Showing : SPIA • reset
1
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2
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429
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Error creating SPIA data for KEGG Orthology (KO) Database KEGG xml files
SPIA
8 months ago Benji Bromberg ▴ 20
0
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0
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821
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plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
4.3 years ago Assa Yeroslaviz ★ 1.5k
0
votes
1
reply
890
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alternative package to SPIA
SPIA pathway enrichment analysis overrepresentation
5.3 years ago asifgeb • 0
1
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2
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2.0k
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Question on graphite/SPIA; extracting DE gene list
graphite spia runSPIA
updated 5.5 years ago by 0 • written 9.3 years ago by • 0
0
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0
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996
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SPIA function error in ToPASeq
ToPASeq SPIA pathway analysis R
6.3 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
6.9 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
7.0 years ago khhgng • 0
5
votes
2
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1.6k
views
SPIA::spia function output
SPIA
updated 7.5 years ago by ▴ 570 • written 7.5 years ago by ▴ 10
1
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1
reply
1.2k
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SPIA plotP giving error
SPIA plotP threshold
7.6 years ago docpriya21 ▴ 10
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0
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1.0k
views
SPIA error in DE-Colorectal
SPIA
8.0 years ago saamar.rajput • 0
1
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2
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2.5k
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(Gene-set)Pathway analysis based on network/pathway topology in R
SPIA functional enrichment pathway topology pathway analysis bioconductor
9.0 years ago svlachavas ▴ 830
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 23 months ago by • 0 • written 9.7 years ago by • 0
0
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0
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1.1k
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R: Re: Deseq2 and differentia expression
SPIA SPIA
10.0 years ago Simon Anders ★ 3.7k
0
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1
reply
1.4k
views
SPIA
Pathways SPIA Pathways SPIA
updated 10.3 years ago by ▴ 570 • written 10.3 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
10.5 years ago array chip ▴ 420
0
votes
1
reply
1.5k
views
makeSPIAdata
SPIA SPIA
updated 10.5 years ago by ▴ 570 • written 10.5 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 10.6 years ago by ▴ 570 • written 10.6 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
11.3 years ago Ian Sudbery ▴ 30
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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
11.3 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
11.4 years ago Tarca, Adi ▴ 570
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0
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1.3k
views
Bioconductor Digest, Vol 119, Issue 5: Overrepresentation pathway with KEGGPROFILE and SPIA
Pathways SPIA KEGGprofile Pathways SPIA KEGGprofile
11.5 years ago Tarca, Adi ▴ 570
0
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0
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1.0k
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Overrepresentation pathway with KEGGPROFILE and SPIA
SPIA SPIA
11.5 years ago gregory voisin ▴ 430
0
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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 12.1 years ago by ▴ 120 • written 12.1 years ago by ▴ 50
0
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2
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2.5k
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 12.5 years ago by ▴ 570 • written 12.5 years ago by ▴ 100
0
votes
0
replies
1.2k
views
Bioconductor resources for immunology
Pathways GO SPIA Pathways GO SPIA
12.5 years ago January Weiner ▴ 240
0
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0
replies
1.4k
views
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
12.6 years ago Jing Huang ▴ 380
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2
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1.4k
views
SPIA package
PROcess SPIA PROcess SPIA
12.8 years ago Jing Huang ▴ 380
0
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0
replies
1.1k
views
question for you on SPIA package
Pathways Organism SPIA Pathways Organism SPIA
12.8 years ago Tarca, Adi ▴ 570
0
votes
2
replies
1.4k
views
question on SPIA pavkage application
Organism SPIA Organism SPIA
updated 12.9 years ago by ▴ 150 • written 12.9 years ago by ▴ 380
0
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1
reply
1.2k
views
a question on SPIA package
Microarray SPIA Microarray SPIA
updated 12.9 years ago by ▴ 650 • written 12.9 years ago by ▴ 380
0
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2
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1.7k
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organism abbreviations (SPIA package)
Microarray Organism SPIA Microarray Organism SPIA
updated 12.9 years ago by ▴ 340 • written 12.9 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 13.4 years ago by ▴ 370 • written 13.4 years ago by ▴ 100
0
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1
reply
1.2k
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Which resources for pathway analysis?
Pathways SPIA Pathways SPIA
updated 13.4 years ago by ▴ 300 • written 13.4 years ago by ▴ 370
0
votes
1
reply
1.2k
views
SPIA package with updated KEGG pathways
Pathways SPIA Pathways SPIA
updated 13.6 years ago by ★ 7.2k • written 13.6 years ago by ▴ 20
0
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0
replies
1.0k
views
Bioconductor Digest, Vol 94, Issue 10
Pathways SPIA Pathways SPIA
13.6 years ago Tarca, Adi ▴ 570
0
votes
0
replies
1.4k
views
Bioconductor Digest, Vol 93, Issue 26: How to create KEGG's pathway data for SPIA?
Organism KEGGgraph SPIA Organism KEGGgraph SPIA
13.6 years ago Tarca, Adi ▴ 570
0
votes
0
replies
998
views
How to create KEGG's pathway data for SPIA?
SPIA SPIA
13.6 years ago Lourdes Peña Castillo ▴ 140
0
votes
4
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1.4k
views
SPIA - changes between 1.4.0 and 1.60.
Pathways SPIA Pathways SPIA
updated 13.8 years ago by ▴ 20 • written 13.8 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
13.9 years ago Will Bush ▴ 10
0
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0
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1.1k
views
SPIA package problem
Microarray GO Cancer Organism hgu95av2 mgug4122a SPIA Microarray GO Cancer Organism
14.1 years ago January Weiner ▴ 370
0
votes
0
replies
972
views
help with SPIA package
Organism limma SPIA Organism limma SPIA
14.1 years ago Barbara Bo-Ju Shih ▴ 40
0
votes
0
replies
875
views
MArray into data.frame for SPIA package
limma marray SPIA limma marray SPIA
14.3 years ago Gordon Smyth 51k
0
votes
1
reply
1.2k
views
SPIA package
graph SPIA graph SPIA
updated 14.3 years ago by ★ 7.4k • written 14.3 years ago by ▴ 200
0
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0
replies
1.4k
views
SPIA: inferring inhibited pathways from up-regulated genes?
Pathways SPIA Pathways SPIA
14.5 years ago Tarca, Adi ▴ 570
0
votes
0
replies
1.3k
views
SPIA, hacked to run with only selected pathways
SystemsBiology Pathways Cancer SPIA SystemsBiology Pathways Cancer SPIA
14.6 years ago Tarca, Adi ▴ 570
46 results • Page 1 of 1
Recent ...
Replies
Comment: Ranking the GSEA Results by Lluís Revilla Sancho ▴ 730
You can have the ranking without the cutoff. If you don't keep any gene set after the cutoff then there is nothing to rank as you said, so…
Answer: Create a Graph w/ Only the Genes Interaction by Antonio • 0
Thank you all, I solved my issue by creating a for loop. Cheers!
Comment: Ranking the GSEA Results by alserg ▴ 270
Apparently, it sends a notification to the developer on a new message after the tags were updated :) but not the change of tags itself
Comment: Ranking the GSEA Results by alserg ▴ 270
Where did you see ranking of genes by `log2FC * (-log10 p-value)`? I don't think I ever saw one and not sure what it should achieve. Aren't…
Comment: Trouble Installing DADA2 (warning: R new user) by shepherl 3.9k
As far as this ERROR for Bioc requires R version, Bioconductor is closely tied to an R release. Depending if you tried to use a premade s…
Votes
Comment: Ranking the GSEA Results
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
Comment: How to get the DMR?
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
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Popular Question to ATpoint ★ 4.2k
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Scholar to Gordon Smyth 51k
Voter to Chris ▴ 20
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