Showing : Pathways • reset
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ISMB talks: Pathview for pathway-based data integration and visualization
Pathways Visualization pathview Pathways Visualization pathview
11.4 years ago Luo Weijun ★ 1.6k
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ECCB 2014
Sequencing Pathways Sequencing Pathways
11.5 years ago Wolfgang Raffelsberger ▴ 60
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PostDoc opportunity
Pathways Network Pathways Network
11.5 years ago Guest User ★ 13k
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Thalassiosira pseudonana
Annotation Pathways GO Annotation Pathways GO
11.5 years ago nooshin ▴ 300
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graphite biopax conversion code?
Pathways graphite Pathways graphite
11.5 years ago Ryan C. Thompson ★ 7.9k
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Can GAGE be used for transcript set pathway analysis
Pathways gage Pathways gage
updated 11.5 years ago by ★ 1.6k • written 11.5 years ago by ▴ 100
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use of voom function with attract package
Pathways GO attract Pathways GO attract
updated 11.6 years ago by 53k • written 11.6 years ago by ★ 13k
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KEGG pathway analysis with ReportingTools
Pathways GO ReportingTools Pathways GO ReportingTools
11.6 years ago Mayte Suarez-Farinas ▴ 510
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[phenoTest package]: gsea.kegg error with absVals parameter
Pathways GO hgu133a hgu95av2 phenoTest Pathways GO hgu133a hgu95av2 phenoTest
11.6 years ago Kostas Kerkentzes ▴ 10
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pathview with tomato and minor species
Pathways pathview Pathways pathview
11.7 years ago Luo Weijun ★ 1.6k
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GAGE/Pathview RNA-Seq Workflows: reference genome issue
Pathways pathview Pathways pathview
11.7 years ago Luo Weijun ★ 1.6k
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SPIA
Pathways SPIA Pathways SPIA
updated 11.7 years ago by ▴ 570 • written 11.7 years ago by ★ 13k
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pathview - plotting multiple samples in the same graph?
Pathways GO pathview Pathways GO pathview
11.7 years ago Peter Davidsen ▴ 210
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Request for installation of software R2.13/Biconductor 2.8
Pathways Pathways
updated 11.7 years ago by ★ 8.2k • written 11.7 years ago by ▴ 10
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GO-Pathways using RDAVIDWebService
Pathways Homo sapiens RDAVIDWebService Pathways Homo sapiens RDAVIDWebService
updated 11.8 years ago by ▴ 370 • written 11.8 years ago by ▴ 50
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pathview vectorized output?
Pathways graph pathview Pathways graph pathview
11.8 years ago Luo Weijun ★ 1.6k
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2.1k
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pathway analysis by SPIA using SPIA package vs graphite package
Pathways SPIA cycle graphite Pathways SPIA cycle graphite
11.8 years ago array chip ▴ 420
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topGO spurious GO terms?
Pathways GO topGO Pathways GO topGO
updated 11.9 years ago by ▴ 50 • written 11.9 years ago by ★ 13k
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Can gage not use large gene sets for pathway analysis?
Pathways gage pathview Pathways gage pathview
updated 12.0 years ago by ★ 1.6k • written 12.0 years ago by ★ 13k
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Metabolomic data analysis with papi / papiHtest() does not work as expected
Pathways PAPi Pathways PAPi
updated 12.0 years ago by ▴ 20 • written 12.0 years ago by ★ 13k
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plot QuSAGE problem
Pathways qusage Pathways qusage
updated 12.0 years ago by ▴ 20 • written 12.0 years ago by ★ 13k
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DESeq2 with GAGE
Pathways cycle gage DESeq2 pathview Pathways cycle gage DESeq2 pathview
12.0 years ago Luo Weijun ★ 1.6k
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Pathview - Problem with PNG output
Pathways graph pathview Pathways graph pathview
updated 12.2 years ago by ★ 1.6k • written 12.2 years ago by ▴ 150
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Change enzyme code (EC) into gene symbol
Pathways graph pathview Pathways graph pathview
12.2 years ago Luo Weijun ★ 1.6k
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2.6k
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pathview puzzle
Pathways pathview Pathways pathview
12.2 years ago Oleg Moskvin ▴ 60
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Pathview for global and overview maps Re: using pathview about hsa01100
Pathways graph PROcess SIM gage pathview Pathways graph PROcess SIM gage pathview
updated 12.3 years ago by ▴ 230 • written 12.3 years ago by ★ 1.6k
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Pathview with non-KEGG organisms?
Microbiome Pathways GO Visualization Organism graph gage pathview Microbiome Pathways GO
12.3 years ago Luo Weijun ★ 1.6k
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Pathview with non-KEGG organisms?
Pathways Organism pathview Pathways Organism pathview
12.3 years ago Luo Weijun ★ 1.6k
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Pathview+GAGE workflow on RNA-seq data pathway analysis and visualization (was: Pathview published in Bioinformatics)
Annotation Pathways Visualization graph PROcess gage pathview Annotation Pathways graph
12.3 years ago Luo Weijun ★ 1.6k
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pathview
Pathways graph pathview Pathways graph pathview
12.4 years ago Luo Weijun ★ 1.6k
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1.1k
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Analyzing Agilent Human DNA Methylation Microarray
Pathways Cancer Pathways Cancer
12.5 years ago Arpit Jain ▴ 10
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1.3k
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looking for tools to study additive expression effects in gene pathways/networks
Pathways Rgraphviz KEGGgraph Pathways Rgraphviz KEGGgraph
12.5 years ago Christopher T Gregg ▴ 210
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Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 4 elements
Pathways Pathways
12.6 years ago Dario Strbenac ★ 1.6k
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Fwd: GO terms: Annotation for HumanMethylation450
Annotation Pathways GO probe annotate Annotation Pathways GO probe annotate
12.6 years ago Jinyan Huang ▴ 110
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Fwd: GO terms: Annotation for HumanMethylation450
Annotation Pathways GO probe annotate Annotation Pathways GO probe annotate
updated 12.6 years ago by ▴ 110 • written 12.6 years ago by ★ 4.2k
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GO terms: Annotation for HumanMethylation450
Annotation Pathways GO probe Annotation Pathways GO probe
updated 12.6 years ago by ▴ 110 • written 12.6 years ago by ★ 7.2k
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Background for test in SPIA package.
Annotation Pathways SPIA Annotation Pathways SPIA
12.6 years ago Ian Sudbery ▴ 30
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1.8k
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GSVA
Microarray Pathways GSVA Microarray Pathways GSVA
12.7 years ago Robert Castelo ★ 3.4k
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2.5k
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Bioconductor Digest, Vol 120, Issue 12
Microarray qPCR Coverage Annotation Pathways Visualization Cancer Breast Organism affy
12.7 years ago Matthew Thornton ▴ 380
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runSPIA() in graphite package
Pathways Breast siggenes PROcess cycle graphite Pathways Breast siggenes PROcess cycle
updated 12.8 years ago by ▴ 20 • written 12.8 years ago by ▴ 420
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LogFC query in Limma
Pathways Cancer probe limma convert Pathways Cancer probe limma convert
updated 12.8 years ago by 53k • written 12.8 years ago by ▴ 130
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3.8k
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LogFC query in Limma
Pathways convert Pathways convert
updated 12.8 years ago by ★ 13k • written 12.8 years ago by ▴ 130
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Overrepresentation pathway with KEGGPROFILE and SPIA
Proteomics Pathways KEGGprofile Proteomics Pathways KEGGprofile
12.9 years ago slzhao ▴ 10
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Bioconductor Digest, Vol 119, Issue 5: Overrepresentation pathway with KEGGPROFILE and SPIA
Pathways SPIA KEGGprofile Pathways SPIA KEGGprofile
12.9 years ago Tarca, Adi ▴ 570
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correlation between two pathways' genes
Microarray Pathways GSEABase Microarray Pathways GSEABase
12.9 years ago Robert Castelo ★ 3.4k
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1.3k
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correlation between two pathways' genes
Pathways Pathways
updated 12.9 years ago by ★ 1.3k • written 12.9 years ago by ▴ 440
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ComBat
Transcription Genetics Pathways Network Survival Cancer Breast Colon Kidney Leukemia HIV
13.0 years ago SSc Array Core ▴ 10
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4
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2.4k
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KEGGgraph
Pathways Organism graph PROcess KEGGgraph Pathways Organism graph PROcess KEGGgraph
13.0 years ago Ricardo Silva ▴ 110
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3
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1.4k
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rna-seq
Microarray Pathways Network goseq Microarray Pathways Network goseq
updated 13.1 years ago by ▴ 350 • written 13.1 years ago by ★ 13k
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GOSEQ help
Pathways GO goseq Pathways GO goseq
13.1 years ago Emma Quinn ▴ 20
246 results • Page 2 of 5
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Replies
Comment: Getting a large intercept with DESeq2 by Michael Love 43k
Thanks James -- Denise you can check the "note on factor levels" in the vignette. And I'd recommend `plotCounts()` for looking at individu…
Comment: Getting a large intercept with DESeq2 by James W. MacDonald 68k
As a trivial example, consider this: ``` > model.matrix(~Treatment, data.frame(Treatment = factor(rep(1:3, each = 4)))) (Intercept) Tre…
Answer: Getting a large intercept with DESeq2 by James W. MacDonald 68k
The default parameterization in R is a treatment-contrasts parameterization that sets one of your groups as the baseline. So the intercept …
Answer: Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single C by ATpoint ★ 5.0k
There is no "MUST", but pseudobulk aggregation is beneficial to a) enable use of tested and robust methods such as limma (though it could u…
Answer: Post translational modifications and phosphoproteomics in limpa? by Gordon Smyth 53k
Yes, we use limpa for PTMs ourselves. I assume your data is preprocessed so that each row corresponds to a PTM. You replace dpcQuant() with…
Votes
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
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