Showing : spia • reset
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4
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SPIA - changes between 1.4.0 and 1.60.
Pathways SPIA Pathways SPIA
updated 13.6 years ago by ▴ 20 • written 13.6 years ago by ▴ 480
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2
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2.4k
views
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 12.3 years ago by ▴ 570 • written 12.3 years ago by ▴ 100
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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 12.7 years ago by ▴ 150 • written 12.7 years ago by ▴ 380
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2
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1.3k
views
SPIA package
PROcess SPIA PROcess SPIA
12.6 years ago Jing Huang ▴ 380
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1
reply
1.3k
views
SPIA
Pathways SPIA Pathways SPIA
updated 10.1 years ago by ▴ 570 • written 10.1 years ago by ★ 13k
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 13.4 years ago by ▴ 20
1
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2
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1.9k
views
Question on graphite/SPIA; extracting DE gene list
graphite spia runSPIA
updated 5.3 years ago by 0 • written 9.1 years ago by • 0
0
votes
1
reply
1.2k
views
SPIA package
graph SPIA graph SPIA
updated 14.1 years ago by ★ 7.4k • written 14.1 years ago by ▴ 200
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votes
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
5
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2
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1.5k
views
SPIA::spia function output
SPIA
updated 7.3 years ago by ▴ 570 • written 7.3 years ago by ▴ 10
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3
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2.6k
views
Kegg pathways overlay with log fold change values
Pathways limma SPIA Pathways limma SPIA
updated 11.9 years ago by ▴ 120 • written 11.9 years ago by ▴ 50
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1
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1.4k
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
0
votes
1
reply
1.1k
views
a question on SPIA package
Microarray SPIA Microarray SPIA
updated 12.7 years ago by ▴ 650 • written 12.7 years ago by ▴ 380
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2
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1.6k
views
organism abbreviations (SPIA package)
Microarray Organism SPIA Microarray Organism SPIA
updated 12.7 years ago by ▴ 340 • written 12.7 years ago by ▴ 380
1
vote
2
replies
373
views
Error creating SPIA data for KEGG Orthology (KO) Database KEGG xml files
SPIA
6 months ago Benji Bromberg ▴ 20
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votes
1
reply
2.5k
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
votes
1
reply
1.4k
views
makeSPIAdata
SPIA SPIA
updated 10.3 years ago by ▴ 570 • written 10.3 years ago by ▴ 10
0
votes
1
reply
1.7k
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pathway analysis by SPIA using SPIA package vs graphite package
Pathways SPIA cycle graphite Pathways SPIA cycle graphite
10.3 years ago array chip ▴ 420
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0
replies
1.0k
views
R: Re: Deseq2 and differentia expression
SPIA SPIA
9.8 years ago Simon Anders ★ 3.7k
0
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1
reply
2.1k
views
SPIA error - names of de are not in reference array
SPIA named vectors pathway analysis
updated 21 months ago by • 0 • written 9.5 years ago by • 0
1
vote
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
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0
replies
1000
views
SPIA error in DE-Colorectal
SPIA
7.8 years ago saamar.rajput • 0
0
votes
1
reply
1.1k
views
SPIA plotP giving error
SPIA plotP threshold
7.4 years ago docpriya21 • 0
0
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0
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1.0k
views
SPIA Package : Activated and Inhibited
SPIA R pathway analysis
6.8 years ago khhgng • 0
0
votes
0
replies
1.2k
views
a possible bug in spia function
SPIA
6.7 years ago slava.ilyntskyy • 0
0
votes
0
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921
views
SPIA function error in ToPASeq
ToPASeq SPIA pathway analysis R
6.1 years ago fawazfebin ▴ 60
0
votes
1
reply
846
views
alternative package to SPIA
SPIA pathway enrichment analysis overrepresentation
5.1 years ago asifgeb • 0
0
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0
replies
770
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plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
4.1 years ago Assa Yeroslaviz ★ 1.5k
0
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0
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1.2k
views
Background for test in SPIA package.
Annotation Pathways SPIA Annotation Pathways SPIA
11.1 years ago Ian Sudbery ▴ 30
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0
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1.4k
views
SPIA: inferring inhibited pathways from up-regulated genes?
Pathways SPIA Pathways SPIA
14.3 years ago Tarca, Adi ▴ 570
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votes
0
replies
850
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MArray into data.frame for SPIA package
limma marray SPIA limma marray SPIA
14.1 years ago Gordon Smyth 50k
0
votes
0
replies
934
views
help with SPIA package
Organism limma SPIA Organism limma SPIA
13.9 years ago Barbara Bo-Ju Shih ▴ 40
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0
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1.0k
views
SPIA package problem
Microarray GO Cancer Organism hgu95av2 mgug4122a SPIA Microarray GO Cancer Organism
13.9 years ago January Weiner ▴ 370
0
votes
0
replies
1.1k
views
SPIA with Mouse Data
Genetics Network Organism SPIA Genetics Network Organism SPIA
13.7 years ago Will Bush ▴ 10
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votes
0
replies
966
views
How to create KEGG's pathway data for SPIA?
SPIA SPIA
13.4 years ago Lourdes Peña Castillo ▴ 140
0
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0
replies
1.3k
views
Bioconductor Digest, Vol 93, Issue 26: How to create KEGG's pathway data for SPIA?
Organism KEGGgraph SPIA Organism KEGGgraph SPIA
13.4 years ago Tarca, Adi ▴ 570
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0
replies
982
views
Bioconductor Digest, Vol 94, Issue 10
Pathways SPIA Pathways SPIA
13.4 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
12.6 years ago Tarca, Adi ▴ 570
0
votes
0
replies
1.2k
views
question for SPIA package
Pathways SPIA Pathways SPIA
12.4 years ago Jing Huang ▴ 380
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votes
0
replies
1.4k
views
SPIA package
Pathways Organism SPIA Pathways Organism SPIA
12.4 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
12.3 years ago January Weiner ▴ 240
0
votes
0
replies
1000
views
Overrepresentation pathway with KEGGPROFILE and SPIA
SPIA SPIA
11.3 years ago gregory voisin ▴ 430
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0
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1.2k
views
Bioconductor Digest, Vol 119, Issue 5: Overrepresentation pathway with KEGGPROFILE and SPIA
Pathways SPIA KEGGprofile Pathways SPIA KEGGprofile
11.3 years ago Tarca, Adi ▴ 570
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0
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1.4k
views
changes in SPIA package: using updated KEGG pathway data
Organism SPIA Organism SPIA
11.2 years ago Tarca, Adi ▴ 570
0
votes
0
replies
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
0
votes
0
replies
1.2k
views
SPIA, hacked to run with only selected pathways
SystemsBiology Pathways Cancer SPIA SystemsBiology Pathways Cancer SPIA
14.4 years ago Tarca, Adi ▴ 570
46 results • Page 1 of 1
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Replies
Comment: How to retrieve gene ontology GO class? by bandconductor • 0
Sorry I wasn't clear before. What I mean is the all the information associated with the go term, such as description and evidence. I have …
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
How am i making the data? I am using the DESeq2 output data which I had generated
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq by Michael Love 41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Answer: Citation for edgeR user guide by Gordon Smyth 50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You are just making up data? What is the point of this exercise?
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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