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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932
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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
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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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0
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796
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SNPRelate handling of missing genotypes
SNPRelate
2.3 years ago serpalma.v ▴ 60
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0
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689
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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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918
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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
1
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1
reply
807
views
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
reply
859
views
Different order of samples in output of snpgdsSlidingWindow to calculate Fst and aggregation method
SNPRelate
updated 5.0 years ago by ▴ 30 • written 5.0 years ago by ▴ 60
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1
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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
1
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1
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978
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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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1
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901
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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
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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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1.6k
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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
1
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2
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1.6k
views
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
reply
1.5k
views
SNPRelate Dendrogram Point Colors and Shapes
SNPRelate R
updated 7.9 years ago by ▴ 30 • written 7.9 years ago by • 0
3
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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
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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
views
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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0
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930
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RADseq chromosomes unknown
snprelate RADseq Stacks
8.5 years ago clive.darwell • 0
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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: 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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Popular Question to Leo Lahti ▴ 40
Scholar to James W. MacDonald 65k
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