User: FreeMindAlex

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FreeMindAlex100
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2 months ago
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Posts by FreeMindAlex

<prev • 43 results • page 1 of 5 • next >
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Comment: C: What do you want to learn about bioinformatics?
... It's going to be a structured online course. Still exploring other aspects. ...
written 17 months ago by FreeMindAlex100
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Forum: What do you want to learn about bioinformatics?
... Hi there, I'm organising a course in bioinformatics and would like to get some insight from prospective students on what they'd like the content of such a course to be. If you're considering doing an online bioinformatics course than I'd really appreciate if you answer all or some of the questions ...
bioinformatics forum course education written 17 months ago by FreeMindAlex100 • updated 17 months ago by genomax84k
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Answer: A: Download all eQTL data for all the 9 tissues from GTEx Portal
... Is all the data from GETx available now?. In addition to significant associations I'm also interested in the P-values for non-significant associations. Are these available now? ...
written 4.2 years ago by FreeMindAlex100
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Comment: C: What'S The Best Way To View And Explore A Large Gene Ontology Dag?
... Is there a tool like REVIGO that can be applied to other gene sets (i.e. not GO terms)? ...
written 4.5 years ago by FreeMindAlex100 • updated 6 months ago by RamRS27k
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Scatter plot for GSEA results analysis
... Hi All, I really like fig 5A in this paper: http://www.nature.com/nbt/journal/v31/n1/full/nbt.2450.html It neatly displays result of the GSEA analysis with an indication of gene set size and P-value. Can anyone help me figure out how to make a graph like this given gene set + enrichment score + P ...
rna-seq written 4.5 years ago by FreeMindAlex100 • updated 3.9 years ago by siabadaba70
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Comment: C: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
... bernatel, Since you mention regioneR - is there a discussion forum where users can contact regioneR developers? I like the permutation strategy but it is extremely slow. I have been running randomizeRegions() function for more than 10min [not finished yet] with no result coming up. The GRange files ...
written 4.8 years ago by FreeMindAlex100
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Comment: C: How to test statistical significance of ChIPseq enrichment in custom BED regions
... Thanks I think I will settle with GenometriCorr for good data visualization functionality.  ...
written 4.9 years ago by FreeMindAlex100
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How to test statistical significance of ChIPseq enrichment in custom BED regions?
... Hello All, Say I have a list of regions in BED format + list of ChIPseq peaks in BED format or ChIPseq BAM alignment file. How can I statistically test that factor's occupancy is enriched in BED regions more than would be expected by chance? Is there any specific program I could use for that purpos ...
chip-seq written 4.9 years ago by FreeMindAlex100 • updated 4.9 years ago by Ian5.6k
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Comment: C: Meaning of differential promoter use (cuffdiff)
... Figure 4 in this paper explains everything http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html  ...
written 4.9 years ago by FreeMindAlex100
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Comment: C: Meaning of differential promoter use (cuffdiff)
... Hi Geek Is differential tss site usage meant by differential promoter use? Thanks ...
written 4.9 years ago by FreeMindAlex100

Latest awards to FreeMindAlex

Popular Question 15 months ago, created a question with more than 1,000 views. For How to test statistical significance of ChIPseq enrichment in custom BED regions?
Great Question 17 months ago, created a question with more than 5,000 views. For How is FDR calculated in MACS?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For How to test statistical significance of ChIPseq enrichment in custom BED regions?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Meaning of differential promoter use (cuffdiff)
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Fundamental flaw in ngs.plot - how to overcome?C
Popular Question 4.2 years ago, created a question with more than 1,000 views. For How to test statistical significance of ChIPseq enrichment in custom BED regions?
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Meaning of differential promoter use (cuffdiff)
Popular Question 4.2 years ago, created a question with more than 1,000 views. For What is the appropriate approach for ChIPseq protein genome occupancy % calculation?
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Fundamental flaw in ngs.plot - how to overcome?C
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Read alignment for ChIPseq
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Scatter plot for GSEA results analysis
Popular Question 4.2 years ago, created a question with more than 1,000 views. For How is FDR calculated in MACS?
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Question about the appropriate FPKM gene expression processing
Popular Question 4.2 years ago, created a question with more than 1,000 views. For GSEA matrix error appears during analysis
Student 4.2 years ago, asked a question with at least 3 up-votes. For How is FDR calculated in MACS?

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