Showing : spia • reset
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plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
2.4 years ago Assa Yeroslaviz ★ 1.5k
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alternative package to SPIA
SPIA pathway enrichment analysis overrepresentation
3.5 years ago asifgeb • 0
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2
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1.4k
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Question on graphite/SPIA; extracting DE gene list
graphite spia runSPIA
updated 3.6 years ago by 0 • written 7.4 years ago by • 0
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553
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SPIA function error in ToPASeq
ToPASeq SPIA pathway analysis R
4.4 years ago fawazfebin ▴ 50
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930
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a possible bug in spia function
SPIA
5.1 years ago slava.ilyntskyy • 0
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597
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SPIA Package : Activated and Inhibited
SPIA R pathway analysis
5.1 years ago khhgng • 0
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2
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999
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SPIA::spia function output
SPIA
updated 5.6 years ago by ▴ 570 • written 5.6 years ago by ▴ 10
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690
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SPIA plotP giving error
SPIA plotP threshold
5.8 years ago docpriya21 • 0
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618
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SPIA error in DE-Colorectal
SPIA
6.1 years ago saamar.rajput • 0
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1.9k
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(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
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1.5k
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SPIA error - names of de are not in reference array
SPIA named vectors pathway analysis
updated 20 days ago by • 0 • written 7.8 years ago by • 0
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731
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R: Re: Deseq2 and differentia expression
SPIA SPIA
8.1 years ago Simon Anders ★ 3.7k
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861
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SPIA
Pathways SPIA Pathways SPIA
updated 8.5 years ago by ▴ 570 • written 8.5 years ago by ★ 12k
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1.2k
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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
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993
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makeSPIAdata
SPIA SPIA
updated 8.6 years ago by ▴ 570 • written 8.6 years ago by ▴ 10
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1.9k
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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 ▴ 570 • written 8.7 years ago by ★ 12k
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Background for test in SPIA package.
Annotation Pathways SPIA Annotation Pathways SPIA
9.4 years ago Ian Sudbery ▴ 30
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1.3k
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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
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changes in SPIA package: using updated KEGG pathway data
Organism SPIA Organism SPIA
9.5 years ago Tarca, Adi ▴ 570
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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
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787
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Overrepresentation pathway with KEGGPROFILE and SPIA
SPIA SPIA
9.6 years ago gregory voisin ▴ 430
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3
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2.0k
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Kegg pathways overlay with log fold change values
Pathways limma SPIA Pathways limma SPIA
updated 10.2 years ago by ▴ 120 • written 10.2 years ago by ▴ 50
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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 10.6 years ago by ▴ 570 • written 10.6 years ago by ▴ 100
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893
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Bioconductor resources for immunology
Pathways GO SPIA Pathways GO SPIA
10.7 years ago January Weiner ▴ 240
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1.0k
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SPIA package
Pathways Organism SPIA Pathways Organism SPIA
10.7 years ago Tarca, Adi ▴ 570
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828
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question for SPIA package
Pathways SPIA Pathways SPIA
10.7 years ago Jing Huang ▴ 380
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2
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881
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SPIA package
PROcess SPIA PROcess SPIA
10.9 years ago Jing Huang ▴ 380
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752
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question for you on SPIA package
Pathways Organism SPIA Pathways Organism SPIA
10.9 years ago Tarca, Adi ▴ 570
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2
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979
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question on SPIA pavkage application
Organism SPIA Organism SPIA
updated 11.0 years ago by ▴ 150 • written 11.0 years ago by ▴ 380
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728
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a question on SPIA package
Microarray SPIA Microarray SPIA
updated 11.0 years ago by ▴ 650 • written 11.0 years ago by ▴ 380
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2
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1.2k
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organism abbreviations (SPIA package)
Microarray Organism SPIA Microarray Organism SPIA
updated 11.0 years ago by ▴ 340 • written 11.0 years ago by ▴ 380
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1.0k
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Which resources for pathway analysis?
Pathways Network SPIA DEGraph Pathways Network SPIA DEGraph
updated 11.5 years ago by ▴ 370 • written 11.5 years ago by ▴ 100
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826
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Which resources for pathway analysis?
Pathways SPIA Pathways SPIA
updated 11.5 years ago by ▴ 300 • written 11.5 years ago by ▴ 370
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1
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838
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SPIA package with updated KEGG pathways
Pathways SPIA Pathways SPIA
updated 11.7 years ago by ★ 7.2k • written 11.7 years ago by ▴ 20
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668
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Bioconductor Digest, Vol 94, Issue 10
Pathways SPIA Pathways SPIA
11.7 years ago Tarca, Adi ▴ 570
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0
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943
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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
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693
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How to create KEGG's pathway data for SPIA?
SPIA SPIA
11.7 years ago Lourdes Peña Castillo ▴ 140
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4
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889
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SPIA - changes between 1.4.0 and 1.60.
Pathways SPIA Pathways SPIA
updated 11.9 years ago by ▴ 20 • written 11.9 years ago by ▴ 480
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746
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SPIA with Mouse Data
Genetics Network Organism SPIA Genetics Network Organism SPIA
12.0 years ago Will Bush ▴ 10
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734
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SPIA package problem
Microarray GO Cancer Organism hgu95av2 mgug4122a SPIA Microarray GO Cancer Organism
12.2 years ago January Weiner ▴ 370
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667
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help with SPIA package
Organism limma SPIA Organism limma SPIA
12.3 years ago Barbara Bo-Ju Shih ▴ 40
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622
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MArray into data.frame for SPIA package
limma marray SPIA limma marray SPIA
12.4 years ago Gordon Smyth 46k
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1
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817
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SPIA package
graph SPIA graph SPIA
updated 12.4 years ago by ★ 7.4k • written 12.4 years ago by ▴ 200
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1.1k
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SPIA: inferring inhibited pathways from up-regulated genes?
Pathways SPIA Pathways SPIA
12.7 years ago Tarca, Adi ▴ 570
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803
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SPIA, hacked to run with only selected pathways
SystemsBiology Pathways Cancer SPIA SystemsBiology Pathways Cancer SPIA
12.7 years ago Tarca, Adi ▴ 570
45 results • Page 1 of 1
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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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