User: gaelgarcia05

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gaelgarcia05210
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UK
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9 months, 1 week ago
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Posts by gaelgarcia05

<prev • 58 results • page 1 of 6 • next >
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Comment: C: Convert a Seurat object to .h5ad file
... Could not have said it better. Thanks! ...
written 9 months ago by gaelgarcia05210
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Convert a Seurat object to .h5ad file
... Hi, I'm trying to build a single-cell browser using [cellxgene][1] from the Chan-Zuckerberg Intiative. However, I need to have a `.h5ad` file from the `annpdata` ackage in Python. I've done all my analysis in R, mainly using Seurat. I was wondering if there's a way to convert a Seurat object to . ...
single-cell R rna-seq seurat scanpy written 9 months ago by gaelgarcia05210 • updated 5 months ago by mmfiruleva10
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Answer: A: how to produce plots like this in R
... This is from the Seurat `DotPlot` function, which is documented here: https://github.com/satijalab/seurat/blob/master/R/plotting.R Essentially, it is a ggplot `geom_point` plot. ...
written 16 months ago by gaelgarcia05210
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Comment: C: Finding Variable Genes in Seurat, scRNA-seq
... Hi @igor , @lishen0709 – did you find a solution to your question about selecting the correct parameters for x and y cutoffs in Seurat's FindVariableGenes? Thanks! ...
written 20 months ago by gaelgarcia05210
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Comment: C: Compare allele frequency of SNPs in my data to their allele frequency in differe
... Thanks @finswimmer - just updated my post to clarify what I'm looking for as output. The output table I have in mind would look something like this: snpID MAF_mysamples MAF_european MAF_finnish MAF_african MAF_se_asian MAF_asian ...
written 2.0 years ago by gaelgarcia05210
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Comment: C: How To Find Major And Minor Alleles From Dbsnp ?
... Thank you for your thorough explanation, Jorge — Are the populations and MAFs per population in the `Population Diversity` table those corresponding to the 1000 Genomes project, or has this table been updated to include ExAC populations and MAFs? ...
written 2.0 years ago by gaelgarcia05210
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Comment: C: tools to calculate Exac population specific frequency
... Hi Jan, Wondering if you ended up finding an effective way to do this? I'm currently trying to do the same thing — except I don't relally understand what you mean by 'MAF files'. ...
written 2.0 years ago by gaelgarcia05210
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Compare allele frequency of SNPs in my data to their allele frequency in different human populations - ExAC vs 1000 Genomes vs Other?
... Hello, I have a list of SNPs (in the form of a VCF) found in our [very] targeted sequencing dataset of ~15,000 individuals. I am looking to compare the MAFs of these SNPs within this 'population' (our dataset) to their MAFs across different populations, such as the populations defined in ExAC or t ...
maf 1000genomes exac snp sequencing written 2.0 years ago by gaelgarcia05210
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Comment: C: Converting VCF to PLINK .bed binary fileset to check for pedigree errors with KI
... Ahh, that explains so much! Thanks! ...
written 2.1 years ago by gaelgarcia05210
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Comment: C: How To Convert Vcf File To Plink Ped Format?
... @alolex, Do you do this using the above mentioned tool from GATK `VariantsToBinaryPed`? Or with PLINK's --make-bed? ...
written 2.1 years ago by gaelgarcia05210

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Scholar 2.1 years ago, created an answer that has been accepted. For A: Full list of KING options and paramenters
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