Showing : SPIA • reset
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SPIA - changes between 1.4.0 and 1.60.
Pathways SPIA Pathways SPIA
updated 13.7 years ago by ▴ 20 • written 13.7 years ago by ▴ 480
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3
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2.7k
views
Kegg pathways overlay with log fold change values
Pathways limma SPIA Pathways limma SPIA
updated 12.0 years ago by ▴ 120 • written 12.0 years ago by ▴ 50
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2
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1.4k
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question on SPIA pavkage application
Organism SPIA Organism SPIA
updated 12.8 years ago by ▴ 150 • written 12.8 years ago by ▴ 380
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2
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SPIA package
PROcess SPIA PROcess SPIA
12.7 years ago Jing Huang ▴ 380
1
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2
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397
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Error creating SPIA data for KEGG Orthology (KO) Database KEGG xml files
SPIA
7 months ago Benji Bromberg ▴ 20
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2
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1.6k
views
organism abbreviations (SPIA package)
Microarray Organism SPIA Microarray Organism SPIA
updated 12.8 years ago by ▴ 340 • written 12.8 years ago by ▴ 380
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2
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1.9k
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Question on graphite/SPIA; extracting DE gene list
graphite spia runSPIA
updated 5.4 years ago by 0 • written 9.2 years ago by • 0
1
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2
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2.4k
views
(Gene-set)Pathway analysis based on network/pathway topology in R
SPIA functional enrichment pathway topology pathway analysis bioconductor
8.8 years ago svlachavas ▴ 830
5
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2
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1.5k
views
SPIA::spia function output
SPIA
updated 7.4 years ago by ▴ 570 • written 7.4 years ago by ▴ 10
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2
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2.4k
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Problem in SPIA: de must be a vector of log2 fold changes. The names of de should be included in the refference array!
Organism limma SPIA Organism limma SPIA
updated 12.4 years ago by ▴ 570 • written 12.4 years ago by ▴ 100
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1
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2.1k
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SPIA error - names of de are not in reference array
SPIA named vectors pathway analysis
updated 22 months ago by • 0 • written 9.6 years ago by • 0
0
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1
reply
1.5k
views
Which resources for pathway analysis?
Pathways Network SPIA DEGraph Pathways Network SPIA DEGraph
updated 13.2 years ago by ▴ 370 • written 13.2 years ago by ▴ 100
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1
reply
866
views
alternative package to SPIA
SPIA pathway enrichment analysis overrepresentation
5.2 years ago asifgeb • 0
0
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1
reply
1.2k
views
SPIA package with updated KEGG pathways
Pathways SPIA Pathways SPIA
updated 13.4 years ago by ★ 7.2k • written 13.5 years ago by ▴ 20
1
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1
reply
1.2k
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SPIA plotP giving error
SPIA plotP threshold
7.5 years ago docpriya21 ▴ 10
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1
reply
1.2k
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a question on SPIA package
Microarray SPIA Microarray SPIA
updated 12.8 years ago by ▴ 650 • written 12.8 years ago by ▴ 380
0
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1
reply
1.2k
views
SPIA package
graph SPIA graph SPIA
updated 14.2 years ago by ★ 7.4k • written 14.2 years ago by ▴ 200
0
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1
reply
1.2k
views
Which resources for pathway analysis?
Pathways SPIA Pathways SPIA
updated 13.2 years ago by ▴ 300 • written 13.2 years ago by ▴ 370
0
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1
reply
1.4k
views
makeSPIAdata
SPIA SPIA
updated 10.4 years ago by ▴ 570 • written 10.4 years ago by ▴ 10
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1
reply
1.7k
views
pathway analysis by SPIA using SPIA package vs graphite package
Pathways SPIA cycle graphite Pathways SPIA cycle graphite
10.4 years ago array chip ▴ 420
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1
reply
1.3k
views
SPIA
Pathways SPIA Pathways SPIA
updated 10.2 years ago by ▴ 570 • written 10.2 years ago by ★ 13k
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1
reply
2.6k
views
SPIA error - Error in density.default(pfstmp, bw = sd(pfstmp)/4) : \'bw\' is not positive.
SPIA cycle SPIA cycle
updated 10.4 years ago by ▴ 570 • written 10.4 years ago by ★ 13k
0
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0
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953
views
SPIA function error in ToPASeq
ToPASeq SPIA pathway analysis R
6.1 years ago fawazfebin ▴ 60
0
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0
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794
views
plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
4.2 years ago Assa Yeroslaviz ★ 1.5k
0
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0
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1.2k
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Background for test in SPIA package.
Annotation Pathways SPIA Annotation Pathways SPIA
11.2 years ago Ian Sudbery ▴ 30
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0
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1.4k
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SPIA: inferring inhibited pathways from up-regulated genes?
Pathways SPIA Pathways SPIA
14.4 years ago Tarca, Adi ▴ 570
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0
replies
861
views
MArray into data.frame for SPIA package
limma marray SPIA limma marray SPIA
14.2 years ago Gordon Smyth 50k
0
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0
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955
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help with SPIA package
Organism limma SPIA Organism limma SPIA
14.0 years ago Barbara Bo-Ju Shih ▴ 40
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0
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1.0k
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SPIA package problem
Microarray GO Cancer Organism hgu95av2 mgug4122a SPIA Microarray GO Cancer Organism
14.0 years ago January Weiner ▴ 370
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0
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1.1k
views
SPIA with Mouse Data
Genetics Network Organism SPIA Genetics Network Organism SPIA
13.8 years ago Will Bush ▴ 10
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0
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984
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How to create KEGG's pathway data for SPIA?
SPIA SPIA
13.5 years ago Lourdes Peña Castillo ▴ 140
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0
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1.3k
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Bioconductor Digest, Vol 93, Issue 26: How to create KEGG's pathway data for SPIA?
Organism KEGGgraph SPIA Organism KEGGgraph SPIA
13.5 years ago Tarca, Adi ▴ 570
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0
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999
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Bioconductor Digest, Vol 94, Issue 10
Pathways SPIA Pathways SPIA
13.5 years ago Tarca, Adi ▴ 570
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0
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1.1k
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question for you on SPIA package
Pathways Organism SPIA Pathways Organism SPIA
12.7 years ago Tarca, Adi ▴ 570
0
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0
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1.2k
views
question for SPIA package
Pathways SPIA Pathways SPIA
12.5 years ago Jing Huang ▴ 380
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0
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1.4k
views
SPIA package
Pathways Organism SPIA Pathways Organism SPIA
12.5 years ago Tarca, Adi ▴ 570
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0
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1.2k
views
Bioconductor resources for immunology
Pathways GO SPIA Pathways GO SPIA
12.4 years ago January Weiner ▴ 240
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0
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1.0k
views
Overrepresentation pathway with KEGGPROFILE and SPIA
SPIA SPIA
11.4 years ago gregory voisin ▴ 430
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0
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1.2k
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Bioconductor Digest, Vol 119, Issue 5: Overrepresentation pathway with KEGGPROFILE and SPIA
Pathways SPIA KEGGprofile Pathways SPIA KEGGprofile
11.4 years ago Tarca, Adi ▴ 570
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0
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1.4k
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changes in SPIA package: using updated KEGG pathway data
Organism SPIA Organism SPIA
11.2 years ago Tarca, Adi ▴ 570
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0
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1.7k
views
SPIA algorithm organisms not included already in the SPIA package
Organism SPIA goseq KEGGREST Organism SPIA goseq KEGGREST
11.2 years ago Tarca, Adi ▴ 570
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0
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1.2k
views
SPIA, hacked to run with only selected pathways
SystemsBiology Pathways Cancer SPIA SystemsBiology Pathways Cancer SPIA
14.5 years ago Tarca, Adi ▴ 570
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0
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1.1k
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R: Re: Deseq2 and differentia expression
SPIA SPIA
9.9 years ago Simon Anders ★ 3.7k
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1.0k
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SPIA error in DE-Colorectal
SPIA
7.9 years ago saamar.rajput • 0
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0
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1.1k
views
SPIA Package : Activated and Inhibited
SPIA R pathway analysis
6.9 years ago khhgng • 0
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0
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1.2k
views
a possible bug in spia function
SPIA
6.8 years ago slava.ilyntskyy • 0
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Answer: recount3 problem downloading data from source sra by Leonardo Collado Torres ★ 1.0k
Hi, I wasn't able to reproduce the issue on both bioc 3.19 (current release version) and 3.18 (closer to your session info). My guess is…
Answer: Running ENmix with mouse methylation manifest: readidat error - Error in readman by minardsmitha ▴ 10
Well it turns out there is a typo in the manifest file name. This particular issue is resolved by correcting the typo. A new error now …
Answer: Documenting resources in an `ExperimentHub` package? by James W. MacDonald 66k
The easiest way to do that IMO is to use emacs/ESS (or I believe there is some newfangled thing called RStudio? Not personally familiar, bu…
Comment: ChAMP installation issue by shepherl 3.9k
We are still waiting for the goseq to respond to our requests but will take action next week if it is not resolved. ChAMP is currently una…
Comment: How to arrange multiple plots into one page in NOISeq? by baptiste.bidon • 0
After facing the same problem, I realise that you can direct your plot in the matrix with the *par()* option `par(..., mfg = c(1,2))`. If i…
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how to control age and gender effect in expression data using DESeq2
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Comment: LRT, more than two conditions and pairwise comparisons
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