Showing : spia • reset
1
vote
2
replies
580
views
Error creating SPIA data for KEGG Orthology (KO) Database KEGG xml files
SPIA
14 months ago Benji Bromberg ▴ 30
0
votes
0
replies
973
views
plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
4.8 years ago Assa Yeroslaviz ★ 1.5k
0
votes
1
reply
1.0k
views
alternative package to SPIA
SPIA pathway enrichment analysis overrepresentation
5.8 years ago asifgeb • 0
1
vote
2
replies
2.2k
views
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
votes
0
replies
1.1k
views
SPIA function error in ToPASeq
ToPASeq SPIA pathway analysis R
6.7 years ago fawazfebin ▴ 60
0
votes
0
replies
1.3k
views
a possible bug in spia function
SPIA
7.4 years ago slava.ilyntskyy • 0
0
votes
0
replies
1.2k
views
SPIA Package : Activated and Inhibited
SPIA R pathway analysis
7.5 years ago khhgng • 0
5
votes
2
replies
1.7k
views
SPIA::spia function output
SPIA
updated 8.0 years ago by ▴ 570 • written 8.0 years ago by ▴ 10
1
vote
1
reply
1.3k
views
SPIA plotP giving error
SPIA plotP threshold
8.1 years ago docpriya21 ▴ 10
0
votes
0
replies
1.2k
views
SPIA error in DE-Colorectal
SPIA
8.5 years ago saamar.rajput • 0
1
vote
2
replies
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
votes
1
reply
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
votes
0
replies
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
votes
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
0
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
votes
0
replies
1.3k
views
Background for test in SPIA package.
Annotation Pathways SPIA Annotation Pathways SPIA
11.7 years ago Ian Sudbery ▴ 30
0
votes
0
replies
1.8k
views
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
votes
0
replies
1.5k
views
changes in SPIA package: using updated KEGG pathway data
Organism SPIA Organism SPIA
11.8 years ago Tarca, Adi ▴ 570
0
votes
0
replies
1.4k
views
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
0
votes
0
replies
1.1k
views
Overrepresentation pathway with KEGGPROFILE and SPIA
SPIA SPIA
12.0 years ago gregory voisin ▴ 430
0
votes
3
replies
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
votes
2
replies
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 13.0 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
votes
2
replies
1.5k
views
SPIA package
PROcess SPIA PROcess SPIA
13.3 years ago Jing Huang ▴ 380
0
votes
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
votes
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
votes
2
replies
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
votes
1
reply
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
votes
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
votes
0
replies
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
replies
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
943
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
Recent ...
Replies
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by anna.cot.anna.cot ▴ 30
Thank you Gordon! Apologies if this is a too basic question-I'm a biologist and want to ensure I understand correctly. Here is my metadata …
Comment: nightmare to make custom txdb for genomes from ToxoDB by rohitsatyam102 ▴ 20
I offer my apologies if the title was misleading. I will change it at once. I wrote txdb because the error emnated from `seqlevelsStyle(txd…
Comment: nightmare to make custom txdb for genomes from ToxoDB by rohitsatyam102 ▴ 20
Hi Herve As I mentioned, for parasites we rely on VEuPathDB databases (such as ToxoDB here: https://toxodb.org/toxo/app/downloads) which p…
Comment: nightmare to make custom txdb for genomes from ToxoDB by Hervé Pagès 16k
`keepStandardChromosomes()` is not smart enough to know what to keep for this assembly. Note that what `keepStandardChromosomes()` means by…
Comment: nightmare to make custom txdb for genomes from ToxoDB by James W. MacDonald 67k
Thanks Hervé! Very helpful. However, I believe that `keepStandardChromosomes` gets called by `gDNAx`, and it appears not to work correctly.…
Votes
Answer: nightmare to make custom txdb for genomes from ToxoDB
Comment: nightmare to make custom txdb for genomes from ToxoDB
Answer: Normalizing batch effects using technical replicates for DGE analysis between tw
Answer: nightmare to make custom txdb for genomes from ToxoDB
A: Advice on correcting for batch effect using DESeq2
Awards • All
Popular Question to Jenny Drnevich ★ 2.0k
Popular Question to martin.grigorov ▴ 10
Scholar to James W. MacDonald 67k
Popular Question to Benjamin ▴ 20
Popular Question to María Calvo • 0
Locations • All
Seattle, WA, United States, 1 minute ago
United States, 1 minute ago
United States, 5 minutes ago
India, 8 minutes ago
United Kingdom, 13 minutes ago
Traffic: 845 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6