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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
18 months ago
m610110001
• 0
0
votes
2
replies
931
views
How to project a new vector onto PCA space using snpgdsPCA( )?
SNPRelate
updated 2.1 years ago by
Stephanie M. Gogarten
▴ 870 • written 2.1 years ago by
MatthaeusCaesar
• 0
0
votes
1
reply
1.1k
views
SNP annotation
SNPRelate
SNP
GWASTools
Annotation
GWASdata
updated 2.3 years ago by
Stephanie M. Gogarten
▴ 870 • written 2.4 years ago by
Adrián
• 0
0
votes
0
replies
795
views
SNPRelate handling of missing genotypes
SNPRelate
2.3 years ago
serpalma.v
▴ 60
0
votes
0
replies
687
views
#SeqSQC error: Problem while converting vcf format to gds format
SNPRelate
gdsfmt
SeqSQC
2.5 years ago
Bhargavi
• 0
0
votes
1
reply
918
views
error when running snpgdsLDpruning: The GDS node "genotype/data" does not exist.
SNPRelate
updated 3.4 years ago by
xiuwen.zheng
• 0 • written 3.4 years ago by
alyssahz
• 0
3
votes
1
reply
1.0k
views
How to add colors to the PCA made using SNPRelate
snprelate
updated 3.6 years ago by
James W. MacDonald
65k • written 3.6 years ago by
zen
• 0
1
vote
1
reply
807
views
What does SNPRelate::snpgdsDiss calculate?
SNPRelate
updated 4.9 years ago by
zhengx
▴ 30 • written 4.9 years ago by
grp2009
• 0
0
votes
1
reply
858
views
Different order of samples in output of snpgdsSlidingWindow to calculate Fst and aggregation method
SNPRelate
updated 5.0 years ago by
zhengx
▴ 30 • written 5.0 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 5.1 years ago by
Stephanie M. Gogarten
▴ 870 • written 5.1 years ago by
cav3gh
• 0
1
vote
1
reply
977
views
PCA axis description SNPRelate
SNPRelate
PCA
updated 5.1 years ago by
Stephanie M. Gogarten
▴ 870 • written 5.1 years ago by
serpalma.v
▴ 60
0
votes
1
reply
3.7k
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
901
views
Using previously calculated PCs in GENESIS
genesis
snprelate
5.6 years ago
Stephanie M. Gogarten
▴ 870
0
votes
1
reply
1.3k
views
Write gds in parallel
gds
SNPRelate
BiocParallel
updated 6.0 years ago by
zhengx
▴ 30 • written 6.0 years ago by
Vinicius Henrique da Silva
▴ 40
0
votes
2
replies
1.6k
views
Error converting vcf to gds
snprelate
vcf
gds
updated 6.1 years ago by
zhengx
▴ 30 • written 6.1 years ago by
annat22
• 0
1
vote
2
replies
1.6k
views
Cannot read plink files correctly
snprelate
Tutorial
updated 6.9 years ago by
zhengx
▴ 30 • written 6.9 years ago by
AR3513
• 0
0
votes
1
reply
1.5k
views
SNPRelate Dendrogram Point Colors and Shapes
SNPRelate
R
updated 7.9 years ago by
zhengx
▴ 30 • written 7.9 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 7.9 years ago by
Adrienne Stilp
▴ 30 • written 7.9 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
2.4k
views
NA values in snpgdsDiss dissimilarity matrix
snprelate
updated 8.4 years ago by
zhengx
▴ 30 • written 8.4 years ago by
blackgore
▴ 10
0
votes
0
replies
930
views
RADseq chromosomes unknown
snprelate
RADseq
Stacks
8.5 years ago
clive.darwell
• 0
0
votes
0
replies
1.9k
views
GWASTools
Organism
GWASTools
Organism
GWASTools
SNPRelate
11.1 years ago
Stephanie M. Gogarten
▴ 870
22 results • Page
1 of 1
Recent ...
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Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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