Showing : SNPRelate • reset
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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
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2
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922
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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
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1.1k
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SNP annotation
SNPRelate SNP GWASTools Annotation GWASdata
updated 2.3 years ago by ▴ 870 • written 2.4 years ago by • 0
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792
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SNPRelate handling of missing genotypes
SNPRelate
2.3 years ago serpalma.v ▴ 60
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684
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#SeqSQC error: Problem while converting vcf format to gds format
SNPRelate gdsfmt SeqSQC
2.5 years ago Bhargavi • 0
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1
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912
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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
3
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1
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1.0k
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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
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1
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803
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What does SNPRelate::snpgdsDiss calculate?
SNPRelate
updated 4.9 years ago by ▴ 30 • written 4.9 years ago by • 0
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1
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854
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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
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1.5k
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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
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970
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PCA axis description SNPRelate
SNPRelate PCA
updated 5.1 years ago by ▴ 870 • written 5.1 years ago by ▴ 60
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1
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3.7k
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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
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896
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Using previously calculated PCs in GENESIS
genesis snprelate
5.6 years ago Stephanie M. Gogarten ▴ 870
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1.3k
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Write gds in parallel
gds SNPRelate BiocParallel
updated 6.0 years ago by ▴ 30 • written 6.0 years ago by ▴ 40
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2
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1.5k
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Error converting vcf to gds
snprelate vcf gds
updated 6.1 years ago by ▴ 30 • written 6.1 years ago by • 0
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2
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1.6k
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Cannot read plink files correctly
snprelate Tutorial
updated 6.9 years ago by ▴ 30 • written 6.9 years ago by • 0
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1
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1.5k
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SNPRelate Dendrogram Point Colors and Shapes
SNPRelate R
updated 7.8 years ago by ▴ 30 • written 7.9 years ago by • 0
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2
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1.7k
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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
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9
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6.2k
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unable to update mgcv package
mgcv snprelate
updated 8.3 years ago by 25k • written 8.3 years ago by • 0
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4
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2.4k
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NA values in snpgdsDiss dissimilarity matrix
snprelate
updated 8.4 years ago by ▴ 30 • written 8.4 years ago by ▴ 10
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925
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RADseq chromosomes unknown
snprelate RADseq Stacks
8.4 years ago clive.darwell • 0
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1.9k
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GWASTools
Organism GWASTools Organism GWASTools SNPRelate
11.1 years ago Stephanie M. Gogarten ▴ 870
22 results • Page 1 of 1
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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
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