Showing : SPIA • reset
1
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2
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578
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Error creating SPIA data for KEGG Orthology (KO) Database KEGG xml files
SPIA
14 months ago Benji Bromberg ▴ 30
0
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0
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972
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plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
4.8 years ago Assa Yeroslaviz ★ 1.5k
0
votes
1
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1.0k
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alternative package to SPIA
SPIA pathway enrichment analysis overrepresentation
5.8 years ago asifgeb • 0
1
vote
2
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2.2k
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Question on graphite/SPIA; extracting DE gene list
graphite spia runSPIA
updated 5.9 years ago by 0 • written 9.8 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
6.7 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
7.4 years ago slava.ilyntskyy • 0
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
7.5 years ago khhgng • 0
5
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2
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1.7k
views
SPIA::spia function output
SPIA
updated 8.0 years ago by ▴ 570 • written 8.0 years ago by ▴ 10
1
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1
reply
1.3k
views
SPIA plotP giving error
SPIA plotP threshold
8.1 years ago docpriya21 ▴ 10
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0
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1.2k
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SPIA error in DE-Colorectal
SPIA
8.5 years ago saamar.rajput • 0
1
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2
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2.7k
views
(Gene-set)Pathway analysis based on network/pathway topology in R
SPIA functional enrichment pathway topology pathway analysis bioconductor
9.4 years ago svlachavas ▴ 840
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 2.4 years ago by • 0 • written 10.1 years ago by • 0
0
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0
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1.2k
views
R: Re: Deseq2 and differentia expression
SPIA SPIA
10.4 years ago Simon Anders ★ 3.8k
0
votes
1
reply
1.5k
views
SPIA
Pathways SPIA Pathways SPIA
updated 10.8 years ago by ▴ 570 • written 10.8 years ago by ★ 13k
0
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1
reply
1.9k
views
pathway analysis by SPIA using SPIA package vs graphite package
Pathways SPIA cycle graphite Pathways SPIA cycle graphite
10.9 years ago array chip ▴ 420
0
votes
1
reply
1.6k
views
makeSPIAdata
SPIA SPIA
updated 11.0 years ago by ▴ 570 • written 11.0 years ago by ▴ 10
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votes
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 11.0 years ago by ▴ 570 • written 11.0 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
11.7 years ago Ian Sudbery ▴ 30
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0
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1.8k
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SPIA algorithm organisms not included already in the SPIA package
Organism SPIA goseq KEGGREST Organism SPIA goseq KEGGREST
11.8 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
11.8 years ago Tarca, Adi ▴ 570
0
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0
replies
1.4k
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Bioconductor Digest, Vol 119, Issue 5: Overrepresentation pathway with KEGGPROFILE and SPIA
Pathways SPIA KEGGprofile Pathways SPIA KEGGprofile
12.0 years ago Tarca, Adi ▴ 570
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0
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1.1k
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Overrepresentation pathway with KEGGPROFILE and SPIA
SPIA SPIA
12.0 years ago gregory voisin ▴ 430
0
votes
3
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2.9k
views
Kegg pathways overlay with log fold change values
Pathways limma SPIA Pathways limma SPIA
updated 12.5 years ago by ▴ 120 • written 12.5 years ago by ▴ 50
0
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2
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2.6k
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 12.9 years ago by ▴ 570 • written 12.9 years ago by ▴ 100
0
votes
0
replies
1.3k
views
Bioconductor resources for immunology
Pathways GO SPIA Pathways GO SPIA
13.0 years ago January Weiner ▴ 240
0
votes
0
replies
1.5k
views
SPIA package
Pathways Organism SPIA Pathways Organism SPIA
13.0 years ago Tarca, Adi ▴ 570
0
votes
0
replies
1.4k
views
question for SPIA package
Pathways SPIA Pathways SPIA
13.0 years ago Jing Huang ▴ 380
0
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2
replies
1.5k
views
SPIA package
PROcess SPIA PROcess SPIA
13.3 years ago Jing Huang ▴ 380
0
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0
replies
1.2k
views
question for you on SPIA package
Pathways Organism SPIA Pathways Organism SPIA
13.3 years ago Tarca, Adi ▴ 570
0
votes
2
replies
1.5k
views
question on SPIA pavkage application
Organism SPIA Organism SPIA
updated 13.3 years ago by ▴ 150 • written 13.3 years ago by ▴ 380
0
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1
reply
1.3k
views
a question on SPIA package
Microarray SPIA Microarray SPIA
updated 13.3 years ago by ▴ 650 • written 13.3 years ago by ▴ 380
0
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2
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1.8k
views
organism abbreviations (SPIA package)
Microarray Organism SPIA Microarray Organism SPIA
updated 13.3 years ago by ▴ 340 • written 13.3 years ago by ▴ 380
0
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1
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1.7k
views
Which resources for pathway analysis?
Pathways Network SPIA DEGraph Pathways Network SPIA DEGraph
updated 13.8 years ago by ▴ 370 • written 13.8 years ago by ▴ 100
0
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1
reply
1.4k
views
Which resources for pathway analysis?
Pathways SPIA Pathways SPIA
updated 13.8 years ago by ▴ 300 • written 13.8 years ago by ▴ 370
0
votes
1
reply
1.4k
views
SPIA package with updated KEGG pathways
Pathways SPIA Pathways SPIA
updated 14.0 years ago by ★ 7.2k • written 14.0 years ago by ▴ 20
0
votes
0
replies
1.1k
views
Bioconductor Digest, Vol 94, Issue 10
Pathways SPIA Pathways SPIA
14.0 years ago Tarca, Adi ▴ 570
0
votes
0
replies
1.5k
views
Bioconductor Digest, Vol 93, Issue 26: How to create KEGG's pathway data for SPIA?
Organism KEGGgraph SPIA Organism KEGGgraph SPIA
14.1 years ago Tarca, Adi ▴ 570
0
votes
0
replies
1.1k
views
How to create KEGG's pathway data for SPIA?
SPIA SPIA
14.1 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 14.3 years ago by ▴ 20 • written 14.3 years ago by ▴ 480
0
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0
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1.2k
views
SPIA with Mouse Data
Genetics Network Organism SPIA Genetics Network Organism SPIA
14.4 years ago Will Bush ▴ 10
0
votes
0
replies
1.2k
views
SPIA package problem
Microarray GO Cancer Organism hgu95av2 mgug4122a SPIA Microarray GO Cancer Organism
14.6 years ago January Weiner ▴ 370
0
votes
0
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1.1k
views
help with SPIA package
Organism limma SPIA Organism limma SPIA
14.6 years ago Barbara Bo-Ju Shih ▴ 40
0
votes
0
replies
940
views
MArray into data.frame for SPIA package
limma marray SPIA limma marray SPIA
14.8 years ago Gordon Smyth 52k
0
votes
1
reply
1.3k
views
SPIA package
graph SPIA graph SPIA
updated 14.8 years ago by ★ 7.4k • written 14.8 years ago by ▴ 200
0
votes
0
replies
1.5k
views
SPIA: inferring inhibited pathways from up-regulated genes?
Pathways SPIA Pathways SPIA
15.0 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
15.0 years ago Tarca, Adi ▴ 570
46 results • Page 1 of 1
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Replies
Comment: Feature Counts - potential bug with outfile.jcounts by chris2.a.white • 0
Hi @gordonsmyth and @weishi, Firstly, thank you for offering your time to develop the junction quantification module further. This is gre…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Hi Tim, Thanks for your reply! Yes, my data is 450K, and it is TCGA methylation data downloaded by TCGAbiolinks. The problem is that I can …
Answer: Error in get_anno_data(ontology) : ontology not supported yet... by Guido Hooiveld ★ 4.1k
Did you check the help page for the function `enrichDO`? Type `?enrichDO`. I am asking, because there it is stated that the argument `ont`…
Comment: Build error on kunpeng2 Linux aarch64 by martin.grigorov ▴ 10
Hi, There was a problem with `icu` and because of that the (r)curl library was not installed. The system/OS curl library is one version ol…
Answer: Standardization of rlog transformed counts before PCA by ATpoint ★ 4.6k
I guess you mean scaling in terms of Z-scoring? There are plenty of posts towards scaling in PCA both here on Bioconductor and in other com…
Votes
Comment: Feature Counts - potential bug with outfile.jcounts
Answer: Feature Counts - potential bug with outfile.jcounts
Comment: Can we get beta values with DMRcate package
Answer: Can we get beta values with DMRcate package
DiffBind giving different results from dba.report() and dba.analyze(..., bRetrieveAnalysis=TRUE)
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