Moderator: Nicolas Rosewick

gravatar for Nicolas Rosewick
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Posts by Nicolas Rosewick

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Comment: C: Help Compiling STAR
... Why not use the binary ? ...
written 15 days ago by Nicolas Rosewick9.3k
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Where to find SNP genotype information for ENCODE samples
... Hi, I'm working on some ChIP-Seq data from ENCODE project. I've a set of SNP of interest that may disrupt a TF binding site. In order to check the impact of these SNPs on the TF binding affinity I would like to stratify the samples by GT. I looked in ENCODE and there is some dataset of genotyping ...
encode genotype written 11 weeks ago by Nicolas Rosewick9.3k
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Comment: C: Should the number of significantly DE genes rise with the number of SVs estimate
... Could you rephrase your question (and maybe give an example), it's not clear. Are you asking if there is a linear relation between SV number and DE genes number ? ...
written 11 weeks ago by Nicolas Rosewick9.3k
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Comment: C: increase spacing between groups in a bar plot
... could you post your ggplot command in order to reproduce your plot ? ...
written 3 months ago by Nicolas Rosewick9.3k
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Comment: C: increase spacing between groups in a bar plot
... quick google search : https://stackoverflow.com/questions/6085238/adding-space-between-bars-in-ggplot2 ...
written 3 months ago by Nicolas Rosewick9.3k
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Comment: C: Strange plots I got from R studio
... without any more information (code, reproducible dataset/example, figures) we can not help you. Please edit your question accordingly ...
written 3 months ago by Nicolas Rosewick9.3k
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Answer: A: What is the VEP Impact column?
... Everything is explained on ENSEMBL website : https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html and here : https://www.ensembl.org/Help/Glossary **Variant impact** A subjective classification of the severity of the variant consequence, based on agreement with SNPEff. **M ...
written 3 months ago by Nicolas Rosewick9.3k
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Comment: C: RNA seq data analysis and building co expression network
... please do not use excel to do bioinformatics (or to handle any kind of genomic data). Please try appropriate tools/language such as R to manipulate gene count tables. ...
written 3 months ago by Nicolas Rosewick9.3k
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Comment: C: Weird results in TopHat2 paired-end alignment
... FYI : https://twitter.com/lpachter/status/937055346987712512?lang=fr ...
written 3 months ago by Nicolas Rosewick9.3k
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Comment: C: GWAS results and linkage disequilibrium issue
... IMO You should try to use a fine-mapping tool e.g. FINEMAP in order to get the causal SNP. Then use this SNP as reference SNP and report all SNPs in the neighborhood that are significant and their associated LD R2 with the reference SNP. Also I would use only the putative causal SNP for the risk sco ...
written 3 months ago by Nicolas Rosewick9.3k

Latest awards to Nicolas Rosewick

Great Question 3 days ago, created a question with more than 5,000 views. For Tophat: How Many Allowed Mismatch ?
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Appreciated 8 days ago, created a post with more than 5 votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Good Answer 11 days ago, created an answer that was upvoted at least 5 times. For A: How Do I Make A Heatmap In R?
Appreciated 11 days ago, created a post with more than 5 votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Great Question 26 days ago, created a question with more than 5,000 views. For Tophat: How Many Allowed Mismatch ?
Good Question 5 weeks ago, asked a question that was upvoted at least 5 times. For Insert Size And Fragment Size ?
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Great Question 8 weeks ago, created a question with more than 5,000 views. For Tophat: How Many Allowed Mismatch ?
Great Question 9 weeks ago, created a question with more than 5,000 views. For Tophat: How Many Allowed Mismatch ?
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Good Answer 9 weeks ago, created an answer that was upvoted at least 5 times. For A: How Do I Make A Heatmap In R?
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: How Do I Make A Heatmap In R?
Appreciated 3 months ago, created a post with more than 5 votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Popular Question 3 months ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Popular Question 3 months ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Appreciated 3 months ago, created a post with more than 5 votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Librarian 3 months ago, created a post with more than 10 bookmarks. For Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
Epic Question 5 months ago, created a question with more than 10,000 views. For bigwig to peak
Prophet 5 months ago, created a post with more than 20 followers. For Insert Size And Fragment Size ?
Great Question 6 months ago, created a question with more than 5,000 views. For bigwig to peak

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