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gage package
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0
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534
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GAGE for non model organism
gage package
gage
4.0 years ago
melkile26
• 0
1
vote
2
replies
623
views
GAGE analysis with the whole or a subset of matrix
gage
gage package
gene expression matrix
gene set analysis
4.1 years ago
atakanekiz
▴ 30
5
votes
7
replies
2.1k
views
Gage package; go.gset() function error: argument "go_id" is missing
gage package
error
updated 4.2 years ago by
James W. MacDonald
60k • written 4.2 years ago by
Miskey, Csaba
▴ 20
0
votes
2
replies
2.4k
views
Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage
gage package
pathview
rna-seq
updated 5 months ago by
Helen
• 0 • written 4.5 years ago by
tarun2
• 0
2
votes
4
replies
813
views
Can't find gene list for KEGG genesets
kegg
geneset
genelist
gage package
updated 5.0 years ago by
Gordon Smyth
46k • written 5.0 years ago by
sup230
▴ 30
1
vote
0
replies
1.0k
views
DESeq2 - GAGE workflow
gage package
deseq2
5.0 years ago
sup230
▴ 30
0
votes
2
replies
965
views
How to extract essential genes from pathway (essGene) using DEseq2/GAGE workflow?
gage
gage package
updated 5.8 years ago by
Luo Weijun
★ 1.5k • written 5.8 years ago by
Michael
• 0
1
vote
2
replies
927
views
Need to convert gene IDs for GAGE pathway analysis of honey bee RNA-seq data
R
gage package
rnaseq
pathview
6.0 years ago
joanito.liberti
• 0
0
votes
1
reply
614
views
Question on Gage
gage package
path.ids
RNA-Seq
6.0 years ago
rl1385
• 0
0
votes
0
replies
643
views
GAGE package statistical tests
t-test
GAGE package
Kolmogorov-Smirnov test
Gene-Set enrichment
6.1 years ago
smt8n
• 0
10 results • Page
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Comment: OPLS-DA: confidence interval for accuracy metric
by
etienne.thevenot
▴ 20
- The bootstrapping approach can be used to compute the CIs: see here for an example: Mendez et al. (2019). « A comparative evaluation …
Comment: Data input for aracne2regulon function in viper package
by
xlal
• 0
You are right!And may be we should check the gene symbols cause when I open the expression matrix in EXCEL,it will change some genes into m…
Comment: unable to install.packages("spatialLIBD")
by
Leonardo Collado Torres
▴ 1000
All the solutions Lori proposed are valid. The `STexampleData` package I think has only 1 of our samples (see https://bioconductor.org/pack…
Answer: how to use Rsamtools to parse extra fields from STAR alignment
by
Martin Morgan
25k
The 'extra columns' are called 'tags' in the SAM specification. Following the documentation `?ScanBamParam` you should add `tag = "NH"`. Se…
Comment: DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscrip
by
Delta._.43
▴ 10
Yes, indeed it is the same error. Here are the first few lines of my count file. ``` "ENSG00000000003":"001" 0 "ENSG00000000003":"002" 1032…
Votes
Answer: spot- vs cell-level data access
Answer: unable to install.packages("spatialLIBD")
Comment: unable to install.packages("spatialLIBD")
error running UniProt.ws
Answer: DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FU
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