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gdcquery
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2.6k
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Workflow type=Star_counts, I want to download FPKM or TPM values, but star_counts for which?
GDCquery
23 months ago • updated 22 months ago
yuanyuan
• 0
0
votes
0
replies
973
views
TCGAbiolinks specific mutation query
TCGAbiolinks
TCGA
Mutation
GDCquery
rnaseq
5.1 years ago
Yonatan Amzaleg
• 0
0
votes
0
replies
1.3k
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Error in value[[3L]](cond) : GDC server down, try to use this package later
GDCquery
5.9 years ago
sechenmo
• 0
0
votes
0
replies
656
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how include slicing to manifest
gdcquery
6.1 years ago
dvortsov
• 0
1
vote
2
replies
1.5k
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TCGABiolinks::GDCquery() suddenly sending back unknown error
software error
error
tcgabiolinks
GDCquery
updated 6.5 years ago by
eshelden
▴ 40 • written 6.5 years ago by
jrlarsen
▴ 10
5 results • Page
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Comment: putting my own expression data in deseq2
by
ATpoint
★ 4.1k
> directly from GEOquery I can tell you that GEOquery retrieves array data not appropriate for DESeq2. For anything else make your questi…
Comment: Assist me in determining whether the analysis process using the limma package ha
by
SSSJec
• 0
Thanks for your reply. I understand the principle of adjusted P-values, but I still want to address that issue. The description of the G…
Comment: Why p value inconsistent when using different number of pathway score?
by
Gordon Smyth
50k
Just a note that fgsea is not classical GSEA. The classical GSEA as described in the Subramanian paper and other papers from the Broad Inst…
Comment: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
by
Chris
• 0
Thank you! The resource I use may mispresent the requirement input of fgsea.
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
by
alserg
▴ 260
fgsea doesn't require the presence of deferentially expressed genes, it takes as the input the differential expression-based ranking of all…
Votes
Answer: Improving the design matrices vignette in RNAseq123
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
Comment: DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
Comment: Why p value inconsistent when using different number of pathway score?
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