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
7 months ago m610110001 • 0
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2
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558
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How to project a new vector onto PCA space using snpgdsPCA( )?
SNPRelate
updated 14 months ago by ▴ 840 • written 14 months ago by • 0
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1
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568
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SNP annotation
SNPRelate SNP GWASTools Annotation GWASdata
updated 16 months ago by ▴ 840 • written 18 months ago by • 0
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449
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SNPRelate handling of missing genotypes
SNPRelate
16 months ago serpalma.v ▴ 60
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363
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#SeqSQC error: Problem while converting vcf format to gds format
SNPRelate gdsfmt SeqSQC
19 months ago Bhargavi • 0
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1
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614
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error when running snpgdsLDpruning: The GDS node "genotype/data" does not exist.
SNPRelate
updated 2.5 years ago by • 0 • written 2.5 years ago by • 0
3
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1
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752
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How to add colors to the PCA made using SNPRelate
snprelate
updated 2.7 years ago by 63k • written 2.7 years ago by • 0
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1
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561
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What does SNPRelate::snpgdsDiss calculate?
SNPRelate
updated 4.0 years ago by ▴ 30 • written 4.0 years ago by • 0
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1
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591
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Different order of samples in output of snpgdsSlidingWindow to calculate Fst and aggregation method
SNPRelate
updated 4.1 years ago by ▴ 30 • written 4.1 years ago by ▴ 60
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1
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1.1k
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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 4.2 years ago by ▴ 840 • written 4.2 years ago by • 0
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690
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PCA axis description SNPRelate
SNPRelate PCA
updated 4.2 years ago by ▴ 840 • written 4.2 years ago by ▴ 60
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1
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3.1k
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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 4.6 years ago by ▴ 30 • written 4.6 years ago by • 0
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1
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630
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Using previously calculated PCs in GENESIS
genesis snprelate
4.7 years ago Stephanie M. Gogarten ▴ 840
0
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1
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850
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Write gds in parallel
gds SNPRelate BiocParallel
updated 5.1 years ago by ▴ 30 • written 5.1 years ago by ▴ 40
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2
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1.2k
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Error converting vcf to gds
snprelate vcf gds
updated 5.2 years ago by ▴ 30 • written 5.2 years ago by • 0
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2
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1.2k
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Cannot read plink files correctly
snprelate Tutorial
updated 6.0 years ago by ▴ 30 • written 6.0 years ago by • 0
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1
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1.2k
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SNPRelate Dendrogram Point Colors and Shapes
SNPRelate R
updated 7.0 years ago by ▴ 30 • written 7.0 years ago by • 0
3
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2
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1.5k
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Minimum allele frequency (MAF) from a Genomic Data Structure (GDS) file
snprelate GWASTools
updated 7.0 years ago by ▴ 30 • written 7.0 years ago by ▴ 40
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9
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5.7k
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unable to update mgcv package
mgcv snprelate
updated 7.4 years ago by 25k • written 7.4 years ago by • 0
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4
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2.0k
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NA values in snpgdsDiss dissimilarity matrix
snprelate
updated 7.5 years ago by ▴ 30 • written 7.5 years ago by ▴ 10
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765
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RADseq chromosomes unknown
snprelate RADseq Stacks
7.6 years ago clive.darwell • 0
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1.6k
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GWASTools
Organism GWASTools Organism GWASTools SNPRelate
10.2 years ago Stephanie M. Gogarten ▴ 840
22 results • Page 1 of 1
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Answer: DESeq2 + analysis question for design with uneven time point design by Michael Love 40k
I'd recommend reaching out to a local statistician or someone familiar with linear models in R. Unfortunately, I have to reserve my time on…
Answer: Genes with highest differential expression have very low read counts for most ge by Michael Love 40k
Have you use `lfcShrink`? Or `results` with `lfcThreshold`? Either of these are recommended for prioritizing DE genes.
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Gordon Smyth 47k
> equivqalent in limma would be like a gene by gene specificic design matrix where no BL time point would exist but a continuous variable t…
Comment: Extract Limma Adjusted Values for Plotting by ATpoint ★ 2.9k
Yes, with normalized counts on log2 scale.
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Anna ▴ 20
A no I never referred to transcriptomic data when I was talking about "standard procedure" I was referring to the way we analyze longitudin…
Votes
A: Ranges from a fasta file
Answer: NA transcript values in my Txdb
Comment: Interpret plot from DiffBind
Answer: Use with_go along with other filters in getBM function
Answer: Use with_go along with other filters in getBM function
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Scholar to Mike Smith ★ 6.0k
Popular Question to Martin Morgan 25k
Teacher to deeenes ▴ 30
Popular Question to Hervé Pagès 16k
Popular Question to Gordon Smyth 47k
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