Showing : spia • reset
1
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Error creating SPIA data for KEGG Orthology (KO) Database KEGG xml files
SPIA
7 months ago Benji Bromberg ▴ 20
0
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0
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788
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plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
4.2 years ago Assa Yeroslaviz ★ 1.5k
0
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1
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862
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alternative package to SPIA
SPIA pathway enrichment analysis overrepresentation
5.2 years ago asifgeb • 0
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 5.4 years ago by 0 • written 9.2 years ago by • 0
0
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0
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945
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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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1.2k
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a possible bug in spia function
SPIA
6.8 years ago slava.ilyntskyy • 0
0
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0
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1.1k
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SPIA Package : Activated and Inhibited
SPIA R pathway analysis
6.9 years ago khhgng • 0
5
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2
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1.5k
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SPIA::spia function output
SPIA
updated 7.4 years ago by ▴ 570 • written 7.4 years ago by ▴ 10
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
0
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0
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1.0k
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SPIA error in DE-Colorectal
SPIA
7.9 years ago saamar.rajput • 0
1
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2
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2.4k
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(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
0
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1
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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 9.6 years ago by • 0
0
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0
replies
1.1k
views
R: Re: Deseq2 and differentia expression
SPIA SPIA
9.8 years ago Simon Anders ★ 3.7k
0
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1
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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
1.7k
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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
0
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1
reply
1.4k
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makeSPIAdata
SPIA SPIA
updated 10.4 years ago by ▴ 570 • written 10.4 years ago by ▴ 10
0
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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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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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1.7k
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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
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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
0
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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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1.0k
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Overrepresentation pathway with KEGGPROFILE and SPIA
SPIA SPIA
11.4 years ago gregory voisin ▴ 430
0
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3
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2.7k
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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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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 12.4 years ago by ▴ 570 • written 12.4 years ago by ▴ 100
0
votes
0
replies
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
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1.4k
views
SPIA package
Pathways Organism SPIA Pathways Organism SPIA
12.4 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
0
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2
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1.3k
views
SPIA package
PROcess SPIA PROcess SPIA
12.7 years ago Jing Huang ▴ 380
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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
votes
2
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1.4k
views
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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1
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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
0
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2
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1.6k
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organism abbreviations (SPIA package)
Microarray Organism SPIA Microarray Organism SPIA
updated 12.7 years ago by ▴ 340 • written 12.7 years ago by ▴ 380
0
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1
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1.5k
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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
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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
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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
0
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0
replies
996
views
Bioconductor Digest, Vol 94, Issue 10
Pathways SPIA Pathways SPIA
13.4 years ago Tarca, Adi ▴ 570
0
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0
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1.3k
views
Bioconductor Digest, Vol 93, Issue 26: How to create KEGG's pathway data for SPIA?
Organism KEGGgraph SPIA Organism KEGGgraph SPIA
13.5 years ago Tarca, Adi ▴ 570
0
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0
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982
views
How to create KEGG's pathway data for SPIA?
SPIA SPIA
13.5 years ago Lourdes Peña Castillo ▴ 140
0
votes
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
0
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0
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1.1k
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SPIA with Mouse Data
Genetics Network Organism SPIA Genetics Network Organism SPIA
13.8 years ago Will Bush ▴ 10
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
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0
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953
views
help with SPIA package
Organism limma SPIA Organism limma SPIA
14.0 years ago Barbara Bo-Ju Shih ▴ 40
0
votes
0
replies
858
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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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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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
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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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Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by makala • 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by Erik Wright ▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by Matthew Thornton ▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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