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gage package
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0
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1.2k
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GAGE for non model organism
gage package
gage
7.2 years ago
melkile26
• 0
1
vote
2
replies
1.6k
views
GAGE analysis with the whole or a subset of matrix
gage
gage package
gene expression matrix
gene set analysis
7.3 years ago
atakanekiz
▴ 30
5
votes
7
replies
3.3k
views
Gage package; go.gset() function error: argument "go_id" is missing
gage package
error
updated 7.4 years ago by
James W. MacDonald
68k • written 7.4 years ago by
Miskey, Csaba
▴ 20
0
votes
2
replies
4.5k
views
Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage
gage package
pathview
rna-seq
updated 3.6 years ago by
Helen
• 0 • written 7.7 years ago by
tarun2
• 0
2
votes
4
replies
2.6k
views
Can't find gene list for KEGG genesets
kegg
geneset
genelist
gage package
updated 8.2 years ago by
Gordon Smyth
53k • written 8.2 years ago by
sup230
▴ 30
1
vote
0
replies
1.8k
views
DESeq2 - GAGE workflow
gage package
deseq2
8.2 years ago
sup230
▴ 30
0
votes
2
replies
2.1k
views
How to extract essential genes from pathway (essGene) using DEseq2/GAGE workflow?
gage
gage package
updated 9.0 years ago by
Luo Weijun
★ 1.6k • written 9.0 years ago by
Michael
• 0
1
vote
2
replies
1.9k
views
Need to convert gene IDs for GAGE pathway analysis of honey bee RNA-seq data
R
gage package
rnaseq
pathview
9.2 years ago
joanito.liberti
• 0
0
votes
1
reply
1.3k
views
Question on Gage
gage package
path.ids
RNA-Seq
9.2 years ago
rl1385
• 0
0
votes
0
replies
1.2k
views
GAGE package statistical tests
t-test
GAGE package
Kolmogorov-Smirnov test
Gene-Set enrichment
9.3 years ago
smt8n
• 0
10 results • Page
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Comment: DESeq2 for candidate gene analysis
by
piffelpaff
▴ 10
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis
by
Michael Love
43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
That's weird. Using the example data works for me. ``` > example(read10xCounts) rd10xC> # Mocking up some 10X genomics output. rd10xC> ex…
Comment: Join BOC Sciences at Drug Discovery Chemistry
by
teamardigen
• 0
Sounds like an exciting event for anyone passionate about small molecule innovation. The focus on discovery and optimization really drives …
Votes
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Join BOC Sciences at Drug Discovery Chemistry
Drug datasets for RNA-seq
Comment: Check removeBatchEffect effectiveness
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