User: User 7754

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User 7754230
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Posts by User 7754

<prev • 82 results • page 1 of 9 • next >
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Find region that full captures association signal
... Hi, Are there any softwares or scripts to define a genomic region around an association signal in GWAS? I know people define usually a set amount (e.g. 200kb) around the most associated SNP, or first find the index SNPs in Plink and then limit these by LD and pvalue, but I was wondering if there i ...
gwas ld pvalue written 5 months ago by User 7754230 • updated 4 months ago by christopher medway440
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Comment: C: How to compute enrichment of one feature in the other across the genome (log fol
... it's only a few datasets that don't have sex chromosome, not one sample, and since I am computing the enrichment for each dataset I don't see why I would need to remove them. Is there any reason I am not seeing? I found this other question that could help actually for enrichment (maybe it is a dupli ...
written 5 months ago by User 7754230
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Comment: C: How to compute enrichment of one feature in the other across the genome (log fol
... Thank you Friederike for your replies! I see the difference now, it is the number of features overlapping, but I would still think that if there is a p-value there must be a way to also say, e.g., it is 3 times more enriched than expected by chance (after taking account of the genome length)? The re ...
written 5 months ago by User 7754230
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Comment: C: How to compute enrichment of one feature in the other across the genome (log fol
... Hi, thank you Jared. 1. Some bed files A have the sex chromosomes, some bed files A do not. So, in cases that do not include the sex chromosomes, I should compute enrichment of bed files A in bed files B after removing the sex files? Then the enrichments of bed files A in bed files B will be all com ...
written 5 months ago by User 7754230
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How to compute enrichment of one feature in the other across the genome (log fold, and pvalue)
... Hi, I have two bed files, and I would like to know if bed file A is enriched in bed file B compared to what is expected, given the genome sizes. I found how to get a p-value for this using Fisher, at least an idea of the baseline: bedtools fisher -a testA.bed -b testB.bed -g chrom_hg19.sizes, ...
genome enrichment written 5 months ago by User 7754230
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Comment: C: Batch download of bed files for all transcription factors associated with a cell
... I didn't know about this resource, thank you! ...
written 6 months ago by User 7754230
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Batch download of bed files for all transcription factors associated with a cell type
... Hi, Are there any web tools for downloading all TF related ChiPSeq experiments in a particular cell type in batch without going through each dataset in ENCODE or in Cistrome db? Thank you ...
chip-seq transcription factors cell-type specific written 6 months ago by User 7754230 • updated 6 months ago by ATpoint24k
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Comment: C: Finding the best model for expression data (RNA-Seq counts)
... Ok that makes sense! If I plot the log (FPKM), it finally looks normal! So the final answer is to use this in a linear regression model. I do think I need to do log(FPKM +1), for the log to work. I just have one more question. I imagine the extra step of "dividing each FPK by the sum of FPKs and mu ...
written 7 months ago by User 7754230
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Comment: C: Finding the best model for expression data (RNA-Seq counts)
... Thank you i.sudbery! That is very clear. Yes, I was actually including gene length as covariate to control for that, so doing: expression ~ conservation + gene_length. I don't know how that would be different but will read the paper you linked. I thought I needed samples to run DESeq2 or edgeR (whi ...
written 7 months ago by User 7754230
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Comment: C: Finding the best model for expression data (RNA-Seq counts)
... Charles, thank you, the paper and links helped so much. Please modify (or let me know how best to modify) the question, so that it is clearer and can help others (can also remove this and put it as an answer?). Thank you for all the help! ...
written 7 months ago by User 7754230

Latest awards to User 7754

Student 7 months ago, asked a question with at least 3 up-votes. For Finding the best model for expression data (RNA-Seq counts)
Supporter 7 months ago, voted at least 25 times.
Great Question 20 months ago, created a question with more than 5,000 views. For Plot Genes In R Under A Regional Manhattan Plot
Popular Question 20 months ago, created a question with more than 1,000 views. For P-value for enrichment of ChIP-Seq peaks within a genomic annotation
Popular Question 20 months ago, created a question with more than 1,000 views. For Definition of splicing eQTLs in RNA-Seq and arrays
Popular Question 20 months ago, created a question with more than 1,000 views. For Tools for alternative splicing of distant genes
Popular Question 20 months ago, created a question with more than 1,000 views. For Circos or circlize plot for overlapping values/colors
Popular Question 20 months ago, created a question with more than 1,000 views. For [SOLVED] Trying to apply overlap to each row of a "GRangesList"
Popular Question 2.0 years ago, created a question with more than 1,000 views. For P-value for enrichment of ChIP-Seq peaks within a genomic annotation
Popular Question 3.0 years ago, created a question with more than 1,000 views. For P-value for enrichment of ChIP-Seq peaks within a genomic annotation
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Tools for alternative splicing of distant genes
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Circos or circlize plot for overlapping values/colors
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Combined Association Of Expression, Genetic, Clinical Phenotypes
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Combined Association Of Expression, Genetic, Clinical Phenotypes
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Combined Association Of Expression, Genetic, Clinical Phenotypes
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Plot Genes In R Under A Regional Manhattan Plot
Commentator 4.9 years ago, created a comment with at least 3 up-votes. For C: Eqtl Database Available?
Popular Question 5.7 years ago, created a question with more than 1,000 views. For Visualise Ld Plots On Whole Chromosome
Popular Question 7.3 years ago, created a question with more than 1,000 views. For Plot Genes In R Under A Regional Manhattan Plot

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