User: Nicolas Rosewick

gravatar for Nicolas Rosewick
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Belgium, Brussels, Université Libre de Bruxelles / Université de Liège
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https://nrosewick.gith...
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nrosewick
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Posts by Nicolas Rosewick

<prev • 723 results • page 1 of 73 • next >
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Answer: A: TMB Tumor Mutation Burden
... You can start by this paper : https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-017-0424-2 In the method part : > TMB was defined as the number of somatic, coding, base substitution, > and indel mutations per megabase of genome examined. ...
written 1 day ago by Nicolas Rosewick6.0k
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Comment: C: Merging raw Illumina FASTQ files with snakemake
... Could you be more specific ? What should we put as input then ? How will the mergeFastqR1 rule looks like ? thanks ...
written 13 days ago by Nicolas Rosewick6.0k
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Answer: A: Scatterplot with hexbin
... You could use geom_hex from ggplot2 : http://ggplot2.tidyverse.org/reference/geom_hex.html and add geom_hline and geom_vline where you want some vertical and horizontal lines. ...
written 6 weeks ago by Nicolas Rosewick6.0k
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Comment: C: Finding fasta files that share the highest number of identical headers
... @Pierre : Your command seems to output the top 10 most redundant headers not the top 10 fasta file names non ? ...
written 8 weeks ago by Nicolas Rosewick6.0k
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Biostars API : retrieve only original questions not answers or comment
... Hi, Using biostars API it's possible to access information concerning all posts from biostars users. Example : https://www.biostars.org/api/post/25/ However is there a way to access only the original questions and not comments or answers. In the returned JSON file, it would be possible to filter ...
biostars api written 8 weeks ago by Nicolas Rosewick6.0k
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Comment: C: Finding fasta files that share the highest number of identical headers
... one-liner always rocks! ...
written 8 weeks ago by Nicolas Rosewick6.0k
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Comment: C: fgbio: Calling consensus reads using UMI
... thanks I'll give a try ! ...
written 8 weeks ago by Nicolas Rosewick6.0k
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Comment: C: word cloud plot
... Please could you give us a little more details. Do you have already the biological process lists ? Or a list of impacted genes ? or raw data ? or nothing ? If you have the biological process lists it's quiet easy. A simple google search gives me a tutorial : https://datascienceplus.com/building-wor ...
written 8 weeks ago by Nicolas Rosewick6.0k
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Chimeric alignment with minimap2
... Hi, On minimap2 github (https://github.com/lh3/minimap2) it says : > For long RNA-seq reads, minimap2 may produce chimeric alignments > potentially caused by gene fusions/structural variations or by an > intron longer than the max intron length -G (200k by default). For > now, it is no ...
minimap2 chimeric nanopore written 9 weeks ago by Nicolas Rosewick6.0k • updated 9 weeks ago by Macspider2.2k
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Answer: A: How can I calculate coverage from the base frequencies file?
... in R : cov <- read_tsv("file.txt",col_names=c("Position","A","C","G","T")) tot <- cov %>% select(A,C,G,T) %>% sum cov <- cov %>% rowwise() %>% mutate(perc=sum(A,C,G,T)*100/tot) And to visualize ggplot(cov,aes(x=Position,y=perc))+geom_ba ...
written 9 weeks ago by Nicolas Rosewick6.0k

Latest awards to Nicolas Rosewick

Popular Question 3 days ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Great Question 12 days ago, created a question with more than 5,000 views. For Tophat Library-Type : Illumina Truseq Stranded Total Rna Sample Prep Kit
Popular Question 13 days ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Great Question 14 days ago, created a question with more than 5,000 views. For Tophat Library-Type : Illumina Truseq Stranded Total Rna Sample Prep Kit
Popular Question 14 days ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Popular Question 18 days ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Teacher 5 weeks 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?
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Scholar 9 weeks ago, created an answer that has been accepted. For C: How to increase cytoscape memory?
Prophet 10 weeks ago, created a post with more than 20 followers. For Tophat Library-Type : Illumina Truseq Stranded Total Rna Sample Prep Kit
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Scholar 11 weeks ago, created an answer that has been accepted. For C: How to increase cytoscape memory?
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
Scholar 3 months ago, created an answer that has been accepted. For C: How to increase cytoscape memory?
Scholar 3 months ago, created an answer that has been accepted. For C: How to increase cytoscape memory?
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
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: What Regulates Alternative Splicing And Intergenic Trans Splicing?

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