Showing : SPIA • reset
1
vote
2
replies
852
views
Error creating SPIA data for KEGG Orthology (KO) Database KEGG xml files
SPIA
2.1 years ago Benji Bromberg ▴ 30
0
votes
0
replies
1.2k
views
plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
5.7 years ago Assa Yeroslaviz ★ 1.5k
0
votes
1
reply
1.2k
views
alternative package to SPIA
SPIA pathway enrichment analysis overrepresentation
6.7 years ago asifgeb • 0
1
vote
2
replies
2.4k
views
Question on graphite/SPIA; extracting DE gene list
graphite spia runSPIA
updated 6.9 years ago by 0 • written 10.7 years ago by • 0
0
votes
0
replies
1.3k
views
SPIA function error in ToPASeq
ToPASeq SPIA pathway analysis R
7.6 years ago fawazfebin ▴ 60
0
votes
0
replies
1.5k
views
a possible bug in spia function
SPIA
8.3 years ago slava.ilyntskyy • 0
0
votes
0
replies
1.4k
views
SPIA Package : Activated and Inhibited
SPIA R pathway analysis
8.4 years ago khhgng • 0
5
votes
2
replies
2.0k
views
SPIA::spia function output
SPIA
updated 8.9 years ago by ▴ 570 • written 8.9 years ago by ▴ 10
1
vote
1
reply
1.5k
views
SPIA plotP giving error
SPIA plotP threshold
9.0 years ago docpriya21 ▴ 10
0
votes
0
replies
1.3k
views
SPIA error in DE-Colorectal
SPIA
9.4 years ago saamar.rajput • 0
1
vote
2
replies
2.9k
views
(Gene-set)Pathway analysis based on network/pathway topology in R
SPIA functional enrichment pathway topology pathway analysis bioconductor
10.3 years ago svlachavas ▴ 840
0
votes
1
reply
2.5k
views
SPIA error - names of de are not in reference array
SPIA named vectors pathway analysis
updated 3.3 years ago by • 0 • written 11.1 years ago by • 0
0
votes
0
replies
1.4k
views
R: Re: Deseq2 and differentia expression
SPIA SPIA
11.4 years ago Simon Anders ★ 3.8k
0
votes
1
reply
1.6k
views
SPIA
Pathways SPIA Pathways SPIA
updated 11.7 years ago by ▴ 570 • written 11.7 years ago by ★ 13k
0
votes
1
reply
2.1k
views
pathway analysis by SPIA using SPIA package vs graphite package
Pathways SPIA cycle graphite Pathways SPIA cycle graphite
11.9 years ago array chip ▴ 420
0
votes
1
reply
1.7k
views
makeSPIAdata
SPIA SPIA
updated 11.9 years ago by ▴ 570 • written 11.9 years ago by ▴ 10
0
votes
1
reply
3.0k
views
SPIA error - Error in density.default(pfstmp, bw = sd(pfstmp)/4) : \'bw\' is not positive.
SPIA cycle SPIA cycle
updated 12.0 years ago by ▴ 570 • written 12.0 years ago by ★ 13k
0
votes
0
replies
1.4k
views
Background for test in SPIA package.
Annotation Pathways SPIA Annotation Pathways SPIA
12.7 years ago Ian Sudbery ▴ 30
0
votes
0
replies
2.0k
views
SPIA algorithm organisms not included already in the SPIA package
Organism SPIA goseq KEGGREST Organism SPIA goseq KEGGREST
12.7 years ago Tarca, Adi ▴ 570
0
votes
0
replies
1.7k
views
changes in SPIA package: using updated KEGG pathway data
Organism SPIA Organism SPIA
12.7 years ago Tarca, Adi ▴ 570
0
votes
0
replies
1.5k
views
Bioconductor Digest, Vol 119, Issue 5: Overrepresentation pathway with KEGGPROFILE and SPIA
Pathways SPIA KEGGprofile Pathways SPIA KEGGprofile
12.9 years ago Tarca, Adi ▴ 570
0
votes
0
replies
1.2k
views
Overrepresentation pathway with KEGGPROFILE and SPIA
SPIA SPIA
12.9 years ago gregory voisin ▴ 430
0
votes
3
replies
3.2k
views
Kegg pathways overlay with log fold change values
Pathways limma SPIA Pathways limma SPIA
updated 13.5 years ago by ▴ 120 • written 13.5 years ago by ▴ 50
0
votes
2
replies
2.9k
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 13.9 years ago by ▴ 570 • written 13.9 years ago by ▴ 100
0
votes
0
replies
1.5k
views
Bioconductor resources for immunology
Pathways GO SPIA Pathways GO SPIA
13.9 years ago January Weiner ▴ 240
0
votes
0
replies
1.6k
views
SPIA package
Pathways Organism SPIA Pathways Organism SPIA
14.0 years ago Tarca, Adi ▴ 570
0
votes
0
replies
1.5k
views
question for SPIA package
Pathways SPIA Pathways SPIA
14.0 years ago Jing Huang ▴ 380
0
votes
2
replies
1.7k
views
SPIA package
PROcess SPIA PROcess SPIA
14.2 years ago Jing Huang ▴ 380
0
votes
0
replies
1.3k
views
question for you on SPIA package
Pathways Organism SPIA Pathways Organism SPIA
14.2 years ago Tarca, Adi ▴ 570
0
votes
2
replies
1.7k
views
question on SPIA pavkage application
Organism SPIA Organism SPIA
updated 14.3 years ago by ▴ 150 • written 14.3 years ago by ▴ 380
0
votes
1
reply
1.5k
views
a question on SPIA package
Microarray SPIA Microarray SPIA
updated 14.3 years ago by ▴ 650 • written 14.3 years ago by ▴ 380
0
votes
2
replies
2.1k
views
organism abbreviations (SPIA package)
Microarray Organism SPIA Microarray Organism SPIA
updated 14.3 years ago by ▴ 340 • written 14.3 years ago by ▴ 380
0
votes
1
reply
1.9k
views
Which resources for pathway analysis?
Pathways Network SPIA DEGraph Pathways Network SPIA DEGraph
updated 14.7 years ago by ▴ 370 • written 14.7 years ago by ▴ 100
0
votes
1
reply
1.5k
views
Which resources for pathway analysis?
Pathways SPIA Pathways SPIA
updated 14.7 years ago by ▴ 300 • written 14.7 years ago by ▴ 370
0
votes
1
reply
1.5k
views
SPIA package with updated KEGG pathways
Pathways SPIA Pathways SPIA
updated 14.9 years ago by ★ 7.2k • written 15.0 years ago by ▴ 20
0
votes
0
replies
1.2k
views
Bioconductor Digest, Vol 94, Issue 10
Pathways SPIA Pathways SPIA
15.0 years ago Tarca, Adi ▴ 570
0
votes
0
replies
1.7k
views
Bioconductor Digest, Vol 93, Issue 26: How to create KEGG's pathway data for SPIA?
Organism KEGGgraph SPIA Organism KEGGgraph SPIA
15.0 years ago Tarca, Adi ▴ 570
0
votes
0
replies
1.2k
views
How to create KEGG's pathway data for SPIA?
SPIA SPIA
15.0 years ago Lourdes Peña Castillo ▴ 140
0
votes
4
replies
1.9k
views
SPIA - changes between 1.4.0 and 1.60.
Pathways SPIA Pathways SPIA
updated 15.2 years ago by ▴ 20 • written 15.2 years ago by ▴ 480
0
votes
0
replies
1.3k
views
SPIA with Mouse Data
Genetics Network Organism SPIA Genetics Network Organism SPIA
15.3 years ago Will Bush ▴ 10
0
votes
0
replies
1.3k
views
SPIA package problem
Microarray GO Cancer Organism hgu95av2 mgug4122a SPIA Microarray GO Cancer Organism
15.5 years ago January Weiner ▴ 370
0
votes
0
replies
1.2k
views
help with SPIA package
Organism limma SPIA Organism limma SPIA
15.5 years ago Barbara Bo-Ju Shih ▴ 40
0
votes
0
replies
1.0k
views
MArray into data.frame for SPIA package
limma marray SPIA limma marray SPIA
15.7 years ago Gordon Smyth 53k
0
votes
1
reply
1.5k
views
SPIA package
graph SPIA graph SPIA
updated 15.7 years ago by ★ 7.4k • written 15.7 years ago by ▴ 200
0
votes
0
replies
1.7k
views
SPIA: inferring inhibited pathways from up-regulated genes?
Pathways SPIA Pathways SPIA
15.9 years ago Tarca, Adi ▴ 570
0
votes
0
replies
1.5k
views
SPIA, hacked to run with only selected pathways
SystemsBiology Pathways Cancer SPIA SystemsBiology Pathways Cancer SPIA
16.0 years ago Tarca, Adi ▴ 570
46 results • Page 1 of 1
Recent ...
Replies
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much, @ATpoint and @kevin , for your valuable insights. I have carefully checked all your suggestions. First, I examined th…
Answer: Finding duplicated entries in GRangesList by Kevin Blighe ★ 4.0k
The duplicated and unique functions operate element-wise on GRangesList objects. This means that they apply the respective function to each…
Answer: DESeq2 on non-RNASeq counts data by Kevin Blighe ★ 4.0k
The use of DESeq2 for count data from artificial sequences is acceptable, as the program models counts via a negative binomial distribution…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hello Rui Tang, The buffer overflow error in featureCounts that you encountered is likely due to a compatibility issue between the Subre…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
The issue that you describe with the tumor mutational burden (TMB) plots appearing linear and lacking consistent TMB values across samples …
Votes
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Identifying differentially expressed genes in individual samples from a large co
Awards • All
Scholar to Gordon Smyth 53k
Popular Question to shepherl 4.2k
Supporter to fabio.marroni • 0
Popular Question to Guido Hooiveld ★ 4.1k
Popular Question to James W. MacDonald 68k
Locations • All
WEHI, Melbourne, Australia, 1 hour ago
United States, 1 hour ago
Pittsburgh, United States, 1 hour ago
United States, 1 hour ago
United States, 2 hours ago
Traffic: 567 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