User: CrazyB

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CrazyB190
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Posts by CrazyB

<prev • 45 results • page 1 of 5 • next >
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Comment: C: looking for large human genomes databases
... @ lltommy, @ genomax, my title said that i am looking for human genomes databases. I've now made the changes in the main text to reflect that. ...
written 10 months ago by CrazyB190
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looking for large human genomes databases
... Other than `ExAC` and `GnomAD`, are there any other public human genome databases available that are searchable? `UK10K` seems like a work-in-progress and data are not compiled (thus searchable per dataset but not searchable as a collective group of genome data). A quick google search did not find a ...
genome written 10 months ago by CrazyB190
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how to re-arrange the gene expression heatmap to maximize the visual effect of the result
... I have the mRNA expression data for 4 groups of samples (2-3 samples per group), based on different genetic backgrounds and treatments. While the dendrogram segregates group #1 from the remaining 3 groups at the first branch of the dendrogram, it is not visually clear from the heatmap. Is it possi ...
heatmap written 12 months ago by CrazyB190 • updated 12 months ago by Jean-Karim Heriche15k
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Comment: C: is there a value of ranking genes based on p-value in RNA-seq data
... - @biofalconch - thanks for pointing this out. I completely missed that aspect of the difference between fold-change and p-value. - @CMosychuk - thanks for the link to the Cell paper. Perhaps I did not fully understand the answer in the linked question, but it appeared that the OP in that ...
written 12 months ago by CrazyB190
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is there a value of ranking genes based on p-value in RNA-seq data
... For my RNA-seq project, my collaborator generally provides a list of DEGs and the output is ranked based on p-value, not fold-change. While I understand the significance of p-value in the multiple-testing problems , I have always assumed once a gene passes the p-value cutoff, there is little differe ...
rna-seq written 13 months ago by CrazyB190 • updated 12 months ago by h.mon15k
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interpreting the untransmitted allele in TdT (transmission disequilibrium test)
... Can anyone help shed light on the interpretation/meaning of untransmitted alleles in the TdT test ? For example, in a cohort study, untransmitted SNP1 and transmitted SNP2 are significantly associated with the disease group. As "transmission" of SNP2 is significantly associated with the disease gr ...
tdt written 20 months ago by CrazyB190
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Comment: C: how to find the haplotype info in population genomic databases
... Thanks ! Ensembl database does have the info. ...
written 23 months ago by CrazyB190
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how to find the haplotype info in population genomic databases
... How do I find the haplotype info from `ExAC` or `1000 Genomes`? `1000 genomes` states that their data released from phase 3 are all phased. But when I use the browser to find SNPs, I could not find much haplotype info of any of the SNPs that I am looking for MacAurther Lab from the Broad Institute ...
1000genomes haplotype exac written 23 months ago by CrazyB190 • updated 23 months ago by Denise - Open Targets4.5k
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how to add pedigree info into VCF
... My VCF does not contain pedigree info and as such when running `PLINK`, it does not compute. `VCFtool` can convert VCF to `.ped` and `.map` but my understanding is that it does not require a pedigree for the conversion and assumes all individuals as unrelated (?). I googled around but did not find ...
vcf pedigree ped written 2.2 years ago by CrazyB190 • updated 2.2 years ago by Ram15k
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Comment: C: phased and unphased genotype results differ ?
... @ Pierre, to clarify, should I check "accept" out of courtesy for all responses or only when I believe the provided answer helps with the question? ...
written 2.3 years ago by CrazyB190

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Great Question 2.7 years ago, created a question with more than 5,000 views. For convert text file to VCF file ?
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