Showing : spia • reset
0
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4
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1.4k
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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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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
0
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2
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1.3k
views
SPIA package
PROcess SPIA PROcess SPIA
12.7 years ago • updated 12.6 years ago Jing Huang ▴ 380
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votes
1
reply
1.3k
views
SPIA
Pathways SPIA Pathways SPIA
updated 10.2 years ago by ▴ 570 • written 10.2 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
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Question on graphite/SPIA; extracting DE gene list
graphite spia runSPIA
updated 5.3 years ago by 0 • written 9.2 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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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
votes
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
0
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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
0
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1
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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
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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votes
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
383
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Error creating SPIA data for KEGG Orthology (KO) Database KEGG xml files
SPIA
6 months ago Benji Bromberg ▴ 20
0
votes
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
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
votes
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
replies
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
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1.0k
views
SPIA error in DE-Colorectal
SPIA
7.9 years ago saamar.rajput • 0
1
vote
1
reply
1.2k
views
SPIA plotP giving error
SPIA plotP threshold
7.5 years ago docpriya21 ▴ 10
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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
0
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0
replies
1.2k
views
a possible bug in spia function
SPIA
6.8 years ago slava.ilyntskyy • 0
0
votes
0
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932
views
SPIA function error in ToPASeq
ToPASeq SPIA pathway analysis R
6.1 years ago fawazfebin ▴ 60
0
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1
reply
856
views
alternative package to SPIA
SPIA pathway enrichment analysis overrepresentation
5.2 years ago asifgeb • 0
0
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0
replies
780
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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
14.4 years ago Tarca, Adi ▴ 570
0
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0
replies
855
views
MArray into data.frame for SPIA package
limma marray SPIA limma marray SPIA
14.1 years ago Gordon Smyth 50k
0
votes
0
replies
946
views
help with SPIA package
Organism limma SPIA Organism limma SPIA
14.0 years ago Barbara Bo-Ju Shih ▴ 40
0
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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
14.0 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
0
votes
0
replies
976
views
How to create KEGG's pathway data for SPIA?
SPIA SPIA
13.5 years ago Lourdes Peña Castillo ▴ 140
0
votes
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
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993
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
views
question for you on SPIA package
Pathways Organism SPIA Pathways Organism SPIA
12.6 years ago Tarca, Adi ▴ 570
0
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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
12.4 years ago January Weiner ▴ 240
0
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0
replies
1.0k
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
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Comment: Couldn't connect to server while using "pathways" by ATpoint ★ 4.1k
Please understand that we neither can see your screen, nor read minds. You at least need to provide the line of code and the name of the pa…
Answer: Method to find pathways different between 2 groups by Gordon Smyth 50k
> When I search camera limma on pubmed, I found 2 papers I am unclear what point you are trying to make. limma's camera method has been fo…
Comment: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R by Patrycja ▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
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