Showing : SPIA • reset
0
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4
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SPIA - changes between 1.4.0 and 1.60.
Pathways SPIA Pathways SPIA
updated 13.6 years ago by ▴ 20 • written 13.6 years ago by ▴ 480
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2
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2.4k
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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 12.3 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
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2
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1.3k
views
SPIA package
PROcess SPIA PROcess SPIA
12.6 years ago Jing Huang ▴ 380
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1
reply
1.3k
views
SPIA
Pathways SPIA Pathways SPIA
updated 10.1 years ago by ▴ 570 • written 10.1 years ago by ★ 13k
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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
views
Question on graphite/SPIA; extracting DE gene list
graphite spia runSPIA
updated 5.3 years ago by 0 • written 9.1 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 13.1 years ago by ▴ 300 • written 13.1 years ago by ▴ 370
5
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2
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1.5k
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SPIA::spia function output
SPIA
updated 7.3 years ago by ▴ 570 • written 7.3 years ago by ▴ 10
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3
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2.6k
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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
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1
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1.4k
views
Which resources for pathway analysis?
Pathways Network SPIA DEGraph Pathways Network SPIA DEGraph
updated 13.1 years ago by ▴ 370 • written 13.1 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
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373
views
Error creating SPIA data for KEGG Orthology (KO) Database KEGG xml files
SPIA
6 months ago Benji Bromberg ▴ 20
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votes
1
reply
2.5k
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
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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 21 months ago by • 0 • written 9.5 years ago by • 0
1
vote
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
8.8 years ago svlachavas ▴ 830
0
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0
replies
999
views
SPIA error in DE-Colorectal
SPIA
7.8 years ago saamar.rajput • 0
0
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1
reply
1.1k
views
SPIA plotP giving error
SPIA plotP threshold
7.4 years ago docpriya21 • 0
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0
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1.0k
views
SPIA Package : Activated and Inhibited
SPIA R pathway analysis
6.8 years ago khhgng • 0
0
votes
0
replies
1.2k
views
a possible bug in spia function
SPIA
6.7 years ago slava.ilyntskyy • 0
0
votes
0
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914
views
SPIA function error in ToPASeq
ToPASeq SPIA pathway analysis R
6.1 years ago fawazfebin ▴ 60
0
votes
1
reply
841
views
alternative package to SPIA
SPIA pathway enrichment analysis overrepresentation
5.1 years ago asifgeb • 0
0
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0
replies
765
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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
14.3 years ago Tarca, Adi ▴ 570
0
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0
replies
848
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
931
views
help with SPIA package
Organism limma SPIA Organism limma SPIA
13.9 years ago Barbara Bo-Ju Shih ▴ 40
0
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0
replies
1.0k
views
SPIA package problem
Microarray GO Cancer Organism hgu95av2 mgug4122a SPIA Microarray GO Cancer Organism
13.9 years ago January Weiner ▴ 370
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0
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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
966
views
How to create KEGG's pathway data for SPIA?
SPIA SPIA
13.4 years ago Lourdes Peña Castillo ▴ 140
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
13.4 years ago Tarca, Adi ▴ 570
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0
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980
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
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question for you on 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
12.4 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
12.3 years ago January Weiner ▴ 240
0
votes
0
replies
998
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
11.1 years ago Tarca, Adi ▴ 570
0
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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
46 results • Page 1 of 1
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Comment: Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia) by christianhilton64 • 0
I'm less familiar with the specifics of GSVA, but I'm curious about the overall goal of this analysis. Could you provide a high-level summa…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
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Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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