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SNPRelate
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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
17 months ago
m610110001
• 0
0
votes
2
replies
891
views
How to project a new vector onto PCA space using snpgdsPCA( )?
SNPRelate
updated 2.0 years ago by
Stephanie M. Gogarten
▴ 870 • written 2.0 years ago by
MatthaeusCaesar
• 0
0
votes
1
reply
1.0k
views
SNP annotation
SNPRelate
SNP
GWASTools
Annotation
GWASdata
updated 2.2 years ago by
Stephanie M. Gogarten
▴ 870 • written 2.3 years ago by
Adrián
• 0
0
votes
0
replies
764
views
SNPRelate handling of missing genotypes
SNPRelate
2.2 years ago
serpalma.v
▴ 60
0
votes
0
replies
654
views
#SeqSQC error: Problem while converting vcf format to gds format
SNPRelate
gdsfmt
SeqSQC
2.5 years ago
Bhargavi
• 0
0
votes
1
reply
887
views
error when running snpgdsLDpruning: The GDS node "genotype/data" does not exist.
SNPRelate
updated 3.3 years ago by
xiuwen.zheng
• 0 • written 3.3 years ago by
alyssahz
• 0
3
votes
1
reply
993
views
How to add colors to the PCA made using SNPRelate
snprelate
updated 3.5 years ago by
James W. MacDonald
65k • written 3.5 years ago by
zen
• 0
1
vote
1
reply
775
views
What does SNPRelate::snpgdsDiss calculate?
SNPRelate
updated 4.8 years ago by
zhengx
▴ 30 • written 4.8 years ago by
grp2009
• 0
0
votes
1
reply
822
views
Different order of samples in output of snpgdsSlidingWindow to calculate Fst and aggregation method
SNPRelate
updated 4.9 years ago by
zhengx
▴ 30 • written 4.9 years ago by
serpalma.v
▴ 60
1
vote
1
reply
1.5k
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 5.0 years ago by
Stephanie M. Gogarten
▴ 870 • written 5.0 years ago by
cav3gh
• 0
1
vote
1
reply
945
views
PCA axis description SNPRelate
SNPRelate
PCA
updated 5.0 years ago by
Stephanie M. Gogarten
▴ 870 • written 5.0 years ago by
serpalma.v
▴ 60
0
votes
1
reply
3.6k
views
SNPrelate, snpgdsFst is excluding all snps on non-autosomes, how can I get it to stop doing that?
snprelate
fst
updated 5.5 years ago by
zhengx
▴ 30 • written 5.5 years ago by
cav3gh
• 0
0
votes
1
reply
871
views
Using previously calculated PCs in GENESIS
genesis
snprelate
5.5 years ago
Stephanie M. Gogarten
▴ 870
0
votes
1
reply
1.2k
views
Write gds in parallel
gds
SNPRelate
BiocParallel
updated 5.9 years ago by
zhengx
▴ 30 • written 5.9 years ago by
Vinicius Henrique da Silva
▴ 40
0
votes
2
replies
1.5k
views
Error converting vcf to gds
snprelate
vcf
gds
updated 6.0 years ago by
zhengx
▴ 30 • written 6.0 years ago by
annat22
• 0
1
vote
2
replies
1.6k
views
Cannot read plink files correctly
snprelate
Tutorial
updated 6.8 years ago by
zhengx
▴ 30 • written 6.8 years ago by
AR3513
• 0
0
votes
1
reply
1.4k
views
SNPRelate Dendrogram Point Colors and Shapes
SNPRelate
R
updated 7.8 years ago by
zhengx
▴ 30 • written 7.8 years ago by
rfriedman22
• 0
3
votes
2
replies
1.7k
views
Minimum allele frequency (MAF) from a Genomic Data Structure (GDS) file
snprelate
GWASTools
updated 7.8 years ago by
Adrienne Stilp
▴ 30 • written 7.8 years ago by
Vinicius Henrique da Silva
▴ 40
0
votes
9
replies
6.2k
views
unable to update mgcv package
mgcv
snprelate
updated 8.3 years ago by
Martin Morgan
25k • written 8.3 years ago by
mail2vignesh1985
• 0
0
votes
4
replies
2.3k
views
NA values in snpgdsDiss dissimilarity matrix
snprelate
updated 8.3 years ago by
zhengx
▴ 30 • written 8.4 years ago by
blackgore
▴ 10
0
votes
0
replies
913
views
RADseq chromosomes unknown
snprelate
RADseq
Stacks
8.4 years ago
clive.darwell
• 0
0
votes
0
replies
1.9k
views
GWASTools
Organism
GWASTools
Organism
GWASTools
SNPRelate
11.0 years ago
Stephanie M. Gogarten
▴ 870
22 results • Page
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Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
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mercedeh.movassagh
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Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
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This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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