Showing : SPIA • reset
1
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2
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402
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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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796
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plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
4.2 years ago Assa Yeroslaviz ★ 1.5k
0
votes
1
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867
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alternative package to SPIA
SPIA pathway enrichment analysis overrepresentation
5.2 years ago asifgeb • 0
1
vote
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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962
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SPIA function error in ToPASeq
ToPASeq SPIA pathway analysis R
6.2 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
views
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
views
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
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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
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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
8.9 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 22 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
9.9 years ago Simon Anders ★ 3.7k
0
votes
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
votes
1
reply
1.7k
views
pathway analysis by SPIA using SPIA package vs graphite package
Pathways SPIA cycle graphite Pathways SPIA cycle graphite
10.4 years ago array chip ▴ 420
0
votes
1
reply
1.4k
views
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 10.5 years ago by ▴ 570 • written 10.5 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
0
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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
11.2 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
11.3 years ago Tarca, Adi ▴ 570
0
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0
replies
1.2k
views
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
0
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0
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1.0k
views
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
views
Kegg pathways overlay with log fold change values
Pathways limma SPIA Pathways limma SPIA
updated 12.0 years ago by ▴ 120 • written 12.0 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
replies
1.4k
views
SPIA package
Pathways Organism SPIA Pathways Organism SPIA
12.5 years ago Tarca, Adi ▴ 570
0
votes
0
replies
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
0
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0
replies
1.1k
views
question for you on SPIA package
Pathways Organism SPIA Pathways Organism SPIA
12.7 years ago Tarca, Adi ▴ 570
0
votes
2
replies
1.4k
views
question on SPIA pavkage application
Organism SPIA Organism SPIA
updated 12.8 years ago by ▴ 150 • written 12.8 years ago by ▴ 380
0
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1
reply
1.2k
views
a question on SPIA package
Microarray SPIA Microarray SPIA
updated 12.8 years ago by ▴ 650 • written 12.8 years ago by ▴ 380
0
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2
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1.6k
views
organism abbreviations (SPIA package)
Microarray Organism SPIA Microarray Organism SPIA
updated 12.8 years ago by ▴ 340 • written 12.8 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
votes
1
reply
1.2k
views
SPIA package with updated KEGG pathways
Pathways SPIA Pathways SPIA
updated 13.5 years ago by ★ 7.2k • written 13.5 years ago by ▴ 20
0
votes
0
replies
1.0k
views
Bioconductor Digest, Vol 94, Issue 10
Pathways SPIA Pathways SPIA
13.5 years ago Tarca, Adi ▴ 570
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
13.5 years ago Tarca, Adi ▴ 570
0
votes
0
replies
986
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
views
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
votes
0
replies
1.1k
views
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
votes
0
replies
957
views
help with SPIA package
Organism limma SPIA Organism limma SPIA
14.0 years ago Barbara Bo-Ju Shih ▴ 40
0
votes
0
replies
863
views
MArray into data.frame for SPIA package
limma marray SPIA limma marray SPIA
14.2 years ago Gordon Smyth 50k
0
votes
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
votes
0
replies
1.2k
views
SPIA, hacked to run with only selected pathways
SystemsBiology Pathways Cancer SPIA SystemsBiology Pathways Cancer SPIA
14.5 years ago Tarca, Adi ▴ 570
46 results • Page 1 of 1
Recent ...
Replies
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2 by BioinfGuru ▴ 30
I would use biomaRt. This is what happens when annotation occurs to early. If possible I would run the DEG analysis on the original output…
Comment: Volcano plot of scRNA-seq data not "centered" by ATpoint ★ 4.2k
My comment was generic. If your experiment causes drastic shifts then the situation might be different. The advise is the same: Try to use …
Comment: conumee with Infinium MethylationEPIC v2.0 by Maximus • 0
Hi Sole, If there is a combined mixture of MSet of 450K, EPIC and EPICv2, how should I create an annotation object? I tried to create anno…
Comment: Volcano plot of scRNA-seq data not "centered" by tjl • 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…
Votes
A: Analyzing data without replicates using DiffBind
A: Analyzing data without replicates using DiffBind
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
DESeq2 swap ensembl gene id rownames with gene symbol column
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
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Popular Question to Gordon Smyth 50k
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