Showing : SPIA • reset
1
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562
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Error creating SPIA data for KEGG Orthology (KO) Database KEGG xml files
SPIA
13 months ago Benji Bromberg ▴ 30
0
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958
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plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
4.7 years ago Assa Yeroslaviz ★ 1.5k
0
votes
1
reply
992
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alternative package to SPIA
SPIA pathway enrichment analysis overrepresentation
5.7 years ago asifgeb • 0
1
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2
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2.1k
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Question on graphite/SPIA; extracting DE gene list
graphite spia runSPIA
updated 5.8 years 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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SPIA function error in ToPASeq
ToPASeq SPIA pathway analysis R
6.6 years ago fawazfebin ▴ 60
0
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0
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1.3k
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a possible bug in spia function
SPIA
7.3 years ago slava.ilyntskyy • 0
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0
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1.2k
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SPIA Package : Activated and Inhibited
SPIA R pathway analysis
7.4 years ago khhgng • 0
5
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2
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1.7k
views
SPIA::spia function output
SPIA
updated 7.9 years ago by ▴ 570 • written 7.9 years ago by ▴ 10
1
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1
reply
1.3k
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SPIA plotP giving error
SPIA plotP threshold
8.0 years ago docpriya21 ▴ 10
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0
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1.1k
views
SPIA error in DE-Colorectal
SPIA
8.4 years ago saamar.rajput • 0
1
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2
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2.6k
views
(Gene-set)Pathway analysis based on network/pathway topology in R
SPIA functional enrichment pathway topology pathway analysis bioconductor
9.3 years ago svlachavas ▴ 830
0
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1
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2.3k
views
SPIA error - names of de are not in reference array
SPIA named vectors pathway analysis
updated 2.3 years ago by • 0 • written 10.0 years ago by • 0
0
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0
replies
1.2k
views
R: Re: Deseq2 and differentia expression
SPIA SPIA
10.3 years ago Simon Anders ★ 3.8k
0
votes
1
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1.5k
views
SPIA
Pathways SPIA Pathways SPIA
updated 10.7 years ago by ▴ 570 • written 10.7 years ago by ★ 13k
0
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1
reply
1.8k
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pathway analysis by SPIA using SPIA package vs graphite package
Pathways SPIA cycle graphite Pathways SPIA cycle graphite
10.8 years ago array chip ▴ 420
0
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1
reply
1.6k
views
makeSPIAdata
SPIA SPIA
updated 10.9 years ago by ▴ 570 • written 10.9 years ago by ▴ 10
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1
reply
2.8k
views
SPIA error - Error in density.default(pfstmp, bw = sd(pfstmp)/4) : \'bw\' is not positive.
SPIA cycle SPIA cycle
updated 10.9 years ago by ▴ 570 • written 10.9 years ago by ★ 13k
0
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0
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1.3k
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Background for test in SPIA package.
Annotation Pathways SPIA Annotation Pathways SPIA
11.6 years ago Ian Sudbery ▴ 30
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0
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1.8k
views
SPIA algorithm organisms not included already in the SPIA package
Organism SPIA goseq KEGGREST Organism SPIA goseq KEGGREST
11.7 years ago Tarca, Adi ▴ 570
0
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0
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1.5k
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changes in SPIA package: using updated KEGG pathway data
Organism SPIA Organism SPIA
11.7 years ago Tarca, Adi ▴ 570
0
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0
replies
1.3k
views
Bioconductor Digest, Vol 119, Issue 5: Overrepresentation pathway with KEGGPROFILE and SPIA
Pathways SPIA KEGGprofile Pathways SPIA KEGGprofile
11.9 years ago Tarca, Adi ▴ 570
0
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0
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1.1k
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Overrepresentation pathway with KEGGPROFILE and SPIA
SPIA SPIA
11.9 years ago gregory voisin ▴ 430
0
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3
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2.8k
views
Kegg pathways overlay with log fold change values
Pathways limma SPIA Pathways limma SPIA
updated 12.4 years ago by ▴ 120 • written 12.4 years ago by ▴ 50
0
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2
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2.6k
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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 12.9 years ago by ▴ 570 • written 12.9 years ago by ▴ 100
0
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0
replies
1.3k
views
Bioconductor resources for immunology
Pathways GO SPIA Pathways GO SPIA
12.9 years ago January Weiner ▴ 240
0
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0
replies
1.5k
views
SPIA package
Pathways Organism SPIA Pathways Organism SPIA
12.9 years ago Tarca, Adi ▴ 570
0
votes
0
replies
1.3k
views
question for SPIA package
Pathways SPIA Pathways SPIA
13.0 years ago Jing Huang ▴ 380
0
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2
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1.5k
views
SPIA package
PROcess SPIA PROcess SPIA
13.2 years ago Jing Huang ▴ 380
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
13.2 years ago Tarca, Adi ▴ 570
0
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2
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1.5k
views
question on SPIA pavkage application
Organism SPIA Organism SPIA
updated 13.2 years ago by ▴ 150 • written 13.2 years ago by ▴ 380
0
votes
1
reply
1.3k
views
a question on SPIA package
Microarray SPIA Microarray SPIA
updated 13.2 years ago by ▴ 650 • written 13.2 years ago by ▴ 380
0
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2
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1.8k
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organism abbreviations (SPIA package)
Microarray Organism SPIA Microarray Organism SPIA
updated 13.2 years ago by ▴ 340 • written 13.2 years ago by ▴ 380
0
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1
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1.6k
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Which resources for pathway analysis?
Pathways Network SPIA DEGraph Pathways Network SPIA DEGraph
updated 13.7 years ago by ▴ 370 • written 13.7 years ago by ▴ 100
0
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1
reply
1.3k
views
Which resources for pathway analysis?
Pathways SPIA Pathways SPIA
updated 13.7 years ago by ▴ 300 • written 13.7 years ago by ▴ 370
0
votes
1
reply
1.3k
views
SPIA package with updated KEGG pathways
Pathways SPIA Pathways SPIA
updated 13.9 years ago by ★ 7.2k • written 13.9 years ago by ▴ 20
0
votes
0
replies
1.1k
views
Bioconductor Digest, Vol 94, Issue 10
Pathways SPIA Pathways SPIA
13.9 years ago Tarca, Adi ▴ 570
0
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0
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1.5k
views
Bioconductor Digest, Vol 93, Issue 26: How to create KEGG's pathway data for SPIA?
Organism KEGGgraph SPIA Organism KEGGgraph SPIA
14.0 years ago Tarca, Adi ▴ 570
0
votes
0
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1.1k
views
How to create KEGG's pathway data for SPIA?
SPIA SPIA
14.0 years ago Lourdes Peña Castillo ▴ 140
0
votes
4
replies
1.6k
views
SPIA - changes between 1.4.0 and 1.60.
Pathways SPIA Pathways SPIA
updated 14.2 years ago by ▴ 20 • written 14.2 years ago by ▴ 480
0
votes
0
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1.2k
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SPIA with Mouse Data
Genetics Network Organism SPIA Genetics Network Organism SPIA
14.3 years ago Will Bush ▴ 10
0
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0
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1.1k
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SPIA package problem
Microarray GO Cancer Organism hgu95av2 mgug4122a SPIA Microarray GO Cancer Organism
14.5 years ago January Weiner ▴ 370
0
votes
0
replies
1.1k
views
help with SPIA package
Organism limma SPIA Organism limma SPIA
14.5 years ago Barbara Bo-Ju Shih ▴ 40
0
votes
0
replies
930
views
MArray into data.frame for SPIA package
limma marray SPIA limma marray SPIA
14.7 years ago Gordon Smyth 51k
0
votes
1
reply
1.3k
views
SPIA package
graph SPIA graph SPIA
updated 14.7 years ago by ★ 7.4k • written 14.7 years ago by ▴ 200
0
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0
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1.5k
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SPIA: inferring inhibited pathways from up-regulated genes?
Pathways SPIA Pathways SPIA
14.9 years ago Tarca, Adi ▴ 570
0
votes
0
replies
1.4k
views
SPIA, hacked to run with only selected pathways
SystemsBiology Pathways Cancer SPIA SystemsBiology Pathways Cancer SPIA
14.9 years ago Tarca, Adi ▴ 570
46 results • Page 1 of 1
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Answer: [How to construct a model.matrix ] by Gordon Smyth 51k
> Initially, I simply used > `lm(Epigenetic_age ~ Age_group + Age + Sex + PC1 + PC2 + PC3 + PC4 + PC5 + B + CD4T + CD8T + Mono + NK + Neutr…
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by rania.alanany • 0
Hi Robert, Thank you for the explanation, But I am still little bit confused, Is the annotation package (TxDb.Hsapiens.UCSC.hg38.knownGene)…
Comment: Merge Replicates vs Mixed Model by abadgerw • 0
@gabrielhoffman any insight?
Comment: makeContrastsDream for Interaction by abadgerw • 0
@gabrielhoffman any insight?
Comment: ColData and ERROR: rows did not converge in beta, labelled in mcols(object)$beta by Michael Love 42k
That is the rows that did converge.
Votes
A: Some questions for remove batch effect by using mnnCorrect
A: Recommendations for combining multiple 10x runs into one SingleCellExperiment
Answer: [How to construct a model.matrix ]
Answer: Handling biological replicates in DESeq2
Comment: biomaRt rnorvegicus_gene_ensembl not available anymore
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