Showing : ChiPpeakAnno • reset
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ChIPpeakAnno
annotate ChIPpeakAnno annotate ChIPpeakAnno
12.7 years ago Julie Zhu ★ 4.3k
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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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build TSS from biomaRt for ChIPpeakAnno, how to decide the mm9 and mm10 assembly?
Mus musculus biomaRt ChIPpeakAnno Mus musculus biomaRt ChIPpeakAnno
12.8 years ago Julie Zhu ★ 4.3k
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ChIPpeakAnno question--peak aggregation over bins from TSS
ChIPpeakAnno ChIPpeakAnno
12.9 years ago Julie Zhu ★ 4.3k
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ChIPpeakAnno question--peak aggregation over bins from TSS
ChIPpeakAnno ChIPpeakAnno
updated 12.9 years ago by ★ 4.3k • written 12.9 years ago by ▴ 40
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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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7
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2.0k
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Problem loading BED file with BED2RangedData
GO ChIPpeakAnno GO ChIPpeakAnno
updated 13.0 years ago by ★ 1.3k • written 13.0 years ago by ▴ 280
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ChIPpeakAnno
Annotation Category ChIPpeakAnno Annotation Category ChIPpeakAnno
13.1 years ago Julie Zhu ★ 4.3k
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3
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1.7k
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ChIPpeakAnno problem w getAllPeakSequence()
GO annotate ChIPpeakAnno GO annotate ChIPpeakAnno
updated 13.1 years ago by ★ 1.3k • written 13.1 years ago by ▴ 50
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ChipPeakAnno - slightly different results between makeVennDiagram and findPeakOverlaps
Genetics GO ChIPpeakAnno Genetics GO ChIPpeakAnno
13.2 years ago Julie Zhu ★ 4.3k
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ChipPeakAnno - slightly different results between makeVennDiagram and findPeakOverlaps
Genetics ChIPpeakAnno Genetics ChIPpeakAnno
updated 13.2 years ago by ★ 1.3k • written 13.2 years ago by ▴ 510
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question regarding ChIPPeakAnno use
Annotation annotate GLAD ChIPpeakAnno Annotation annotate GLAD ChIPpeakAnno
13.2 years ago Julie Zhu ★ 4.3k
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3
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1.6k
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RE ChIPPEAKANNO
miRNA Genetics ChIPpeakAnno miRNA Genetics ChIPpeakAnno
13.3 years ago Julie Zhu ★ 4.3k
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4
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1.6k
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ChIPpeakAnno
convert ChIPpeakAnno convert ChIPpeakAnno
13.3 years ago Julie Zhu ★ 4.3k
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1
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1.4k
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Question about ChIPpeakAnno R package
AnnotationData annotate ChIPpeakAnno BayesPeak AnnotationData annotate ChIPpeakAnno
13.3 years ago Julie Zhu ★ 4.3k
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ChIPpeakAnno to find peaks nearest to miRNA
miRNA Annotation GO BSgenome biomaRt BSgenome ChIPpeakAnno miRNA Annotation GO BSgenome
13.3 years ago Julie Zhu ★ 4.3k
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4
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1.6k
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more question about makeVennDiagram
GO ChIPpeakAnno GO ChIPpeakAnno
13.3 years ago Julie Zhu ★ 4.3k
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3
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2.2k
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ChIPpeakAnno to find peaks nearest to miRNA
miRNA GO BSgenome BSgenome ChIPpeakAnno miRNA GO BSgenome BSgenome ChIPpeakAnno
updated 13.4 years ago by ★ 4.3k • written 13.4 years ago by ▴ 350
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ChIPpeakAnno - Annotation of miRNA
miRNA GO BSgenome BSgenome ChIPpeakAnno miRNA GO BSgenome BSgenome ChIPpeakAnno
13.4 years ago Paolo Kunderfranco ▴ 350
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1.9k
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[ChIPpeakAnno] Can not start ChIPpeakAnno after update to version 2.5.9
ChIPpeakAnno ChIPpeakAnno
updated 13.5 years ago by ★ 13k • written 13.5 years ago by ▴ 90
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ChIPPeakAnno query (overlaps)
ChIPpeakAnno ChIPpeakAnno
13.6 years ago Julie Zhu ★ 4.3k
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2
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1.3k
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ChIPpeakAnno: Inquiry for Worm Analysis
Annotation GO annotate convert ChIPpeakAnno Annotation GO annotate convert ChIPpeakAnno
13.8 years ago • updated 13.7 years ago Julie Zhu ★ 4.3k
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1.1k
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ChIPpeakAnno - Request of information
Annotation annotate ChIPpeakAnno Annotation annotate ChIPpeakAnno
updated 13.7 years ago by ★ 1.3k • written 13.7 years ago by ★ 4.3k
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ChIPpeakAnno findVennCounts
ChIPpeakAnno ChIPpeakAnno
updated 13.7 years ago by ▴ 10 • written 13.7 years ago by ★ 4.3k
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1.7k
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question regarding ChIPPeakAnno use
ChIPpeakAnno ChIPpeakAnno
updated 13.7 years ago by ▴ 20 • written 13.7 years ago by ★ 4.3k
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1
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1.2k
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ChIPpeakAnno on pathway enrichment
Pathways GO ChIPpeakAnno Pathways GO ChIPpeakAnno
updated 13.7 years ago by ▴ 240 • written 13.7 years ago by ★ 4.3k
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ChipPeakAnno question about file conversion
convert ChIPpeakAnno convert ChIPpeakAnno
13.7 years ago Julie Zhu ★ 4.3k
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4
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2.7k
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ChIPpeakAnno as.data.frame error
GO AnnotationData annotate convert ChIPpeakAnno GO AnnotationData annotate convert
updated 13.8 years ago by ★ 4.3k • written 13.8 years ago by ▴ 910
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2
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1.9k
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ChIPpeakAnno
GO BSgenome annotate BSgenome ChIPpeakAnno GO BSgenome annotate BSgenome ChIPpeakAnno
updated 13.8 years ago by ▴ 10 • written 13.8 years ago by ▴ 10
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1.1k
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ChiPpeakAnno: findOverlappingPeaks: running time
GO ChIPpeakAnno GO ChIPpeakAnno
updated 13.9 years ago by ★ 4.3k • written 13.9 years ago by ★ 13k
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1.0k
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ChIPpeakAnno, makeVennDiagram
Transcription ChIPpeakAnno Transcription ChIPpeakAnno
14.1 years ago Julie Zhu ★ 4.3k
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938
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ChIPpeakAnno - for genes with multiple isoforms
Transcription Annotation annotate ChIPpeakAnno Transcription Annotation annotate
14.2 years ago Julie Zhu ★ 4.3k
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3.1k
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more stupid *Ranges questions...
Transcription ChIPpeakAnno GenomicRanges Transcription ChIPpeakAnno GenomicRanges
updated 14.2 years ago by ★ 11k • written 14.2 years ago by ★ 4.2k
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[Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch problems in R2.13/ChIPpeakAnno_1.8.0 and R2.13/ChIPpeakAnno_2.0.2
Annotation GO BSgenome BSgenome ChIPpeakAnno Annotation GO BSgenome BSgenome ChIPpeakAnno
14.3 years ago • updated 14.2 years ago Julie Zhu ★ 4.3k
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1.9k
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ChIPpeakAnno, getAnnotation question
Annotation microRNA ChIPpeakAnno Annotation microRNA ChIPpeakAnno
14.3 years ago Julie Zhu ★ 4.3k
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1.6k
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chippeakanno:::addGeneID for adding gene symbol etc. to annotatedPeak or enrichedGO
Annotation convert biomaRt bridge ChIPpeakAnno Annotation convert biomaRt bridge
updated 14.3 years ago by ▴ 810 • written 14.3 years ago by ★ 4.3k
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1.2k
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Regarding ChIPpeakAnno::getEnrichedGO function
GO ChIPpeakAnno GO ChIPpeakAnno
updated 14.4 years ago by ▴ 20 • written 14.4 years ago by ★ 4.3k
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ChIPpeakAnno package - filter annotatedPeak for GO enrichment analysis
ChIPSeq Annotation GO biomaRt chipseq ChIPpeakAnno ChIPSeq Annotation GO biomaRt chipseq
14.4 years ago Julie Zhu ★ 4.3k
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2
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1.5k
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Hypergeometric test in ChIPpeakAnno
annotate ChIPpeakAnno annotate ChIPpeakAnno
updated 14.4 years ago by ▴ 20 • written 14.4 years ago by ★ 4.3k
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1.1k
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Information needed for ChIPpeakAnno package
annotate ChIPpeakAnno annotate ChIPpeakAnno
14.4 years ago Julie Zhu ★ 4.3k
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911
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choice of biomaRt feature from annotatePeakInBatch
ChIPSeq Annotation biomaRt chipseq ChIPpeakAnno ChIPSeq Annotation biomaRt chipseq
14.5 years ago Julie Zhu ★ 4.3k
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930
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ChIPpeakAnno
annotate IRanges ChIPpeakAnno annotate IRanges ChIPpeakAnno
14.5 years ago Julie Zhu ★ 4.3k
0
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1
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847
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IRanges question!
annotate IRanges ChIPpeakAnno annotate IRanges ChIPpeakAnno
updated 14.5 years ago by ★ 11k • written 14.5 years ago by ▴ 290
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995
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4-way venn diagram with ChIPpeakAnno
ChIPpeakAnno ChIPpeakAnno
14.5 years ago Julie Zhu ★ 4.3k
0
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1
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1.1k
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Create an non-mainstream organism-specific database for ChIP-chip analysis
Organism ChIPpeakAnno Organism ChIPpeakAnno
updated 14.6 years ago by ★ 7.2k • written 14.6 years ago by ▴ 40
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1.5k
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Using ChIPpeakAnno on a non-mainstream organism
Transcription Annotation GO AnnotationData Organism BSgenome biomaRt BSgenome ChIPpeakAnno
14.6 years ago Julie Zhu ★ 4.3k
0
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1
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1.5k
views
An error while installing RWebService
limma biomaRt RWebServices IRanges microRNA SJava ChIPpeakAnno limma biomaRt RWebServices
updated 14.7 years ago by ★ 8.2k • written 14.7 years ago by ▴ 120
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[ENQUIRY] chIPpeakAnno annotatePeakInBatch
GO AnnotationData ChIPpeakAnno GO AnnotationData ChIPpeakAnno
14.7 years ago Julie Zhu ★ 4.3k
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3
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1.4k
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Help on ChIPpeakAnno
probe ChIPpeakAnno probe ChIPpeakAnno
14.7 years ago Prashantha Hebbar ▴ 260
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1.3k
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Call for help about your Chippeakanno R package
Annotation Cancer AnnotationData ChIPpeakAnno Annotation Cancer AnnotationData ChIPpeakAnno
14.8 years ago Julie Zhu ★ 4.3k
179 results • Page 3 of 4
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It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
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Answered here: https://support.bioconductor.org/p/16318/
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Thank you very much! will take that into consideration
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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
Comment: upstream git branches of bioc-release
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