Showing : SNPRelate • reset
0
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9
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6.2k
views
unable to update mgcv package
mgcv snprelate
updated 8.3 years ago by 25k • written 8.3 years ago by • 0
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 ▴ 30 • written 5.5 years ago by • 0
0
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4
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2.4k
views
NA values in snpgdsDiss dissimilarity matrix
snprelate
updated 8.4 years ago by ▴ 30 • written 8.4 years ago by ▴ 10
0
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0
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1.9k
views
GWASTools
Organism GWASTools Organism GWASTools SNPRelate
11.1 years ago Stephanie M. Gogarten ▴ 870
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 ▴ 30 • written 7.9 years ago by ▴ 40
1
vote
2
replies
1.6k
views
Cannot read plink files correctly
snprelate Tutorial
updated 6.9 years ago by ▴ 30 • written 6.9 years ago by • 0
0
votes
2
replies
1.5k
views
Error converting vcf to gds
snprelate vcf gds
updated 6.1 years ago by ▴ 30 • written 6.1 years ago by • 0
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 ▴ 870 • written 5.1 years ago by • 0
0
votes
1
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1.5k
views
SNPRelate Dendrogram Point Colors and Shapes
SNPRelate R
updated 7.8 years ago by ▴ 30 • written 7.9 years ago by • 0
0
votes
1
reply
1.3k
views
Write gds in parallel
gds SNPRelate BiocParallel
updated 6.0 years ago by ▴ 30 • written 6.0 years ago by ▴ 40
0
votes
1
reply
1.1k
views
SNP annotation
SNPRelate SNP GWASTools Annotation GWASdata
updated 2.3 years ago by ▴ 870 • written 2.4 years ago by • 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 65k • written 3.6 years ago by • 0
1
vote
1
reply
972
views
PCA axis description SNPRelate
SNPRelate PCA
updated 5.1 years ago by ▴ 870 • written 5.1 years ago by ▴ 60
0
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2
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927
views
How to project a new vector onto PCA space using snpgdsPCA( )?
SNPRelate
updated 2.1 years ago by ▴ 870 • written 2.1 years ago by • 0
0
votes
0
replies
926
views
RADseq chromosomes unknown
snprelate RADseq Stacks
8.4 years ago clive.darwell • 0
0
votes
1
reply
915
views
error when running snpgdsLDpruning: The GDS node "genotype/data" does not exist.
SNPRelate
updated 3.4 years ago by • 0 • written 3.4 years ago by • 0
0
votes
1
reply
898
views
Using previously calculated PCs in GENESIS
genesis snprelate
5.6 years ago Stephanie M. Gogarten ▴ 870
0
votes
1
reply
856
views
Different order of samples in output of snpgdsSlidingWindow to calculate Fst and aggregation method
SNPRelate
updated 4.9 years ago by ▴ 30 • written 5.0 years ago by ▴ 60
1
vote
1
reply
804
views
What does SNPRelate::snpgdsDiss calculate?
SNPRelate
updated 4.9 years ago by ▴ 30 • written 4.9 years ago by • 0
0
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0
replies
794
views
SNPRelate handling of missing genotypes
SNPRelate
2.3 years ago serpalma.v ▴ 60
0
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0
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685
views
#SeqSQC error: Problem while converting vcf format to gds format
SNPRelate gdsfmt SeqSQC
2.5 years ago Bhargavi • 0
0
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0
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471
views
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
22 results • Page 1 of 1
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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by SamGG ▴ 350
Is useless the assumption that the majority of genes have no variation in expression (bearing in mind that they are distributed over the en…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Votes
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
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