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snprelate
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116
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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 months ago
m610110001
• 0
0
votes
2
replies
442
views
How to project a new vector onto PCA space using snpgdsPCA( )?
SNPRelate
updated 10 months ago by
Stephanie M. Gogarten
▴ 820 • written 10 months ago by
MatthaeusCaesar
• 0
0
votes
1
reply
445
views
SNP annotation
SNPRelate
SNP
GWASTools
Annotation
GWASdata
updated 12 months ago by
Stephanie M. Gogarten
▴ 820 • written 14 months ago by
Adrián
• 0
0
votes
0
replies
302
views
SNPRelate handling of missing genotypes
SNPRelate
12 months ago
serpalma.v
▴ 60
0
votes
0
replies
286
views
#SeqSQC error: Problem while converting vcf format to gds format
SNPRelate
gdsfmt
SeqSQC
15 months ago
Bhargavi
• 0
0
votes
1
reply
541
views
error when running snpgdsLDpruning: The GDS node "genotype/data" does not exist.
SNPRelate
updated 2.1 years ago by
xiuwen.zheng
• 0 • written 2.1 years ago by
alyssahz
• 0
3
votes
1
reply
655
views
How to add colors to the PCA made using SNPRelate
snprelate
updated 2.4 years ago by
James W. MacDonald
62k • written 2.4 years ago by
zen
• 0
1
vote
1
reply
489
views
What does SNPRelate::snpgdsDiss calculate?
SNPRelate
updated 3.6 years ago by
zhengx
▴ 30 • written 3.6 years ago by
grp2009
• 0
0
votes
1
reply
535
views
Different order of samples in output of snpgdsSlidingWindow to calculate Fst and aggregation method
SNPRelate
updated 3.7 years ago by
zhengx
▴ 30 • written 3.7 years ago by
serpalma.v
▴ 60
1
vote
1
reply
934
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 3.8 years ago by
Stephanie M. Gogarten
▴ 820 • written 3.8 years ago by
cav3gh
• 0
1
vote
1
reply
595
views
PCA axis description SNPRelate
SNPRelate
PCA
updated 3.9 years ago by
Stephanie M. Gogarten
▴ 820 • written 3.9 years ago by
serpalma.v
▴ 60
0
votes
1
reply
2.8k
views
SNPrelate, snpgdsFst is excluding all snps on non-autosomes, how can I get it to stop doing that?
snprelate
fst
updated 4.3 years ago by
zhengx
▴ 30 • written 4.3 years ago by
cav3gh
• 0
0
votes
1
reply
560
views
Using previously calculated PCs in GENESIS
genesis
snprelate
4.4 years ago
Stephanie M. Gogarten
▴ 820
0
votes
1
reply
750
views
Write gds in parallel
gds
SNPRelate
BiocParallel
updated 4.8 years ago by
zhengx
▴ 30 • written 4.8 years ago by
Vinicius Henrique da Silva
▴ 40
0
votes
2
replies
1.1k
views
Error converting vcf to gds
snprelate
vcf
gds
updated 4.8 years ago by
zhengx
▴ 30 • written 4.9 years ago by
annat22
• 0
1
vote
2
replies
1.2k
views
Cannot read plink files correctly
snprelate
Tutorial
updated 5.7 years ago by
zhengx
▴ 30 • written 5.7 years ago by
AR3513
• 0
0
votes
1
reply
1.2k
views
SNPRelate Dendrogram Point Colors and Shapes
SNPRelate
R
updated 6.6 years ago by
zhengx
▴ 30 • written 6.6 years ago by
rfriedman22
• 0
3
votes
2
replies
1.4k
views
Minimum allele frequency (MAF) from a Genomic Data Structure (GDS) file
snprelate
GWASTools
updated 6.7 years ago by
Adrienne Stilp
▴ 30 • written 6.7 years ago by
Vinicius Henrique da Silva
▴ 40
0
votes
9
replies
5.5k
views
unable to update mgcv package
mgcv
snprelate
updated 7.1 years ago by
Martin Morgan
25k • written 7.1 years ago by
mail2vignesh1985
• 0
0
votes
4
replies
1.9k
views
NA values in snpgdsDiss dissimilarity matrix
snprelate
updated 7.2 years ago by
zhengx
▴ 30 • written 7.2 years ago by
blackgore
▴ 10
0
votes
0
replies
711
views
RADseq chromosomes unknown
snprelate
RADseq
Stacks
7.2 years ago
clive.darwell
• 0
0
votes
0
replies
1.5k
views
GWASTools
Organism
GWASTools
Organism
GWASTools
SNPRelate
9.9 years ago
Stephanie M. Gogarten
▴ 820
22 results • Page
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Comment: pathview says my nonmodel species is unknown: "species invalid"
by
Guido Hooiveld
★ 3.5k
Does a restart of R help? Does a reinstall of the library `png` help? In a fresh R-session, what is the output from `BiocManager::valid()…
Comment: Don't let TopGo to trimm long GO names
by
James W. MacDonald
62k
Did you not notice that this has been answered *as part of this thread that you posted in?*
Comment: pathview says my nonmodel species is unknown: "species invalid"
by
nute11a
• 0
Hi Luo, thank you so much for your helpful comment. While I was able to get this to work and visualize my interesting KEGG pathways (yay!) …
Comment: Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
by
Wolfgang Huber
13k
Hi Ben, your first step should be to upgrade to the current versions of R and Bioconductor. There is really little point in trouble-shooti…
Answer: Is ther an annotation package for sheep (Ovis aries)
by
Guido Hooiveld
★ 3.5k
Yes, there is! An `EnsDb` for sheep can be obtained through the so-called `AnnotationHub`. See James' and my posts in the thread linked t…
Votes
FDR and padj in deseq and edger
FDR and padj in deseq and edger
Comment: Mutect version, matched normal and manual curation in PureCN
Answer: Is ther an annotation package for sheep (Ovis aries)
Is ther an annotation package for sheep (Ovis aries)
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James W. MacDonald
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Michael Love
39k
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twtoal
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▴ 40
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