Showing : annotate • reset
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ChIPpeakAnno Question, regarding BED scores
Annotation annotate ChIPpeakAnno Annotation annotate ChIPpeakAnno
12.2 years ago Julie Zhu ★ 4.3k
3
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5
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5.9k
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getBM returns shorter vectors than values
annotate biomaRt oligo annotate biomaRt oligo
updated 12.3 years ago by ▴ 540 • written 12.2 years ago by ▴ 380
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Annotating Results for HuEx 1.0 STv2 - Oligo
annotate oligo annotate oligo
12.3 years ago Bade ▴ 310
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ChIPpeakAnno::assignChromosomeRegion
annotate annotate
12.3 years ago Julie Zhu ★ 4.3k
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3
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1.4k
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Annotate blastSequences Returns No Result
annotate annotate
updated 12.3 years ago by 25k • written 12.3 years ago by ★ 1.6k
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2
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2.0k
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GViz - successes and a few hopes
annotate Gviz annotate Gviz
updated 12.3 years ago by ★ 1.6k • written 12.4 years ago by ★ 1.6k
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1.4k
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答复: an error in AnnotationForge
Annotation ChipName annotate affy AnnotationForge Annotation ChipName annotate affy
12.3 years ago joseph ▴ 50
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1.3k
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an error in AnnotationForge
Annotation ChipName annotate affy AnnotationForge Annotation ChipName annotate affy
updated 12.4 years ago by ★ 7.2k • written 12.4 years ago by ▴ 50
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Venn diagrams using ChIPpeakAnno
annotate ChIPpeakAnno annotate ChIPpeakAnno
12.4 years ago Julie Zhu ★ 4.3k
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4
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2.1k
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FeatureExpressionSet using list.files() in place of read.xysfiles()
Microarray Annotation GO Organism probe annotate limma convert pdInfoBuilder sva GO sva
updated 12.5 years ago by ★ 4.3k • written 12.5 years ago by ▴ 140
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Error in makeOrgPackageFromNCBI
GO OrgDb annotate GOstats GO OrgDb annotate GOstats
12.5 years ago Chris Whelan ▴ 60
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10
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3.8k
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PAIR files -- feature set table
Microarray Annotation Organism annotate pdInfoBuilder Microarray Annotation Organism
updated 12.5 years ago by ★ 4.3k • written 12.5 years ago by ★ 13k
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2
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1.4k
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Reading Affy CEL files
annotate affy convert oligo annotate affy convert oligo
updated 12.5 years ago by ▴ 40 • written 12.5 years ago by ▴ 10
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4
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2.0k
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Howto annotate blast subject.id with AnnotationDbi
Alignment GO annotate AnnotationDbi Alignment GO annotate AnnotationDbi
updated 12.5 years ago by ★ 7.2k • written 12.5 years ago by ▴ 40
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2
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Annotation of Human Exon 1.0 ST
annotate biomaRt oligo annotate biomaRt oligo
updated 12.6 years ago by ★ 4.3k • written 12.6 years ago by ★ 13k
0
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1
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1.3k
views
Add new affy organism platform
Microarray Annotation Organism cdf db0 probe annotate affy Microarray Annotation cdf
updated 12.6 years ago by ★ 7.2k • written 12.6 years ago by ▴ 50
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where can I obtain the package of hugene20st.db
probe annotate probe annotate
12.6 years ago Guannan Sun ▴ 10
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1.8k
views
biomaRt not returning expected results
Annotation annotate biomaRt Annotation annotate biomaRt
updated 12.6 years ago by ▴ 540 • written 12.6 years ago by ★ 13k
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RE : ChIPpeakAnno_2.8.0 assignCromosomeRegion
annotate Category ChIPpeakAnno annotate Category ChIPpeakAnno
12.6 years ago Julie Zhu ★ 4.3k
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1.3k
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Annotated a snp list to find where these snp are located.
SNP annotate SNP annotate
updated 12.7 years ago by ★ 6.8k • written 12.7 years ago by ▴ 970
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7
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2.3k
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Fwd: GO terms: Annotation for HumanMethylation450
Annotation Pathways GO probe annotate Annotation Pathways GO probe annotate
12.7 years ago Jinyan Huang ▴ 110
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2
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1.2k
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Fwd: GO terms: Annotation for HumanMethylation450
Annotation Pathways GO probe annotate Annotation Pathways GO probe annotate
updated 12.7 years ago by ▴ 110 • written 12.7 years ago by ★ 4.2k
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2
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1.5k
views
ChIPpeakAnno
annotate ChIPpeakAnno annotate ChIPpeakAnno
12.7 years ago Julie Zhu ★ 4.3k
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949
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Annotating Illumina Mouse Ref8 array in BRB
annotate annotate
12.7 years ago Tejas Tirodkar ▴ 10
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2
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1.6k
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ChIPpeakAnno query
Microarray Annotation Cancer Prostate annotate affy convert biomaRt ChIPpeakAnno Cancer
updated 12.7 years ago by ▴ 10 • written 12.7 years ago by ★ 4.3k
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1.3k
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DEXseq: transcript plot
annotate annotate
12.7 years ago Vincenzo Capece ▴ 140
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4
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3.5k
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how to annotate Illumina HumanHT-12 v3 chips?
annotate annotate
updated 12.8 years ago by ▴ 90 • written 12.8 years ago by ▴ 110
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How to annotate Illumina HumanHT-12 v3 chips?
annotate annotate
12.8 years ago Feng Tian ▴ 110
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1.7k
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How to annotate Illumina HumanHT-12 v 3 expression beadchip?
annotate annotate
12.8 years ago Feng Tian ▴ 110
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2
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3.9k
views
mm10 goseq supported genome
annotate goseq annotate goseq
updated 12.9 years ago by ▴ 320 • written 12.9 years ago by ▴ 140
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2
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views
GSEABase error parsing msigdb_v3.1.xml
GO Infrastructure hgu95av2 Biobase annotate graph Category AnnotationDbi BiocGenerics GO
updated 12.9 years ago by 25k • written 12.9 years ago by ▴ 80
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3
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Filtering out duplicate probes in Affy data
Annotation mouse4302 annotate affy Annotation mouse4302 annotate affy
updated 12.9 years ago by 68k • written 12.9 years ago by ▴ 180
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importing data problem with methyAnalysis package
Biophysics Annotation Preprocessing annotate lumi methyAnalysis Biophysics Annotation lumi
12.9 years ago Pan Du ▴ 440
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3
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2.3k
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Use ChIPpeakAnno to find two-sided nearest genes to a peak
AnnotationData annotate ChIPpeakAnno AnnotationData annotate ChIPpeakAnno
13.0 years ago Julie Zhu ★ 4.3k
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5
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oligo package
Microarray Annotation annotate PROcess Microarray Annotation annotate PROcess
updated 13.0 years ago by 68k • written 13.0 years ago by ★ 13k
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2.5k
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locateVariants - error with GRanges query?
annotate annotate
13.0 years ago Lescai, Francesco ▴ 380
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3
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1.8k
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VariantAnnotation - dots in the INFO field give an error
annotate annotate
written 13.1 years ago by ▴ 40
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1.3k
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SNP6.0 annotation
SNP Annotation probe annotate SIM SNP Annotation probe annotate SIM
13.1 years ago Guest User ★ 13k
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1
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1.5k
views
How to get Gene ontology (GO) terms per probe
GO Clustering rat2302 annotate GO Clustering rat2302 annotate
updated 13.1 years ago by 68k • written 13.1 years ago by ★ 13k
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450K annotation: discrepancy between GEO GPL and Bioconductor annotation
Annotation db0 probe annotate PROcess GenomicFeatures GenomicRanges Annotation db0 probe
13.1 years ago Marc Carlson ★ 7.2k
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3
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1.7k
views
ChIPpeakAnno problem w getAllPeakSequence()
GO annotate ChIPpeakAnno GO annotate ChIPpeakAnno
updated 13.2 years ago by ★ 1.3k • written 13.2 years ago by ▴ 50
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3
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2.0k
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Assigning gene symbols to Affymetrix data and averaging probes
Annotation annotate affy limma convert Annotation annotate affy limma convert
updated 13.2 years ago by 68k • written 13.2 years ago by ▴ 50
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984
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findOverlappingPeaks in ChipPeakAnno
annotate annotate
13.2 years ago Julie Zhu ★ 4.3k
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1.4k
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question regarding ChIPPeakAnno use
Annotation annotate GLAD ChIPpeakAnno Annotation annotate GLAD ChIPpeakAnno
13.2 years ago Julie Zhu ★ 4.3k
0
votes
1
reply
1.5k
views
Annotate Affy SNP6 probes in bioc
hgu133a annotate hgu133a annotate
updated 13.3 years ago by 6.7k • written 13.3 years ago by ▴ 170
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4
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4.0k
views
How to combine VCF-class and data.frame with annotations
GO annotate convert ggbio GO annotate convert ggbio
written 13.3 years ago by ▴ 70
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3
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5.1k
views
Affymetrix annotation using R or NetAffx
annotate annotate
updated 13.3 years ago by 68k • written 13.3 years ago by ▴ 440
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1
reply
1.4k
views
Question about ChIPpeakAnno R package
AnnotationData annotate ChIPpeakAnno BayesPeak AnnotationData annotate ChIPpeakAnno
13.3 years ago Julie Zhu ★ 4.3k
0
votes
0
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857
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how to do GO analysis if i have some sequences
Annotation GO annotate Annotation GO annotate
13.4 years ago wang peter ★ 2.0k
0
votes
1
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1.1k
views
LIMMA -- obtaining values used to calculate lfc
probe annotate probe annotate
updated 13.4 years ago by 68k • written 13.4 years ago by ★ 13k
346 results • Page 2 of 7
Recent ...
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Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
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