User: CrazyB

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CrazyB180
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2 months ago
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4 years, 9 months ago
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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 3 months ago by CrazyB180
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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 3 months ago by CrazyB180
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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 5 months ago by CrazyB180 • updated 5 months ago by Jean-Karim Heriche13k
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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 6 months ago by CrazyB180
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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 6 months ago by CrazyB180 • updated 6 months ago by h.mon9.2k
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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 13 months ago by CrazyB180
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Comment: C: how to find the haplotype info in population genomic databases
... Thanks ! Ensembl database does have the info. ...
written 16 months ago by CrazyB180
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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 16 months ago by CrazyB180 • updated 16 months ago by Denise - Open Targets4.1k
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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 20 months ago by CrazyB180 • updated 20 months ago by Ram12k
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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 21 months ago by CrazyB180

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Popular Question 13 months ago, created a question with more than 1,000 views. For a question about some "basic numbers" for rna-seq experiments
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Popular Question 13 months ago, created a question with more than 1,000 views. For convert text file to VCF file ?
Popular Question 16 months ago, created a question with more than 1,000 views. For convert text file to VCF file ?
Popular Question 16 months ago, created a question with more than 1,000 views. For What Is Considered A Good Coverage Depth In Exon Capture Seq
Popular Question 20 months ago, created a question with more than 1,000 views. For What Is Considered A Good Coverage Depth In Exon Capture Seq
Epic Question 20 months ago, created a question with more than 10,000 views. For convert text file to VCF file ?
Popular Question 20 months ago, created a question with more than 1,000 views. For convert text file to VCF file ?
Popular Question 20 months ago, created a question with more than 1,000 views. For Multiplex In Exome Seq And "Customized/Capture" Seq Kits
Great Question 2.1 years ago, created a question with more than 5,000 views. For convert text file to VCF file ?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Multiplex In Exome Seq And "Customized/Capture" Seq Kits
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Negative B-Statistic Values In Limma/Microarray Differential Expression
Student 4.5 years ago, asked a question with at least 3 up-votes. For Need Help Interpreting The Genotype Fields In A Vcf Formatted Data
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Student 4.7 years ago, asked a question with at least 3 up-votes. For What Is Considered A Good Coverage Depth In Exon Capture Seq

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