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spia
•
reset
0
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replies
289
views
plotting Signalling Pathways using SPIA
SPIA
functional-analysis
Pathways
KEGG
2.4 years ago
Assa Yeroslaviz
★ 1.5k
0
votes
1
reply
341
views
alternative package to SPIA
SPIA
pathway enrichment analysis
overrepresentation
3.5 years ago
asifgeb
• 0
1
vote
2
replies
1.4k
views
Question on graphite/SPIA; extracting DE gene list
graphite
spia
runSPIA
updated 3.6 years ago by
Bioconductor Community
0 • written 7.4 years ago by
rgamini
• 0
0
votes
0
replies
553
views
SPIA function error in ToPASeq
ToPASeq
SPIA
pathway analysis
R
4.4 years ago
fawazfebin
▴ 50
0
votes
0
replies
930
views
a possible bug in spia function
SPIA
5.1 years ago
slava.ilyntskyy
• 0
0
votes
0
replies
597
views
SPIA Package : Activated and Inhibited
SPIA
R
pathway analysis
5.1 years ago
khhgng
• 0
5
votes
2
replies
999
views
SPIA::spia function output
SPIA
updated 5.6 years ago by
Tarca, Adi
▴ 570 • written 5.6 years ago by
theobroma22
▴ 10
0
votes
1
reply
690
views
SPIA plotP giving error
SPIA
plotP
threshold
5.8 years ago
docpriya21
• 0
0
votes
0
replies
618
views
SPIA error in DE-Colorectal
SPIA
6.1 years ago
saamar.rajput
• 0
1
vote
2
replies
1.9k
views
(Gene-set)Pathway analysis based on network/pathway topology in R
SPIA
functional enrichment
pathway topology
pathway analysis
bioconductor
7.1 years ago
svlachavas
▴ 800
0
votes
1
reply
1.5k
views
SPIA error - names of de are not in reference array
SPIA
named vectors
pathway analysis
updated 20 days ago by
a.ghosh
• 0 • written 7.8 years ago by
A Eelmur
• 0
0
votes
0
replies
731
views
R: Re: Deseq2 and differentia expression
SPIA
SPIA
8.1 years ago
Simon Anders
★ 3.7k
0
votes
1
reply
861
views
SPIA
Pathways
SPIA
Pathways
SPIA
updated 8.5 years ago by
Tarca, Adi
▴ 570 • written 8.5 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
8.6 years ago
array chip
▴ 420
0
votes
1
reply
993
views
makeSPIAdata
SPIA
SPIA
updated 8.6 years ago by
Tarca, Adi
▴ 570 • written 8.6 years ago by
David Price
▴ 10
0
votes
1
reply
1.9k
views
SPIA error - Error in density.default(pfstmp, bw = sd(pfstmp)/4) : \'bw\' is not positive.
SPIA
cycle
SPIA
cycle
updated 8.7 years ago by
Tarca, Adi
▴ 570 • written 8.7 years ago by
Guest User
★ 12k
0
votes
0
replies
885
views
Background for test in SPIA package.
Annotation
Pathways
SPIA
Annotation
Pathways
SPIA
9.4 years ago
Ian Sudbery
▴ 30
0
votes
0
replies
1.3k
views
SPIA algorithm organisms not included already in the SPIA package
Organism
SPIA
goseq
KEGGREST
Organism
SPIA
goseq
KEGGREST
9.5 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
9.5 years ago
Tarca, Adi
▴ 570
0
votes
0
replies
919
views
Bioconductor Digest, Vol 119, Issue 5: Overrepresentation pathway with KEGGPROFILE and SPIA
Pathways
SPIA
KEGGprofile
Pathways
SPIA
KEGGprofile
9.6 years ago
Tarca, Adi
▴ 570
0
votes
0
replies
787
views
Overrepresentation pathway with KEGGPROFILE and SPIA
SPIA
SPIA
9.6 years ago
gregory voisin
▴ 430
0
votes
3
replies
2.0k
views
Kegg pathways overlay with log fold change values
Pathways
limma
SPIA
Pathways
limma
SPIA
updated 10.2 years ago by
alessandro brozzi
▴ 120 • written 10.2 years ago by
Amit Kumar Kashyap
▴ 50
0
votes
2
replies
1.8k
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 10.6 years ago by
Tarca, Adi
▴ 570 • written 10.6 years ago by
Moritz Kebschull
▴ 100
0
votes
0
replies
893
views
Bioconductor resources for immunology
Pathways
GO
SPIA
Pathways
GO
SPIA
10.7 years ago
January Weiner
▴ 240
0
votes
0
replies
1.0k
views
SPIA package
Pathways
Organism
SPIA
Pathways
Organism
SPIA
10.7 years ago
Tarca, Adi
▴ 570
0
votes
0
replies
828
views
question for SPIA package
Pathways
SPIA
Pathways
SPIA
10.7 years ago
Jing Huang
▴ 380
0
votes
2
replies
881
views
SPIA package
PROcess
SPIA
PROcess
SPIA
10.9 years ago
Jing Huang
▴ 380
0
votes
0
replies
752
views
question for you on SPIA package
Pathways
Organism
SPIA
Pathways
Organism
SPIA
10.9 years ago
Tarca, Adi
▴ 570
0
votes
2
replies
979
views
question on SPIA pavkage application
Organism
SPIA
Organism
SPIA
updated 11.0 years ago by
Freudenberg, Johannes NIH/NIEHS [E]
▴ 150 • written 11.0 years ago by
Jing Huang
▴ 380
0
votes
1
reply
728
views
a question on SPIA package
Microarray
SPIA
Microarray
SPIA
updated 11.0 years ago by
Alex Gutteridge
▴ 650 • written 11.0 years ago by
Jing Huang
▴ 380
0
votes
2
replies
1.2k
views
organism abbreviations (SPIA package)
Microarray
Organism
SPIA
Microarray
Organism
SPIA
updated 11.0 years ago by
Manca Marco PATH
▴ 340 • written 11.0 years ago by
Jing Huang
▴ 380
0
votes
1
reply
1.0k
views
Which resources for pathway analysis?
Pathways
Network
SPIA
DEGraph
Pathways
Network
SPIA
DEGraph
updated 11.5 years ago by
January Weiner
▴ 370 • written 11.5 years ago by
laurent jacob
▴ 100
0
votes
1
reply
826
views
Which resources for pathway analysis?
Pathways
SPIA
Pathways
SPIA
updated 11.5 years ago by
Gilbert Feng
▴ 300 • written 11.5 years ago by
January Weiner
▴ 370
0
votes
1
reply
838
views
SPIA package with updated KEGG pathways
Pathways
SPIA
Pathways
SPIA
updated 11.7 years ago by
Marc Carlson
★ 7.2k • written 11.7 years ago by
Bhaskar Dutta
▴ 20
0
votes
0
replies
668
views
Bioconductor Digest, Vol 94, Issue 10
Pathways
SPIA
Pathways
SPIA
11.7 years ago
Tarca, Adi
▴ 570
0
votes
0
replies
943
views
Bioconductor Digest, Vol 93, Issue 26: How to create KEGG's pathway data for SPIA?
Organism
KEGGgraph
SPIA
Organism
KEGGgraph
SPIA
11.7 years ago
Tarca, Adi
▴ 570
0
votes
0
replies
693
views
How to create KEGG's pathway data for SPIA?
SPIA
SPIA
11.7 years ago
Lourdes Peña Castillo
▴ 140
0
votes
4
replies
889
views
SPIA - changes between 1.4.0 and 1.60.
Pathways
SPIA
Pathways
SPIA
updated 11.9 years ago by
Sorin Draghici
▴ 20 • written 11.9 years ago by
Lavinia Gordon
▴ 480
0
votes
0
replies
746
views
SPIA with Mouse Data
Genetics
Network
Organism
SPIA
Genetics
Network
Organism
SPIA
12.0 years ago
Will Bush
▴ 10
0
votes
0
replies
734
views
SPIA package problem
Microarray
GO
Cancer
Organism
hgu95av2
mgug4122a
SPIA
Microarray
GO
Cancer
Organism
12.2 years ago
January Weiner
▴ 370
0
votes
0
replies
667
views
help with SPIA package
Organism
limma
SPIA
Organism
limma
SPIA
12.3 years ago
Barbara Bo-Ju Shih
▴ 40
0
votes
0
replies
622
views
MArray into data.frame for SPIA package
limma
marray
SPIA
limma
marray
SPIA
12.4 years ago
Gordon Smyth
46k
0
votes
1
reply
817
views
SPIA package
graph
SPIA
graph
SPIA
updated 12.4 years ago by
Seth Falcon
★ 7.4k • written 12.4 years ago by
Marcos Pinho
▴ 200
0
votes
0
replies
1.1k
views
SPIA: inferring inhibited pathways from up-regulated genes?
Pathways
SPIA
Pathways
SPIA
12.7 years ago
Tarca, Adi
▴ 570
0
votes
0
replies
803
views
SPIA, hacked to run with only selected pathways
SystemsBiology
Pathways
Cancer
SPIA
SystemsBiology
Pathways
Cancer
SPIA
12.7 years ago
Tarca, Adi
▴ 570
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Comment: pathview says my nonmodel species is unknown: "species invalid"
by
Guido Hooiveld
★ 3.3k
What is the non-model organism that you are working with?
Comment: `emptyDrops()` calling 'too many' non-empty droplets
by
Peter Hickey
▴ 560
I've had some further and ongoing discussion with 10x tech support. I've copied the initial reply below and will add any useful updates. I…
Comment: `emptyDrops()` calling 'too many' non-empty droplets
by
Peter Hickey
▴ 560
Interestingly, `DropletUtils::emptyDropsCellRanger()` gave ~20,000 non-empty droplets for the problematic capture, `C120_batch13_1`, with o…
Comment: `emptyDrops()` calling 'too many' non-empty droplets
by
Peter Hickey
▴ 560
Thank you, Imran, for your response. I hope to look more closely at those 'real barcode' and 'false positive barcodes' at some point and ma…
Comment: Can I create my own, private ExperimentHub instance?
by
sandmann.t
▴ 70
That's awesome. Thanks a lot for the pointer to the BiocHubServer!
Votes
edgeR: problem with the quasi-likelihood F-test
A: edgeR: problem with the quasi-likelihood F-test
Answer: `emptyDrops()` calling 'too many' non-empty droplets
Answer: `emptyDrops()` calling 'too many' non-empty droplets
Comment: Bioconductor teaching week
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