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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
21 months ago
m610110001
• 0
0
votes
2
replies
1.1k
views
How to project a new vector onto PCA space using snpgdsPCA( )?
SNPRelate
updated 2.4 years ago by
Stephanie M. Gogarten
▴ 870 • written 2.4 years ago by
MatthaeusCaesar
• 0
0
votes
1
reply
1.2k
views
SNP annotation
SNPRelate
SNP
GWASTools
Annotation
GWASdata
updated 2.5 years ago by
Stephanie M. Gogarten
▴ 870 • written 2.7 years ago by
Adrián
• 0
0
votes
0
replies
913
views
SNPRelate handling of missing genotypes
SNPRelate
2.5 years ago
serpalma.v
▴ 60
0
votes
0
replies
759
views
#SeqSQC error: Problem while converting vcf format to gds format
SNPRelate
gdsfmt
SeqSQC
2.8 years ago
Bhargavi
• 0
0
votes
1
reply
1.0k
views
error when running snpgdsLDpruning: The GDS node "genotype/data" does not exist.
SNPRelate
updated 3.6 years ago by
xiuwen.zheng
• 0 • written 3.6 years ago by
alyssahz
• 0
3
votes
1
reply
1.1k
views
How to add colors to the PCA made using SNPRelate
snprelate
updated 3.8 years ago by
James W. MacDonald
66k • written 3.8 years ago by
zen
• 0
1
vote
1
reply
861
views
What does SNPRelate::snpgdsDiss calculate?
SNPRelate
updated 5.1 years ago by
zhengx
▴ 30 • written 5.1 years ago by
grp2009
• 0
0
votes
1
reply
929
views
Different order of samples in output of snpgdsSlidingWindow to calculate Fst and aggregation method
SNPRelate
updated 5.2 years ago by
zhengx
▴ 30 • written 5.2 years ago by
serpalma.v
▴ 60
1
vote
1
reply
1.7k
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 5.3 years ago by
Stephanie M. Gogarten
▴ 870 • written 5.3 years ago by
cav3gh
• 0
1
vote
1
reply
1.0k
views
PCA axis description SNPRelate
SNPRelate
PCA
updated 5.3 years ago by
Stephanie M. Gogarten
▴ 870 • written 5.3 years ago by
serpalma.v
▴ 60
0
votes
1
reply
3.8k
views
SNPrelate, snpgdsFst is excluding all snps on non-autosomes, how can I get it to stop doing that?
snprelate
fst
updated 5.8 years ago by
zhengx
▴ 30 • written 5.8 years ago by
cav3gh
• 0
0
votes
1
reply
964
views
Using previously calculated PCs in GENESIS
genesis
snprelate
5.8 years ago
Stephanie M. Gogarten
▴ 870
0
votes
1
reply
1.3k
views
Write gds in parallel
gds
SNPRelate
BiocParallel
updated 6.2 years ago by
zhengx
▴ 30 • written 6.2 years ago by
Vinicius Henrique da Silva
▴ 40
0
votes
2
replies
1.7k
views
Error converting vcf to gds
snprelate
vcf
gds
updated 6.3 years ago by
zhengx
▴ 30 • written 6.3 years ago by
annat22
• 0
1
vote
2
replies
1.7k
views
Cannot read plink files correctly
snprelate
Tutorial
updated 7.2 years ago by
zhengx
▴ 30 • written 7.2 years ago by
AR3513
• 0
0
votes
1
reply
1.5k
views
SNPRelate Dendrogram Point Colors and Shapes
SNPRelate
R
updated 8.1 years ago by
zhengx
▴ 30 • written 8.1 years ago by
rfriedman22
• 0
3
votes
2
replies
1.8k
views
Minimum allele frequency (MAF) from a Genomic Data Structure (GDS) file
snprelate
GWASTools
updated 8.2 years ago by
Adrienne Stilp
▴ 30 • written 8.2 years ago by
Vinicius Henrique da Silva
▴ 40
0
votes
9
replies
6.4k
views
unable to update mgcv package
mgcv
snprelate
updated 8.6 years ago by
Martin Morgan
25k • written 8.6 years ago by
mail2vignesh1985
• 0
0
votes
4
replies
2.5k
views
NA values in snpgdsDiss dissimilarity matrix
snprelate
updated 8.7 years ago by
zhengx
▴ 30 • written 8.7 years ago by
blackgore
▴ 10
0
votes
0
replies
982
views
RADseq chromosomes unknown
snprelate
RADseq
Stacks
8.7 years ago
clive.darwell
• 0
0
votes
0
replies
1.9k
views
GWASTools
Organism
GWASTools
Organism
GWASTools
SNPRelate
11.4 years ago
Stephanie M. Gogarten
▴ 870
22 results • Page
1 of 1
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Replies
Comment: 'path' must be string
by
James W. MacDonald
66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string
by
cpierce2
• 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest
by
Robert
• 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta
by
Guido Hooiveld
★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta
by
Michael Love
42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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Lluís Revilla Sancho
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