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seqarray
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SeqArray_1.19.2, SeqArray::info() for example gds data does not return correct character list for `AA` column
SeqArray
info
SeqArray::info()
6.4 years ago
qliu7
• 0
1
vote
3
replies
1.2k
views
seqVCF2GDS Error Converting VCF to GDS file
software error
SeqArray
seqVCF2GDS
updated 4.7 years ago by
zhengx
▴ 30 • written 4.7 years ago by
winstondunnmd
▴ 10
0
votes
2
replies
942
views
SeqArray problem in seqVCF2GDS and convert back to vcf
SeqArray
updated 5.2 years ago by
zhengx
▴ 30 • written 5.2 years ago by
miyouduniu
• 0
0
votes
2
replies
1.4k
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Seq Array converting VCF to GDS using seqVCF2GDS, unable to find file problems with vcf.fn
seqarray
updated 5.7 years ago by
Stephanie M. Gogarten
▴ 870 • written 5.7 years ago by
cav3gh
• 0
4
votes
2
replies
1.8k
views
Imputed dosages in GENESIS
genesis
gwastools
seqarray
5.6 years ago • updated 5.2 years ago
Stephanie M. Gogarten
▴ 870
1
vote
1
reply
1.4k
views
How to imports DS field from VCF files with SeqArray seqVCF2GDS()
seqArray
seqVCF2GDS
updated 3.9 years ago by
Stephanie M. Gogarten
▴ 870 • written 3.9 years ago by
ealopera
• 0
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Comment: Too many significant genes when integrating gtex and tcga
by
ATpoint
★ 4.1k
These two datasets are from completely different experiments / batches. It is utterly meaningless to compare them. I would suggest comparat…
Answer: fgsea significant result
by
ATpoint
★ 4.1k
Set a fixed seed before running this. Note that a FDR of 0.25 in fgsea is wildly and overly lenient. See https://support.bioconductor.o…
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
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Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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