Showing : Pathways • reset
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3
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error in plotKEGGGraph
Pathways KEGGgraph Pathways KEGGgraph
updated 15.2 years ago by ▴ 30 • written 15.2 years ago by ▴ 340
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4
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1.9k
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SPIA - changes between 1.4.0 and 1.60.
Pathways SPIA Pathways SPIA
updated 15.2 years ago by ▴ 20 • written 15.2 years ago by ▴ 480
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2
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1.4k
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KEGG orthology linking (K numbers )?
Pathways Pathways
updated 15.3 years ago by 6.7k • written 15.3 years ago by ▴ 30
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1
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1.6k
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error in plotKEGGGraph
Pathways KEGGgraph Pathways KEGGgraph
updated 15.3 years ago by ▴ 340 • written 15.4 years ago by ▴ 280
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3
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1.7k
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KEGG data missing from KEGG.db
Annotation Pathways Annotation Pathways
15.3 years ago Chris Fjell ▴ 60
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1
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990
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What to do with this data? Question on deconfouding and GO analysis
Microarray Pathways GO Microarray Pathways GO
updated 15.5 years ago by ★ 13k • written 15.5 years ago by ▴ 370
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3
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1.8k
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tool for drawing interaction network
Pathways Network Pathways Network
updated 15.5 years ago by ▴ 220 • written 15.5 years ago by ★ 4.1k
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5
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1.5k
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anybody parsing BioPAX 2?
Pathways Pathways
updated 15.5 years ago by ▴ 10 • written 15.5 years ago by ★ 1.1k
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1
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1.1k
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GOstats/Category hyperGTest gene universe problem
Annotation Pathways GO Annotation Pathways GO
updated 15.5 years ago by ★ 7.2k • written 15.5 years ago by ▴ 610
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1
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1.1k
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intersection between genes and pathways
Pathways Pathways
updated 15.7 years ago by ▴ 30 • written 15.7 years ago by ▴ 420
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1
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1.8k
views
KEGGSOAP, hgu95av2.db: limited functionality
Pathways hgu95av2 probe KEGGSOAP Pathways hgu95av2 probe KEGGSOAP
updated 15.7 years ago by ★ 7.2k • written 15.7 years ago by ▴ 70
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6
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2.0k
views
Regarding KEGGgraph
Pathways Network PROcess Pathways Network PROcess
updated 15.9 years ago by ★ 13k • written 15.9 years ago by ▴ 270
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0
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1.3k
views
how to get gene list after hyperGTest (Yue, Chen - BMD)
Annotation Pathways affy GOstats Category AnnotationDbi Annotation Pathways affy GOstats
15.9 years ago Bucher Elmar ▴ 80
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2
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2.1k
views
Bioconductor Digest, Vol 82, Issue 20
Annotation Pathways affy GOstats Category AnnotationDbi Annotation Pathways affy GOstats
updated 15.9 years ago by ▴ 70 • written 15.9 years ago by ▴ 60
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0
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1.7k
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SPIA: inferring inhibited pathways from up-regulated genes?
Pathways SPIA Pathways SPIA
15.9 years ago Tarca, Adi ▴ 570
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2
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2.0k
views
KEGGgraph: any way to obtain 'outcome' nodes?
Pathways KEGGgraph Pathways KEGGgraph
updated 15.9 years ago by ▴ 270 • written 15.9 years ago by ★ 1.1k
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1
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1.4k
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domainsignatures with non-human KEGG pathways
Pathways Organism domainsignatures Pathways Organism domainsignatures
15.9 years ago Robert Castelo ★ 3.4k
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0
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1.5k
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SPIA, hacked to run with only selected pathways
SystemsBiology Pathways Cancer SPIA SystemsBiology Pathways Cancer SPIA
15.9 years ago Tarca, Adi ▴ 570
0
votes
1
reply
1.9k
views
KEGGgraph bug
Pathways Organism SIM KEGGgraph Pathways Organism SIM KEGGgraph
updated 15.9 years ago by ★ 7.2k • written 15.9 years ago by ▴ 270
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1
reply
1.3k
views
KEGGgraph query
Pathways graph KEGGgraph Pathways graph KEGGgraph
updated 16.0 years ago by ▴ 340 • written 16.0 years ago by ▴ 270
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3
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2.0k
views
GeneSetCollection using EntrezID
Annotation Pathways GSEABase Annotation Pathways GSEABase
updated 16.0 years ago by 25k • written 16.0 years ago by ▴ 840
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0
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1.4k
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Job advertisement
Transcription Sequencing Microarray Normalization Pathways PROcess Transcription Sequencing
16.1 years ago Alexandre Kuhn ▴ 60
0
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2
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1.3k
views
YEAST package
Pathways Yeast Pathways Yeast
16.2 years ago suman Duvvuru ▴ 20
0
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2
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1.3k
views
error with "retrain" method of gene2pathway package
Pathways GO Organism Homo sapiens hgu133plus2 gene2pathway Pathways GO Organism
updated 16.2 years ago by 68k • written 16.2 years ago by ▴ 340
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1
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1.5k
views
(no subject)
Pathways Clustering goTools GOstats Pathways Clustering goTools GOstats
updated 16.3 years ago by ▴ 270 • written 16.3 years ago by ▴ 300
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1
reply
842
views
Checking for pathway membership
Pathways Pathways
16.3 years ago anupam sinha ▴ 270
0
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1
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1.2k
views
problem with the structure of a list of pathways
Genetics Pathways probe annaffy Genetics Pathways probe annaffy
updated 16.4 years ago by 68k • written 16.4 years ago by ▴ 60
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0
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732
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problem about saveHTML
Pathways Pathways
16.4 years ago Alberto Goldoni ▴ 420
0
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1
reply
1.2k
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pathway score for individual arrays
Pathways Pathways
updated 16.5 years ago by ▴ 400 • written 16.5 years ago by ★ 4.1k
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3
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1.7k
views
KEGGSOAP: problem with get.pathways.by.genes()
Pathways convert KEGGSOAP Pathways convert KEGGSOAP
updated 16.5 years ago by ▴ 400 • written 16.5 years ago by ▴ 30
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2
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1.7k
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problem of cMAP package
Pathways Pathways
updated 16.5 years ago by ★ 5.5k • written 16.5 years ago by ▴ 10
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0
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2.2k
views
Post Doc position, Berlin Germany
Sequencing Microarray Proteomics Pathways Network Cancer Sequencing Microarray Proteomics
16.6 years ago Paul Hammer ▴ 220
0
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4
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1.5k
views
Rredland installation difficulties
Pathways graph Rredland Pathways graph Rredland
updated 16.6 years ago by ★ 1.6k • written 16.6 years ago by ★ 1.1k
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3
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3.1k
views
Visualizing KEGG pathways
Pathways graph Pathways graph
updated 16.6 years ago by ▴ 400 • written 16.6 years ago by ★ 1.1k
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0
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1.2k
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PFAM analysis packages?
Pathways GOstats Pathways GOstats
16.6 years ago Paul Evans ▴ 180
0
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0
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1.2k
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Visulising KEGG pathways using KEGGSOAP - example code
Pathways geneplotter KEGGSOAP biomaRt GEOquery Pathways geneplotter KEGGSOAP biomaRt
16.6 years ago michael watson IAH-C ★ 3.4k
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4
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1.8k
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Up- or down- regulated pathways or GO terms?
Microarray Pathways GO Microarray Pathways GO
updated 16.6 years ago by ▴ 140 • written 16.6 years ago by ▴ 640
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1
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1.5k
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KEGGgraph question
Pathways KEGGgraph Pathways KEGGgraph
16.7 years ago Sim, Fraser ▴ 350
0
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0
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1.3k
views
Assistant/Associate Professor Department of Biostatistics
Pathways Bayesian Cancer charm Pathways Bayesian Cancer charm
16.7 years ago Kellie J. Archer, Ph.D. ▴ 120
0
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0
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1.1k
views
Gostats and custom list
Annotation Pathways GO Yeast convert GOstats Category Annotation Pathways GO Yeast
16.7 years ago Iain Wallace ▴ 50
0
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0
replies
1.7k
views
GSEA to discover co-regulated genes
Transcription Annotation Pathways Infrastructure probe convert GSEABase Transcription
16.8 years ago Paul Geeleher ★ 1.3k
0
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1
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1.2k
views
GSEA to discover co-regulated genes
Transcription Pathways Transcription Pathways
updated 16.8 years ago by 6.7k • written 16.8 years ago by ★ 1.3k
0
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7
replies
2.4k
views
Kegg pathway --> gene network
Pathways Network Pathways Network
updated 16.9 years ago by 25k • written 16.9 years ago by ▴ 40
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0
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1.0k
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biomaRt with multiple databases/datasets?
Pathways GO biomaRt Pathways GO biomaRt
17.0 years ago T Joshi ▴ 90
0
votes
0
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1.1k
views
Mean Plots and Heat Maps for Chromosome Bands
Pathways hgu95av2 Pathways hgu95av2
17.0 years ago McGee, Monnie ▴ 300
0
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0
replies
1.3k
views
KEGG pathway layout/rendering
Pathways graph PROcess Pathways graph PROcess
17.0 years ago Sim, Fraser ▴ 350
0
votes
1
reply
1.3k
views
globaltest mulitple testing correction
Pathways globaltest Pathways globaltest
updated 17.1 years ago by ▴ 340 • written 17.1 years ago by ▴ 90
0
votes
1
reply
1.5k
views
global test multiple testing correction
Pathways globaltest Pathways globaltest
updated 17.1 years ago by ▴ 40 • written 17.1 years ago by ▴ 60
0
votes
0
replies
782
views
BioPAX
Pathways Pathways
17.1 years ago Michal Kolář ▴ 60
0
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0
replies
1.9k
views
Postdoc positions at the Cancer Research UK Cambridge Research Institute
SNP Genetics Pathways Cancer CGH microRNA SNP Genetics Pathways Cancer CGH microRNA
17.1 years ago Florian Markowetz ▴ 20
246 results • Page 4 of 5
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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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