Moderator: Nicolas Rosewick

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Posts by Nicolas Rosewick

<prev • 818 results • page 1 of 82 • next >
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Comment: C: Overlapping SNPs in R
... Try findOverlaps function from GenomicRanges package in R. ...
written 1 day ago by Nicolas Rosewick6.9k
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Answer: A: Align RNA-seq data to a custom list of exons?
... Yes you can directly change the gtf file to add the exon of interest. Then use featurecounts to count the number of reads per exon (using `-t exon -g exon_id` (if there is an exon_id in the gtf file). ...
written 2 days ago by Nicolas Rosewick6.9k
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Answer: A: Histogram of p values for all tests
... Start reading this excellent article here : http://varianceexplained.org/statistics/interpreting-pvalue-histogram/ These two peaks at the right tail are strange. Did you use the nominal pvalue or the corrected one (you should use the nominal for the plot) ? Otherwise the distribution seems to b ...
written 4 days ago by Nicolas Rosewick6.9k
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Comment: C: How do concatenate different fasta file
... that's a good point ! ...
written 7 days ago by Nicolas Rosewick6.9k
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Answer: A: 3' UTR FASTA back to genes
... Blast the 3'UTR on ENSEMBL website. Then take the gene id found and extract the protein sequence in ENSEMBL biomart. ...
written 7 days ago by Nicolas Rosewick6.9k
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Answer: A: How do concatenate different fasta file
... As Genomax commented : In a unix shell : cat file1.fasa file2.fastq file3.fasta > merged_file.fasta or even easier if all your fasta files are in a directory and ends by .fasta cat *.fasta > merged_file.fasta ...
written 9 days ago by Nicolas Rosewick6.9k
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Comment: C: Correlation between lncRNA and protein coding genes
... You should maybe start by reading about statistics before going further into your analysis 😉 ...
written 18 days ago by Nicolas Rosewick6.9k
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Answer: A: Correlation between lncRNA and protein coding genes
... If your lncRNA is on the ith line in the matrix then in R if count is your matrix cor <- apply(count,1,function(x){cor(x,count[i,])}) You may choose Pearson or Spearman for the correlation ...
written 19 days ago by Nicolas Rosewick6.9k
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Answer: C: Can I compute Tumour Mutational Burden from rnaseq fastq files?
... check this post : https://www.biostars.org/p/178634/ ...
written 19 days ago by Nicolas Rosewick6.9k
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Comment: C: R visualization package : Genome-wide distribution and orientation of translocat
... Try to contact the author of the publication for the source code of this plot. ...
written 22 days ago by Nicolas Rosewick6.9k

Latest awards to Nicolas Rosewick

Teacher 27 days ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Scholar 27 days ago, created an answer that has been accepted. For C: How to increase cytoscape memory?
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Scholar 5 weeks ago, created an answer that has been accepted. For C: How to increase cytoscape memory?
Epic Question 6 weeks ago, created a question with more than 10,000 views. For Download Rrna Sequences
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Scholar 7 weeks ago, created an answer that has been accepted. For C: How to increase cytoscape memory?
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Scholar 8 weeks ago, created an answer that has been accepted. For C: How to increase cytoscape memory?
Popular Question 8 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 featureCounts exon counting problem
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Popular Question 3 months ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Popular Question 4 months ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Great Question 4 months ago, created a question with more than 5,000 views. For bigwig to peak
Popular Question 4 months ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: How Do I Make A Heatmap In R?
Appreciated 4 months ago, created a post with more than 5 votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Popular Question 4 months ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Great Question 4 months ago, created a question with more than 5,000 views. For bigwig to peak
Student 5 months ago, asked a question with at least 3 up-votes. For tRNA expression analysis from RNA-Seq
Popular Question 5 months ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Epic Question 5 months ago, created a question with more than 10,000 views. For Download Rrna Sequences
Popular Question 5 months ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data

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