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SPIA
•
reset
0
votes
0
replies
255
views
plotting Signalling Pathways using SPIA
SPIA
functional-analysis
Pathways
KEGG
2.2 years ago
Assa Yeroslaviz
★ 1.5k
0
votes
1
reply
309
views
alternative package to SPIA
SPIA
pathway enrichment analysis
overrepresentation
3.2 years ago
asifgeb
• 0
1
vote
2
replies
1.4k
views
Question on graphite/SPIA; extracting DE gene list
graphite
spia
runSPIA
updated 3.4 years ago by
Bioconductor Community
0 • written 7.2 years ago by
rgamini
• 0
0
votes
0
replies
519
views
SPIA function error in ToPASeq
ToPASeq
SPIA
pathway analysis
R
4.1 years ago
fawazfebin
▴ 30
0
votes
0
replies
909
views
a possible bug in spia function
SPIA
4.8 years ago
slava.ilyntskyy
• 0
0
votes
0
replies
569
views
SPIA Package : Activated and Inhibited
SPIA
R
pathway analysis
4.9 years ago
khhgng
• 0
5
votes
2
replies
952
views
SPIA::spia function output
SPIA
updated 5.4 years ago by
Tarca, Adi
▴ 570 • written 5.4 years ago by
theobroma22
▴ 10
0
votes
1
reply
647
views
SPIA plotP giving error
SPIA
plotP
threshold
5.5 years ago
docpriya21
• 0
0
votes
0
replies
593
views
SPIA error in DE-Colorectal
SPIA
5.9 years ago
saamar.rajput
• 0
1
vote
2
replies
1.8k
views
(Gene-set)Pathway analysis based on network/pathway topology in R
SPIA
functional enrichment
pathway topology
pathway analysis
bioconductor
6.8 years ago
svlachavas
▴ 780
0
votes
0
replies
1.4k
views
SPIA error - names of de are not in reference array
SPIA
named vectors
pathway analysis
7.6 years ago
A Eelmur
• 0
0
votes
0
replies
706
views
R: Re: Deseq2 and differentia expression
SPIA
SPIA
7.9 years ago
Simon Anders
★ 3.7k
0
votes
1
reply
824
views
SPIA
Pathways
SPIA
Pathways
SPIA
updated 8.2 years ago by
Tarca, Adi
▴ 570 • written 8.2 years ago by
Guest User
★ 12k
0
votes
1
reply
1.2k
views
pathway analysis by SPIA using SPIA package vs graphite package
Pathways
SPIA
cycle
graphite
Pathways
SPIA
cycle
graphite
8.3 years ago
array chip
▴ 420
0
votes
1
reply
958
views
makeSPIAdata
SPIA
SPIA
updated 8.4 years ago by
Tarca, Adi
▴ 570 • written 8.4 years ago by
David Price
▴ 10
0
votes
1
reply
1.8k
views
SPIA error - Error in density.default(pfstmp, bw = sd(pfstmp)/4) : \'bw\' is not positive.
SPIA
cycle
SPIA
cycle
updated 8.4 years ago by
Tarca, Adi
▴ 570 • written 8.4 years ago by
Guest User
★ 12k
0
votes
0
replies
861
views
Background for test in SPIA package.
Annotation
Pathways
SPIA
Annotation
Pathways
SPIA
9.2 years ago
Ian Sudbery
▴ 30
0
votes
0
replies
1.2k
views
SPIA algorithm organisms not included already in the SPIA package
Organism
SPIA
goseq
KEGGREST
Organism
SPIA
goseq
KEGGREST
9.2 years ago
Tarca, Adi
▴ 570
0
votes
0
replies
1.0k
views
changes in SPIA package: using updated KEGG pathway data
Organism
SPIA
Organism
SPIA
9.2 years ago
Tarca, Adi
▴ 570
0
votes
0
replies
879
views
Bioconductor Digest, Vol 119, Issue 5: Overrepresentation pathway with KEGGPROFILE and SPIA
Pathways
SPIA
KEGGprofile
Pathways
SPIA
KEGGprofile
9.4 years ago
Tarca, Adi
▴ 570
0
votes
0
replies
762
views
Overrepresentation pathway with KEGGPROFILE and SPIA
SPIA
SPIA
9.4 years ago
gregory voisin
▴ 430
0
votes
3
replies
1.9k
views
Kegg pathways overlay with log fold change values
Pathways
limma
SPIA
Pathways
limma
SPIA
updated 9.9 years ago by
alessandro brozzi
▴ 120 • written 9.9 years ago by
Amit Kumar Kashyap
▴ 50
0
votes
2
replies
1.7k
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 10.4 years ago by
Tarca, Adi
▴ 570 • written 10.4 years ago by
Moritz Kebschull
▴ 100
0
votes
0
replies
868
views
Bioconductor resources for immunology
Pathways
GO
SPIA
Pathways
GO
SPIA
10.4 years ago
January Weiner
▴ 240
0
votes
0
replies
999
views
SPIA package
Pathways
Organism
SPIA
Pathways
Organism
SPIA
10.5 years ago
Tarca, Adi
▴ 570
0
votes
0
replies
803
views
question for SPIA package
Pathways
SPIA
Pathways
SPIA
10.5 years ago
Jing Huang
▴ 380
0
votes
2
replies
853
views
SPIA package
PROcess
SPIA
PROcess
SPIA
10.7 years ago
Jing Huang
▴ 380
0
votes
0
replies
720
views
question for you on SPIA package
Pathways
Organism
SPIA
Pathways
Organism
SPIA
10.7 years ago
Tarca, Adi
▴ 570
0
votes
2
replies
954
views
question on SPIA pavkage application
Organism
SPIA
Organism
SPIA
updated 10.7 years ago by
Freudenberg, Johannes NIH/NIEHS [E]
▴ 150 • written 10.7 years ago by
Jing Huang
▴ 380
0
votes
1
reply
703
views
a question on SPIA package
Microarray
SPIA
Microarray
SPIA
updated 10.7 years ago by
Alex Gutteridge
▴ 650 • written 10.8 years ago by
Jing Huang
▴ 380
0
votes
2
replies
1.2k
views
organism abbreviations (SPIA package)
Microarray
Organism
SPIA
Microarray
Organism
SPIA
updated 10.7 years ago by
Manca Marco PATH
▴ 340 • written 10.7 years ago by
Jing Huang
▴ 380
0
votes
1
reply
997
views
Which resources for pathway analysis?
Pathways
Network
SPIA
DEGraph
Pathways
Network
SPIA
DEGraph
updated 11.2 years ago by
January Weiner
▴ 370 • written 11.2 years ago by
laurent jacob
▴ 100
0
votes
1
reply
794
views
Which resources for pathway analysis?
Pathways
SPIA
Pathways
SPIA
updated 11.2 years ago by
Gilbert Feng
▴ 300 • written 11.2 years ago by
January Weiner
▴ 370
0
votes
1
reply
805
views
SPIA package with updated KEGG pathways
Pathways
SPIA
Pathways
SPIA
updated 11.4 years ago by
Marc Carlson
★ 7.2k • written 11.5 years ago by
Bhaskar Dutta
▴ 20
0
votes
0
replies
649
views
Bioconductor Digest, Vol 94, Issue 10
Pathways
SPIA
Pathways
SPIA
11.4 years ago
Tarca, Adi
▴ 570
0
votes
0
replies
921
views
Bioconductor Digest, Vol 93, Issue 26: How to create KEGG's pathway data for SPIA?
Organism
KEGGgraph
SPIA
Organism
KEGGgraph
SPIA
11.5 years ago
Tarca, Adi
▴ 570
0
votes
0
replies
666
views
How to create KEGG's pathway data for SPIA?
SPIA
SPIA
11.5 years ago
Lourdes Peña Castillo
▴ 140
0
votes
4
replies
853
views
SPIA - changes between 1.4.0 and 1.60.
Pathways
SPIA
Pathways
SPIA
updated 11.7 years ago by
Sorin Draghici
▴ 20 • written 11.7 years ago by
Lavinia Gordon
▴ 480
0
votes
0
replies
718
views
SPIA with Mouse Data
Genetics
Network
Organism
SPIA
Genetics
Network
Organism
SPIA
11.8 years ago
Will Bush
▴ 10
0
votes
0
replies
709
views
SPIA package problem
Microarray
GO
Cancer
Organism
hgu95av2
mgug4122a
SPIA
Microarray
GO
Cancer
Organism
12.0 years ago
January Weiner
▴ 370
0
votes
0
replies
645
views
help with SPIA package
Organism
limma
SPIA
Organism
limma
SPIA
12.0 years ago
Barbara Bo-Ju Shih
▴ 40
0
votes
0
replies
598
views
MArray into data.frame for SPIA package
limma
marray
SPIA
limma
marray
SPIA
12.2 years ago
Gordon Smyth
45k
0
votes
1
reply
792
views
SPIA package
graph
SPIA
graph
SPIA
updated 12.2 years ago by
Seth Falcon
★ 7.4k • written 12.2 years ago by
Marcos Pinho
▴ 200
0
votes
0
replies
1.0k
views
SPIA: inferring inhibited pathways from up-regulated genes?
Pathways
SPIA
Pathways
SPIA
12.4 years ago
Tarca, Adi
▴ 570
0
votes
0
replies
775
views
SPIA, hacked to run with only selected pathways
SystemsBiology
Pathways
Cancer
SPIA
SystemsBiology
Pathways
Cancer
SPIA
12.4 years ago
Tarca, Adi
▴ 570
45 results • Page
1 of 1
Recent ...
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Comment: R: problem with running time-series analysis software: Mfuzz
by
Kevin Blighe
3.5k
Cross-posted: https://www.biostars.org/p/9524023/
Comment: ROC plot for OPLS-DA
by
Eddie
• 0
Hi, That was helpful. Thank you. How to do the same for the testing data?
Comment: ChIP-seq peak annotation to gene in ChIPseeker
by
Gyan Prakash Mishra
• 0
After going through the package, I think all the peaks are annotated to genes irrespective of distance to TSS. There is also another functi…
Comment: lpsymphony compilation trouble
by
Cankun
• 0
It's 2022 and it still works for lpsymphony_1.24.0
Comment: UniprotKB AC/ID to Entrez ID Conversion
by
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59k
I fixed this when Bioc 3.13 was the release version, so it should work in 3.14 and the current release. ``` > up <- UniProt.ws() > input …
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to
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3.5k
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SamGG
▴ 270
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johnmcma
▴ 10
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