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
3.1 years ago m610110001 • 0
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2
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How to project a new vector onto PCA space using snpgdsPCA( )?
SNPRelate
updated 3.7 years ago by ▴ 890 • written 3.7 years ago by • 0
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1.9k
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SNP annotation
SNPRelate SNP GWASTools Annotation GWASdata
updated 3.9 years ago by ▴ 890 • written 4.0 years ago by • 0
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SNPRelate handling of missing genotypes
SNPRelate
3.9 years ago serpalma.v ▴ 60
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#SeqSQC error: Problem while converting vcf format to gds format
SNPRelate gdsfmt SeqSQC
4.2 years ago Bhargavi • 0
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1.4k
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error when running snpgdsLDpruning: The GDS node "genotype/data" does not exist.
SNPRelate
updated 5.0 years ago by • 0 • written 5.0 years ago by • 0
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1.5k
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How to add colors to the PCA made using SNPRelate
snprelate
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
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1.2k
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What does SNPRelate::snpgdsDiss calculate?
SNPRelate
updated 6.5 years ago by ▴ 30 • written 6.5 years ago by • 0
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1.3k
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Different order of samples in output of snpgdsSlidingWindow to calculate Fst and aggregation method
SNPRelate
updated 6.6 years ago by ▴ 30 • written 6.6 years ago by ▴ 60
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2.2k
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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 6.7 years ago by ▴ 890 • written 6.7 years ago by • 0
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1.4k
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PCA axis description SNPRelate
SNPRelate PCA
updated 6.7 years ago by ▴ 890 • written 6.7 years ago by ▴ 60
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4.7k
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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 7.2 years ago by ▴ 30 • written 7.2 years ago by • 0
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1.3k
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Using previously calculated PCs in GENESIS
genesis snprelate
7.2 years ago Stephanie M. Gogarten ▴ 890
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1.8k
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Write gds in parallel
gds SNPRelate BiocParallel
updated 7.6 years ago by ▴ 30 • written 7.6 years ago by ▴ 40
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2
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2.1k
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Error converting vcf to gds
snprelate vcf gds
updated 7.7 years ago by ▴ 30 • written 7.7 years ago by • 0
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2
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2.2k
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Cannot read plink files correctly
snprelate Tutorial
updated 8.5 years ago by ▴ 30 • written 8.5 years ago by • 0
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1
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2.0k
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SNPRelate Dendrogram Point Colors and Shapes
SNPRelate R
updated 9.5 years ago by ▴ 30 • written 9.5 years ago by • 0
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2
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2.3k
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Minimum allele frequency (MAF) from a Genomic Data Structure (GDS) file
snprelate GWASTools
updated 9.5 years ago by ▴ 30 • written 9.5 years ago by ▴ 40
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7.4k
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unable to update mgcv package
mgcv snprelate
updated 10.0 years ago by 25k • written 10.0 years ago by • 0
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4
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3.1k
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NA values in snpgdsDiss dissimilarity matrix
snprelate
updated 10.0 years ago by ▴ 30 • written 10.1 years ago by ▴ 10
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1.2k
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RADseq chromosomes unknown
snprelate RADseq Stacks
10.1 years ago clive.darwell • 0
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2.2k
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GWASTools
Organism GWASTools Organism GWASTools SNPRelate
12.7 years ago Stephanie M. Gogarten ▴ 890
22 results • Page 1 of 1
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
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