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SNPRelate
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872
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Database for exploring annotations of the coding genome at variants, such as candidate regulatory SNPs at disease-associated loci.
SNP
ExomeSeqData
snapcount
SNAData
SNPRelate
3.0 years ago
m610110001
• 0
0
votes
2
replies
1.5k
views
How to project a new vector onto PCA space using snpgdsPCA( )?
SNPRelate
updated 3.6 years ago by
Stephanie M. Gogarten
▴ 890 • written 3.6 years ago by
MatthaeusCaesar
• 0
0
votes
1
reply
1.8k
views
SNP annotation
SNPRelate
SNP
GWASTools
Annotation
GWASdata
updated 3.8 years ago by
Stephanie M. Gogarten
▴ 890 • written 3.9 years ago by
Adrián
• 0
0
votes
0
replies
1.4k
views
SNPRelate handling of missing genotypes
SNPRelate
3.8 years ago
serpalma.v
▴ 60
0
votes
0
replies
1.1k
views
#SeqSQC error: Problem while converting vcf format to gds format
SNPRelate
gdsfmt
SeqSQC
4.1 years ago
Bhargavi
• 0
0
votes
1
reply
1.4k
views
error when running snpgdsLDpruning: The GDS node "genotype/data" does not exist.
SNPRelate
updated 4.9 years ago by
xiuwen.zheng
• 0 • written 4.9 years ago by
alyssahz
• 0
3
votes
1
reply
1.5k
views
How to add colors to the PCA made using SNPRelate
snprelate
updated 5.1 years ago by
James W. MacDonald
68k • written 5.1 years ago by
zen
• 0
1
vote
1
reply
1.2k
views
What does SNPRelate::snpgdsDiss calculate?
SNPRelate
updated 6.4 years ago by
zhengx
▴ 30 • written 6.4 years ago by
grp2009
• 0
0
votes
1
reply
1.3k
views
Different order of samples in output of snpgdsSlidingWindow to calculate Fst and aggregation method
SNPRelate
updated 6.5 years ago by
zhengx
▴ 30 • written 6.5 years ago by
serpalma.v
▴ 60
1
vote
1
reply
2.1k
views
VCF file does not include snp.id, can I still run SNPRelate for Relatedness Analysis? Data is output from STACKS for mangroves
SNPRelate
VCF
updated 6.6 years ago by
Stephanie M. Gogarten
▴ 890 • written 6.6 years ago by
cav3gh
• 0
1
vote
1
reply
1.4k
views
PCA axis description SNPRelate
SNPRelate
PCA
updated 6.6 years ago by
Stephanie M. Gogarten
▴ 890 • written 6.6 years ago by
serpalma.v
▴ 60
0
votes
1
reply
4.6k
views
SNPrelate, snpgdsFst is excluding all snps on non-autosomes, how can I get it to stop doing that?
snprelate
fst
updated 7.0 years ago by
zhengx
▴ 30 • written 7.0 years ago by
cav3gh
• 0
0
votes
1
reply
1.3k
views
Using previously calculated PCs in GENESIS
genesis
snprelate
7.1 years ago
Stephanie M. Gogarten
▴ 890
0
votes
1
reply
1.8k
views
Write gds in parallel
gds
SNPRelate
BiocParallel
updated 7.5 years ago by
zhengx
▴ 30 • written 7.5 years ago by
Vinicius Henrique da Silva
▴ 40
0
votes
2
replies
2.1k
views
Error converting vcf to gds
snprelate
vcf
gds
updated 7.6 years ago by
zhengx
▴ 30 • written 7.6 years ago by
annat22
• 0
1
vote
2
replies
2.2k
views
Cannot read plink files correctly
snprelate
Tutorial
updated 8.4 years ago by
zhengx
▴ 30 • written 8.4 years ago by
AR3513
• 0
0
votes
1
reply
1.9k
views
SNPRelate Dendrogram Point Colors and Shapes
SNPRelate
R
updated 9.4 years ago by
zhengx
▴ 30 • written 9.4 years ago by
rfriedman22
• 0
3
votes
2
replies
2.2k
views
Minimum allele frequency (MAF) from a Genomic Data Structure (GDS) file
snprelate
GWASTools
updated 9.4 years ago by
Adrienne Stilp
▴ 30 • written 9.4 years ago by
Vinicius Henrique da Silva
▴ 40
0
votes
9
replies
7.3k
views
unable to update mgcv package
mgcv
snprelate
updated 9.9 years ago by
Martin Morgan
25k • written 9.9 years ago by
mail2vignesh1985
• 0
0
votes
4
replies
3.0k
views
NA values in snpgdsDiss dissimilarity matrix
snprelate
updated 9.9 years ago by
zhengx
▴ 30 • written 10.0 years ago by
blackgore
▴ 10
0
votes
0
replies
1.2k
views
RADseq chromosomes unknown
snprelate
RADseq
Stacks
10.0 years ago
clive.darwell
• 0
0
votes
0
replies
2.2k
views
GWASTools
Organism
GWASTools
Organism
GWASTools
SNPRelate
12.6 years ago
Stephanie M. Gogarten
▴ 890
22 results • Page
1 of 1
Recent ...
Replies
Comment: "Watched Tags" are being erased rather than updated
by
shepherl
4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated
by
shepherl
4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts
by
Michael Love
43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts
by
empty_mt
• 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
Comment: deseq2 filter the low counts
by
Michael Love
43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
Votes
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
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