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gtex
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reset
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3
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1.1k
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Can i perform DEseq2 from 2 different rse objects download from RECOUNT database
DESeq2
recount
GTEx
TCGA
recount3
updated 13 months ago by
ATpoint
★ 4.2k • written 13 months ago by
David
▴ 20
2
votes
2
replies
2.0k
views
Create TPM gene tables/dataframe from ReCount3
recount3
TCGA
GTEx
DESeq2
2.0 years ago
David
▴ 20
2
votes
2
replies
1.3k
views
Gene Selection GTex for DESeq2 Analysis
DESeq2
GTEx
3.3 years ago
Bine
▴ 50
0
votes
1
reply
3.4k
views
Is GTEx age and sex data available via the recount package?
recount
gtex
updated 5.6 years ago by
Leonardo Collado Torres
★ 1.1k • written 5.6 years ago by
abe
• 0
2
votes
2
replies
1.2k
views
Error in ebayes in limma when analyzing GTEx data
limma
voom
gtex
6.2 years ago
mico
• 0
1
vote
2
replies
1.8k
views
DESeq2 for differential gene expression on GTEx dataset
rnaseq
deseq2
gtex
updated 6.6 years ago by
Michael Love
42k • written 6.6 years ago by
vikram
• 0
2
votes
0
replies
4.0k
views
Tutorial:
BoF Bioc2017: Analyzing publicly available cancer genomics data from GTEx and TCGA with Bioconductor
public data
TCGA
GTEx
Tutorial
6.9 years ago
shepherl
3.9k
7 results • Page
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Comment: gds in GEOmetadb 2023-06-26 version is empty
by
Frederico Moraes Ferreira
▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter
by
James W. MacDonald
66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat
by
Michael Love
42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Comment: Most enriched pathway is not expressed when modifying universe parameter
by
adripel
• 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Answer: Design formula, numeric contrast, and lfcshrink in deseq2
by
Michael Love
42k
For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…
Votes
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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