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
2.5 years ago m610110001 • 0
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How to project a new vector onto PCA space using snpgdsPCA( )?
SNPRelate
updated 3.1 years ago by ▴ 890 • written 3.1 years ago by • 0
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SNP annotation
SNPRelate SNP GWASTools Annotation GWASdata
updated 3.3 years ago by ▴ 890 • written 3.4 years ago by • 0
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SNPRelate handling of missing genotypes
SNPRelate
3.3 years ago serpalma.v ▴ 60
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#SeqSQC error: Problem while converting vcf format to gds format
SNPRelate gdsfmt SeqSQC
3.5 years ago Bhargavi • 0
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error when running snpgdsLDpruning: The GDS node "genotype/data" does not exist.
SNPRelate
updated 4.4 years ago by • 0 • written 4.4 years ago by • 0
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How to add colors to the PCA made using SNPRelate
snprelate
updated 4.6 years ago by 68k • written 4.6 years ago by • 0
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What does SNPRelate::snpgdsDiss calculate?
SNPRelate
updated 5.9 years ago by ▴ 30 • written 5.9 years ago by • 0
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Different order of samples in output of snpgdsSlidingWindow to calculate Fst and aggregation method
SNPRelate
updated 6.0 years ago by ▴ 30 • written 6.0 years ago by ▴ 60
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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 6.1 years ago by ▴ 890 • written 6.1 years ago by • 0
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PCA axis description SNPRelate
SNPRelate PCA
updated 6.1 years ago by ▴ 890 • written 6.1 years ago by ▴ 60
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4.4k
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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 6.5 years ago by ▴ 30 • written 6.5 years ago by • 0
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1.1k
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Using previously calculated PCs in GENESIS
genesis snprelate
6.6 years ago Stephanie M. Gogarten ▴ 890
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1.6k
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Write gds in parallel
gds SNPRelate BiocParallel
updated 7.0 years ago by ▴ 30 • written 7.0 years ago by ▴ 40
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2.0k
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Error converting vcf to gds
snprelate vcf gds
updated 7.1 years ago by ▴ 30 • written 7.1 years ago by • 0
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2
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2.1k
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Cannot read plink files correctly
snprelate Tutorial
updated 7.9 years ago by ▴ 30 • written 7.9 years ago by • 0
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1.8k
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SNPRelate Dendrogram Point Colors and Shapes
SNPRelate R
updated 8.9 years ago by ▴ 30 • written 8.9 years ago by • 0
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Minimum allele frequency (MAF) from a Genomic Data Structure (GDS) file
snprelate GWASTools
updated 8.9 years ago by ▴ 30 • written 8.9 years ago by ▴ 40
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unable to update mgcv package
mgcv snprelate
updated 9.3 years ago by 25k • written 9.3 years ago by • 0
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2.8k
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NA values in snpgdsDiss dissimilarity matrix
snprelate
updated 9.4 years ago by ▴ 30 • written 9.4 years ago by ▴ 10
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RADseq chromosomes unknown
snprelate RADseq Stacks
9.4 years ago clive.darwell • 0
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GWASTools
Organism GWASTools Organism GWASTools SNPRelate
12.1 years ago Stephanie M. Gogarten ▴ 890
22 results • Page 1 of 1
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Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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