Showing : SPIA • reset
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Kegg pathways overlay with log fold change values
Pathways limma SPIA Pathways limma SPIA
updated 12.8 years ago by ▴ 120 • written 12.8 years ago by ▴ 50
0
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1
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2.9k
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SPIA error - Error in density.default(pfstmp, bw = sd(pfstmp)/4) : \'bw\' is not positive.
SPIA cycle SPIA cycle
updated 11.3 years ago by ▴ 570 • written 11.3 years ago by ★ 13k
1
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2
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2.8k
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(Gene-set)Pathway analysis based on network/pathway topology in R
SPIA functional enrichment pathway topology pathway analysis bioconductor
9.7 years ago svlachavas ▴ 840
0
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2
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2.7k
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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 13.2 years ago by ▴ 570 • written 13.2 years ago by ▴ 100
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1
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2.4k
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SPIA error - names of de are not in reference array
SPIA named vectors pathway analysis
updated 2.7 years ago by • 0 • written 10.4 years ago by • 0
1
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2
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2.2k
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Question on graphite/SPIA; extracting DE gene list
graphite spia runSPIA
updated 6.2 years ago by 0 • written 10.0 years ago by • 0
0
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1
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1.9k
views
pathway analysis by SPIA using SPIA package vs graphite package
Pathways SPIA cycle graphite Pathways SPIA cycle graphite
11.2 years ago array chip ▴ 420
0
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0
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1.9k
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SPIA algorithm organisms not included already in the SPIA package
Organism SPIA goseq KEGGREST Organism SPIA goseq KEGGREST
12.1 years ago Tarca, Adi ▴ 570
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2
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1.9k
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organism abbreviations (SPIA package)
Microarray Organism SPIA Microarray Organism SPIA
updated 13.6 years ago by ▴ 340 • written 13.6 years ago by ▴ 380
5
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2
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1.8k
views
SPIA::spia function output
SPIA
updated 8.2 years ago by ▴ 570 • written 8.2 years ago by ▴ 10
0
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1
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1.7k
views
Which resources for pathway analysis?
Pathways Network SPIA DEGraph Pathways Network SPIA DEGraph
updated 14.1 years ago by ▴ 370 • written 14.1 years ago by ▴ 100
0
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4
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1.7k
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SPIA - changes between 1.4.0 and 1.60.
Pathways SPIA Pathways SPIA
updated 14.5 years ago by ▴ 20 • written 14.5 years ago by ▴ 480
0
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1
reply
1.6k
views
makeSPIAdata
SPIA SPIA
updated 11.2 years ago by ▴ 570 • written 11.2 years ago by ▴ 10
0
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2
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1.6k
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question on SPIA pavkage application
Organism SPIA Organism SPIA
updated 13.6 years ago by ▴ 150 • written 13.6 years ago by ▴ 380
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0
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1.6k
views
changes in SPIA package: using updated KEGG pathway data
Organism SPIA Organism SPIA
12.1 years ago Tarca, Adi ▴ 570
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0
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1.6k
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SPIA package
Pathways Organism SPIA Pathways Organism SPIA
13.3 years ago Tarca, Adi ▴ 570
0
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0
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1.6k
views
SPIA: inferring inhibited pathways from up-regulated genes?
Pathways SPIA Pathways SPIA
15.3 years ago Tarca, Adi ▴ 570
0
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2
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1.6k
views
SPIA package
PROcess SPIA PROcess SPIA
13.6 years ago • updated 13.5 years ago Jing Huang ▴ 380
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0
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1.5k
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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
14.3 years ago Tarca, Adi ▴ 570
0
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1
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1.5k
views
SPIA
Pathways SPIA Pathways SPIA
updated 11.1 years ago by ▴ 570 • written 11.1 years ago by ★ 13k
0
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0
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1.4k
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SPIA, hacked to run with only selected pathways
SystemsBiology Pathways Cancer SPIA SystemsBiology Pathways Cancer SPIA
15.3 years ago Tarca, Adi ▴ 570
0
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1
reply
1.4k
views
SPIA package with updated KEGG pathways
Pathways SPIA Pathways SPIA
updated 14.3 years ago by ★ 7.2k • written 14.3 years ago by ▴ 20
0
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0
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1.4k
views
Bioconductor Digest, Vol 119, Issue 5: Overrepresentation pathway with KEGGPROFILE and SPIA
Pathways SPIA KEGGprofile Pathways SPIA KEGGprofile
12.2 years ago Tarca, Adi ▴ 570
0
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1
reply
1.4k
views
Which resources for pathway analysis?
Pathways SPIA Pathways SPIA
updated 14.1 years ago by ▴ 300 • written 14.1 years ago by ▴ 370
0
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0
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1.4k
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question for SPIA package
Pathways SPIA Pathways SPIA
13.3 years ago Jing Huang ▴ 380
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0
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1.4k
views
Bioconductor resources for immunology
Pathways GO SPIA Pathways GO SPIA
13.3 years ago January Weiner ▴ 240
1
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1
reply
1.4k
views
SPIA plotP giving error
SPIA plotP threshold
8.4 years ago docpriya21 ▴ 10
0
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0
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1.4k
views
a possible bug in spia function
SPIA
7.7 years ago slava.ilyntskyy • 0
0
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1
reply
1.4k
views
SPIA package
graph SPIA graph SPIA
updated 15.0 years ago by ★ 7.4k • written 15.0 years ago by ▴ 200
0
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0
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1.4k
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Background for test in SPIA package.
Annotation Pathways SPIA Annotation Pathways SPIA
12.0 years ago Ian Sudbery ▴ 30
0
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1
reply
1.3k
views
a question on SPIA package
Microarray SPIA Microarray SPIA
updated 13.6 years ago by ▴ 650 • written 13.6 years ago by ▴ 380
0
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0
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1.3k
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SPIA Package : Activated and Inhibited
SPIA R pathway analysis
7.8 years ago khhgng • 0
0
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0
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1.3k
views
R: Re: Deseq2 and differentia expression
SPIA SPIA
10.7 years ago Simon Anders ★ 3.8k
0
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0
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1.2k
views
question for you on SPIA package
Pathways Organism SPIA Pathways Organism SPIA
13.5 years ago Tarca, Adi ▴ 570
0
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0
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1.2k
views
SPIA with Mouse Data
Genetics Network Organism SPIA Genetics Network Organism SPIA
14.6 years ago Will Bush ▴ 10
0
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0
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1.2k
views
SPIA error in DE-Colorectal
SPIA
8.8 years ago saamar.rajput • 0
0
votes
0
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1.2k
views
SPIA package problem
Microarray GO Cancer Organism hgu95av2 mgug4122a SPIA Microarray GO Cancer Organism
14.8 years ago January Weiner ▴ 370
0
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0
replies
1.2k
views
Bioconductor Digest, Vol 94, Issue 10
Pathways SPIA Pathways SPIA
14.3 years ago Tarca, Adi ▴ 570
0
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0
replies
1.2k
views
SPIA function error in ToPASeq
ToPASeq SPIA pathway analysis R
7.0 years ago fawazfebin ▴ 60
0
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0
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1.1k
views
Overrepresentation pathway with KEGGPROFILE and SPIA
SPIA SPIA
12.2 years ago gregory voisin ▴ 430
0
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0
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1.1k
views
How to create KEGG's pathway data for SPIA?
SPIA SPIA
14.3 years ago Lourdes Peña Castillo ▴ 140
0
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0
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1.1k
views
help with SPIA package
Organism limma SPIA Organism limma SPIA
14.9 years ago Barbara Bo-Ju Shih ▴ 40
0
votes
1
reply
1.1k
views
alternative package to SPIA
SPIA pathway enrichment analysis overrepresentation
6.1 years ago asifgeb • 0
0
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0
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1.0k
views
plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
5.0 years ago Assa Yeroslaviz ★ 1.5k
0
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0
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977
views
MArray into data.frame for SPIA package
limma marray SPIA limma marray SPIA
15.0 years ago Gordon Smyth 52k
1
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2
replies
660
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Error creating SPIA data for KEGG Orthology (KO) Database KEGG xml files
SPIA
17 months ago Benji Bromberg ▴ 30
46 results • Page 1 of 1
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Answer: Mismatch between Illumina Mouse Methylation BeadChip annotation and genome brows by James W. MacDonald 68k
The annotation data that is provided for this array is simply a repackaging of data that we get from Illumina, so any apparent inconsistenc…
Answer: Package developing and interoperation with Bioconductor by James W. MacDonald 68k
Ideally you would have S4 methods that dispatch on the incoming data structure, so people could call your main function using a `data.frame…
Comment: ComBat with repeated measures by ATpoint ★ 4.8k
It looks to me that you do not need the batch information since subject is nested with batch so correcting for subject will do a paired ana…
Comment: Surprising behavior for DEXseq dispersion estimate plot? by ATpoint ★ 4.8k
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Comment: Merging EPICV1 and V2 betas by Garbayo • 0
[BitLife][1]: Life Simulator, usually referred to as BitLife, is a mobile life simulator game created by developer CandyWriter LLC on Septe…
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Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
Answer: Explannation for ROAST results
A: How DiffBind run PCA based on peak data?
Looking for equivalent EPIC chip v1 vs. v2 annotation variables
Properly constructing a hypergeometric test
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