k • written 15.7 years ago by ▴ 310
0
votes
9
replies
1.7k
views
metadata - annotation package changes
Annotation moe430a probe Annotation moe430a probe
updated 18.7 years ago by ★ 2.9k • written 18.7 years ago by ▴ 160
0
votes
9
replies
1.6k
views
removing packages from the workspace - is this ok?
Annotation PROcess Annotation PROcess
updated 12.9 years ago by ★ 13k • written 12.9 years ago by ★ 1.9k
2
votes
9
replies
3.4k
views
GEOquery error
Annotation PROcess Annotation PROcess
updated 8.1 years ago by 6.7k • written 10.0 years ago by 65k
4
votes
9
replies
2.5k
views
Common workflow to build an microarray annatation package, like hgu133a.db
annotation
updated 8.3 years ago by 65k • written 8.3 years ago by • 0
0
votes
9
replies
1.8k
views
Mapping microarray probes to the genome using findOverlaps
Microarray Alignment Annotation zebrafish probe Biostrings GenomicFeatures Microarray
updated 13.1 years ago by 21k • written 13.1 years ago by 16k
3
votes
9
replies
2.4k
views
Annotation problem while quering hgug4112a.db with function select and duplicates for agilent microarray dataset
limma annotation agilent hgug4112a microarray
8.2 years ago Konstantinos Yeles ▴ 80
50 results • Page 1 of 1
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Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
Thank you for your suggestions! Here is the MA plot: ![enter image description here][1] I tried several normalization methods with DiffBi…
Answer: OrgDb for maize by Guido Hooiveld ★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question by Garrett • 0
Thanks Peter!
Comment: FGSEA pre-ranked input in increasing order or decreasing by sropri • 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing by alserg ▴ 240
They are reorder in the decreasing order.
Votes
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
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