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gage package
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GAGE for non model organism
gage package
gage
5.8 years ago
melkile26
• 0
1
vote
2
replies
1.1k
views
GAGE analysis with the whole or a subset of matrix
gage
gage package
gene expression matrix
gene set analysis
5.8 years ago
atakanekiz
▴ 30
5
votes
7
replies
2.7k
views
Gage package; go.gset() function error: argument "go_id" is missing
gage package
error
updated 6.0 years ago by
James W. MacDonald
65k • written 6.0 years ago by
Miskey, Csaba
▴ 20
0
votes
2
replies
3.7k
views
Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage
gage package
pathview
rna-seq
updated 2.2 years ago by
Helen
• 0 • written 6.2 years ago by
tarun2
• 0
2
votes
4
replies
1.7k
views
Can't find gene list for KEGG genesets
kegg
geneset
genelist
gage package
updated 6.7 years ago by
Gordon Smyth
50k • written 6.7 years ago by
sup230
▴ 30
1
vote
0
replies
1.4k
views
DESeq2 - GAGE workflow
gage package
deseq2
6.8 years ago
sup230
▴ 30
0
votes
2
replies
1.6k
views
How to extract essential genes from pathway (essGene) using DEseq2/GAGE workflow?
gage
gage package
updated 7.5 years ago by
Luo Weijun
★ 1.6k • written 7.6 years ago by
Michael
• 0
1
vote
2
replies
1.4k
views
Need to convert gene IDs for GAGE pathway analysis of honey bee RNA-seq data
R
gage package
rnaseq
pathview
7.7 years ago
joanito.liberti
• 0
0
votes
1
reply
935
views
Question on Gage
gage package
path.ids
RNA-Seq
7.7 years ago
rl1385
• 0
0
votes
0
replies
913
views
GAGE package statistical tests
t-test
GAGE package
Kolmogorov-Smirnov test
Gene-Set enrichment
7.8 years ago
smt8n
• 0
10 results • Page
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Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Votes
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
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tangming2005
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James W. MacDonald
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