User: fusion.slope

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fusion.slope200
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Posts by fusion.slope

<prev • 95 results • page 1 of 10 • next >
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create null sequences with gkmSVM for mouse genome mm10
... Hello, does anybody of you has never tried to generate null model of DNA sequences in mouse using the gkmSVM package? It works perfectly for human but for mouse it does not. I am wondering if any of you have never used this package for mice and had the same problem. The error problem when I u ...
R gkmsvm dna written 12 days ago by fusion.slope200
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Comment: C: eQTL analysis considering P-values
... you can select cut-off threshold to work with significant SNP. The cut-off threshold should be selected according to sample size to avoid false positive results. A P.val <= 0.01 is a good start but again, select a cut off for eQTL or GWAS or QTL depends on the number of SNPs that you are testing ...
written 5 weeks ago by fusion.slope200
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Comment: C: eQTL analysis considering P-values
... you have a table that might be the output of a tool that is performing such eQTL or QTL analysis, so please formulate again your question. What do you want to know? ...
written 5 weeks ago by fusion.slope200
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Comment: C: eQTL analysis considering P-values
... make a screenshot of the dataset and I can tell you more. I am not in the condition now to download 63.3 Mb of a file. ...
written 5 weeks ago by fusion.slope200
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Comment: C: eQTL analysis considering P-values
... Yes i can confirm, I also highly recommend Matrix eQTL, it is extremely fast and you can add covariates if any in your experimental design. ...
written 5 weeks ago by fusion.slope200
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Comment: C: Use Hypergeometric analysis to model data from RNAseq
... I have a similar problem: I have a list of genes differentially expressed in cell B between "control vs Knock Out" experiment. I want to see if there is an overlap (and via hypergeometric test that is not just by chance) between the genes down-regulated in the Knock out cell B with genes that ar ...
written 5 weeks ago by fusion.slope200
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Comment: C: Probability of gene list overlap
... are the 2 lists from the same cell type? ...
written 5 weeks ago by fusion.slope200
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Hypergeometric test with different cell types
... Hello, I have to select the background for a hypergeometric test that I have to perform. The problem is as follow: I have a list of genes differentially expressed in cell B between "control vs Knock Out" experiment. I want to see if there is an overlap (and via hypergeometric test that is not j ...
R background selection rna-seq hypergeometric written 5 weeks ago by fusion.slope200
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Comment: C: gene_Id in ENCODE gene expression table
... oh thanks a lot, I have scrolled a bit the file but did not go down enough to see the ENSEMBL gene annotation! much appreciated genomax! ...
written 11 weeks ago by fusion.slope200
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Comment: C: gene_Id in ENCODE gene expression table
... thanks a lot, i think alex already answered my question :) but to confirm i should check rsem output to see which gene_id reference they use.. ...
written 11 weeks ago by fusion.slope200

Latest awards to fusion.slope

Appreciated 23 days ago, created a post with more than 5 votes. For A: Where can I find public Singel Cell RNAseq data?
Popular Question 10 weeks ago, created a question with more than 1,000 views. For how is obtained the BED score values (the 5th column of the bed files) in BED files
Popular Question 7 months ago, created a question with more than 1,000 views. For cis-eQTL Results Visualization
Popular Question 7 months ago, created a question with more than 1,000 views. For Rpkm Computation
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Where can I find public Singel Cell RNAseq data?
Popular Question 12 months ago, created a question with more than 1,000 views. For cis-eQTL Results Visualization
Student 14 months ago, asked a question with at least 3 up-votes. For How to interpret and extract from a Vcf file Genotype informations as values
Popular Question 19 months ago, created a question with more than 1,000 views. For cis-eQTL Results Visualization
Popular Question 24 months ago, created a question with more than 1,000 views. For cis-eQTL Results Visualization
Popular Question 2.1 years ago, created a question with more than 1,000 views. For How to interpret and extract from a Vcf file Genotype informations as values
Supporter 2.2 years ago, voted at least 25 times.
Popular Question 2.5 years ago, created a question with more than 1,000 views. For How to interpret and extract from a Vcf file Genotype informations as values

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