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spia
•
reset
1
vote
2
replies
432
views
Error creating SPIA data for KEGG Orthology (KO) Database KEGG xml files
SPIA
8 months ago
Benji Bromberg
▴ 20
0
votes
0
replies
822
views
plotting Signalling Pathways using SPIA
SPIA
functional-analysis
Pathways
KEGG
4.3 years ago
Assa Yeroslaviz
★ 1.5k
0
votes
1
reply
892
views
alternative package to SPIA
SPIA
pathway enrichment analysis
overrepresentation
5.3 years ago
asifgeb
• 0
1
vote
2
replies
2.0k
views
Question on graphite/SPIA; extracting DE gene list
graphite
spia
runSPIA
updated 5.5 years ago by
Bioconductor Community
0 • written 9.3 years ago by
rgamini
• 0
0
votes
0
replies
996
views
SPIA function error in ToPASeq
ToPASeq
SPIA
pathway analysis
R
6.3 years ago
fawazfebin
▴ 60
0
votes
0
replies
1.2k
views
a possible bug in spia function
SPIA
6.9 years ago
slava.ilyntskyy
• 0
0
votes
0
replies
1.1k
views
SPIA Package : Activated and Inhibited
SPIA
R
pathway analysis
7.0 years ago
khhgng
• 0
5
votes
2
replies
1.6k
views
SPIA::spia function output
SPIA
updated 7.5 years ago by
Tarca, Adi
▴ 570 • written 7.5 years ago by
theobroma22
▴ 10
1
vote
1
reply
1.2k
views
SPIA plotP giving error
SPIA
plotP
threshold
7.6 years ago
docpriya21
▴ 10
0
votes
0
replies
1.0k
views
SPIA error in DE-Colorectal
SPIA
8.0 years ago
saamar.rajput
• 0
1
vote
2
replies
2.5k
views
(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
votes
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
a.ghosh
• 0 • written 9.7 years ago by
A Eelmur
• 0
0
votes
0
replies
1.1k
views
R: Re: Deseq2 and differentia expression
SPIA
SPIA
10.0 years ago
Simon Anders
★ 3.7k
0
votes
1
reply
1.4k
views
SPIA
Pathways
SPIA
Pathways
SPIA
updated 10.3 years ago by
Tarca, Adi
▴ 570 • written 10.3 years ago by
Guest User
★ 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
10.5 years ago
array chip
▴ 420
0
votes
1
reply
1.5k
views
makeSPIAdata
SPIA
SPIA
updated 10.5 years ago by
Tarca, Adi
▴ 570 • written 10.5 years ago by
David Price
▴ 10
0
votes
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
Tarca, Adi
▴ 570 • written 10.6 years ago by
Guest User
★ 13k
0
votes
0
replies
1.2k
views
Background for test in SPIA package.
Annotation
Pathways
SPIA
Annotation
Pathways
SPIA
11.3 years ago
Ian Sudbery
▴ 30
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
11.4 years ago
Tarca, Adi
▴ 570
0
votes
0
replies
1.4k
views
changes in SPIA package: using updated KEGG pathway data
Organism
SPIA
Organism
SPIA
11.4 years ago
Tarca, Adi
▴ 570
0
votes
0
replies
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
votes
0
replies
1.0k
views
Overrepresentation pathway with KEGGPROFILE and SPIA
SPIA
SPIA
11.5 years ago
gregory voisin
▴ 430
0
votes
3
replies
2.7k
views
Kegg pathways overlay with log fold change values
Pathways
limma
SPIA
Pathways
limma
SPIA
updated 12.1 years ago by
alessandro brozzi
▴ 120 • written 12.1 years ago by
Amit Kumar Kashyap
▴ 50
0
votes
2
replies
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
Tarca, Adi
▴ 570 • written 12.5 years ago by
Moritz Kebschull
▴ 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
votes
0
replies
1.4k
views
SPIA package
Pathways
Organism
SPIA
Pathways
Organism
SPIA
12.6 years ago
Tarca, Adi
▴ 570
0
votes
0
replies
1.3k
views
question for SPIA package
Pathways
SPIA
Pathways
SPIA
12.6 years ago
Jing Huang
▴ 380
0
votes
2
replies
1.4k
views
SPIA package
PROcess
SPIA
PROcess
SPIA
12.8 years ago
Jing Huang
▴ 380
0
votes
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
Freudenberg, Johannes NIH/NIEHS [E]
▴ 150 • written 12.9 years ago by
Jing Huang
▴ 380
0
votes
1
reply
1.2k
views
a question on SPIA package
Microarray
SPIA
Microarray
SPIA
updated 12.9 years ago by
Alex Gutteridge
▴ 650 • written 12.9 years ago by
Jing Huang
▴ 380
0
votes
2
replies
1.7k
views
organism abbreviations (SPIA package)
Microarray
Organism
SPIA
Microarray
Organism
SPIA
updated 12.9 years ago by
Manca Marco PATH
▴ 340 • written 12.9 years ago by
Jing Huang
▴ 380
0
votes
1
reply
1.5k
views
Which resources for pathway analysis?
Pathways
Network
SPIA
DEGraph
Pathways
Network
SPIA
DEGraph
updated 13.4 years ago by
January Weiner
▴ 370 • written 13.4 years ago by
laurent jacob
▴ 100
0
votes
1
reply
1.3k
views
Which resources for pathway analysis?
Pathways
SPIA
Pathways
SPIA
updated 13.4 years ago by
Gilbert Feng
▴ 300 • written 13.4 years ago by
January Weiner
▴ 370
0
votes
1
reply
1.3k
views
SPIA package with updated KEGG pathways
Pathways
SPIA
Pathways
SPIA
updated 13.6 years ago by
Marc Carlson
★ 7.2k • written 13.6 years ago by
Bhaskar Dutta
▴ 20
0
votes
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
999
views
How to create KEGG's pathway data for SPIA?
SPIA
SPIA
13.6 years ago
Lourdes Peña Castillo
▴ 140
0
votes
4
replies
1.4k
views
SPIA - changes between 1.4.0 and 1.60.
Pathways
SPIA
Pathways
SPIA
updated 13.8 years ago by
Sorin Draghici
▴ 20 • written 13.8 years ago by
Lavinia Gordon
▴ 480
0
votes
0
replies
1.1k
views
SPIA with Mouse Data
Genetics
Network
Organism
SPIA
Genetics
Network
Organism
SPIA
13.9 years ago
Will Bush
▴ 10
0
votes
0
replies
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
877
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
Seth Falcon
★ 7.4k • written 14.3 years ago by
Marcos Pinho
▴ 200
0
votes
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: limma comparison for small sample size and how to get covariance matrix
by
Gordon Smyth
51k
Your MDS plot is better than before, but you are still not following the recommendation for making for making such plots given in the limma…
Comment: Mapping Between GenBank ID's and Uniprot
by
James W. MacDonald
66k
Also, ``` > result <- mapUniProt( from = "EMBL-GenBank-DDBJ_CDS", to = "UniProtKB", query = c("ACF95883.1") ) > result From…
Comment: Mapping Between GenBank ID's and Uniprot
by
James W. MacDonald
66k
Ugh, here's the link https://www.uniprot.org/id-mapping/uniprotkb/dd08aa16774d98ef087dc3bd708582012bba49e2/overview?fields=accession%2Cre…
Answer: Mapping Between GenBank ID's and Uniprot
by
James W. MacDonald
66k
The input should be 'EMBL-GenBank-DDBJ_CDS", as that is a GenBank ID.
Answer: XCMS2 of orbitrap data
by
Elodie
• 0
Hi, I have the same question, I have acquired MS2 data with PRM analysis and inclusion lists of several ions. I have a list of product ion…
Votes
Answer: EPIC array hg38 annotation?
Answer: Why does DESeq2 give negative log2 fold change in treatment vs control for some
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: Ranking the GSEA Results
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
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