User: Nicolas Rosewick

gravatar for Nicolas Rosewick
Reputation:
5,320
Status:
Trusted
Location:
Belgium, Brussels, Université Libre de Bruxelles / Université de Liège
Website:
https://nrosewick.gith...
Twitter:
nrosewick
Scholar ID:
Google Scholar Page
Last seen:
3 days, 9 hours ago
Joined:
6 years, 1 month ago
Email:
n***************@gmail.com

Posts by Nicolas Rosewick

<prev • 647 results • page 1 of 65 • next >
1
vote
0
answers
136
views
0
answers
Comment: C: R: How to test for trend of risk scores
... As phenotype is either 0 or 1 could you just do a fisher test as : fisher.test(score,phenotype) Could also be nice to plot the data as boxplots (x is the data.frame containing your data): ggplot(x,aes(x=score,y=score))+geom_boxplot() ...
written 11 days ago by Nicolas Rosewick5.3k
3
votes
1
answer
196
views
1
answers
Comment: C: No ensemble ID for gene ID
... FYI it's ENSEMBL not ENSEMBL**E** ;) ...
written 16 days ago by Nicolas Rosewick5.3k
1
vote
1
answer
174
views
1
answers
Comment: C: Differential expressed genes in DESeq
... Yes. You can check the normalized read counts for ENSG00000132002 to be sure. norm_count <- counts(dds,normalized=T) ...
written 18 days ago by Nicolas Rosewick5.3k
0
votes
1
answer
174
views
1
answers
Comment: C: Differential expressed genes in DESeq
... Yes , as Devon explain the sign of the log2FC tells you the direction of change. In the case of ENSG00000132002.6 the log2FC is -1.3096108594, thus foldchange = 2^-1.3096108594 = 0.4034297 so 2.478747 (1/0.4034297) times less expressed. ...
written 18 days ago by Nicolas Rosewick5.3k
1
vote
2
answers
170
views
2
answers
Comment: C: how to combine multiple fasta file into a larger fasta file
... use command line : `cat * > all.fasta` ...
written 24 days ago by Nicolas Rosewick5.3k
2
votes
2
answers
329
views
2
answers
Answer: A: Is this RNA-seq data reliable?
... prior alignment you could also use fastqc : https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ to assess the quality of your reads ...
written 4 weeks ago by Nicolas Rosewick5.3k
0
votes
2
answers
233
views
2
answers
Answer: A: Is it fair to compare the significance of overlap of 2 different sized gene sets
... You can use superExactTest R package for this : https://cran.r-project.org/web/packages/SuperExactTest/vignettes/set_html.html ...
written 6 weeks ago by Nicolas Rosewick5.3k
0
votes
1
answer
226
views
1
answers
Comment: C: Is PICARD CollectInsertSizeMetrics use soft-clipping information to compute the
... ok thanks. FYI I used bowtie2 ...
written 6 weeks ago by Nicolas Rosewick5.3k
2
votes
1
answer
226
views
1
answer
Is PICARD CollectInsertSizeMetrics use soft-clipping information to compute the insert size ?
... Hi, I've a basic question concerning picard CollectInsertSizeMetrics (tool that computes insert size metrics). Are the soft-clipping bases take into account for the insert size measure ? Here's a quick draw of my question. So is the insert size computed x (without soft-clipping) or y (with soft-cl ...
picard insert size soft-clipping written 6 weeks ago by Nicolas Rosewick5.3k • updated 6 weeks ago by Pierre Lindenbaum98k
0
votes
0
answers
158
views
0
answers
GRanges : setdiff and keep extra columns
... Hi, I've two GRanges as : > gene.pos.gr GRanges object with 63677 ranges and 1 metadata column: seqnames ranges strand | ensembl_gene_id | [1] HG991_PATCH [66119285, 66465398] + | ENSG00000261 ...
genomicranges written 9 weeks ago by Nicolas Rosewick5.3k

Latest awards to Nicolas Rosewick

Great Question 10 days ago, created a question with more than 5,000 views. For Tophat: Compressed Fastq File (Gz)
Great Question 12 days ago, created a question with more than 5,000 views. For Tophat: Compressed Fastq File (Gz)
Student 12 days ago, asked a question with at least 3 up-votes. For Tophat: Compressed Fastq File (Gz)
Commentator 16 days ago, created a comment with at least 3 up-votes. For C: What Regulates Alternative Splicing And Intergenic Trans Splicing?
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Good Question 6 weeks ago, asked a question that was upvoted at least 5 times. For Best Bioinformatic And Molecular Biology Software Package
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Scholar 10 weeks ago, created an answer that has been accepted. For C: How to increase cytoscape memory?
Teacher 10 weeks 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
Student 3 months ago, asked a question with at least 3 up-votes. For Tophat: Compressed Fastq File (Gz)
Popular Question 3 months 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
Student 4 months ago, asked a question with at least 3 up-votes. For Tophat: Compressed Fastq File (Gz)
Popular Question 4 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 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
Scholar 5 months ago, created an answer that has been accepted. For C: How to increase cytoscape memory?
Popular Question 6 months ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Student 7 months ago, asked a question with at least 3 up-votes. For Tophat: Compressed Fastq File (Gz)
Popular Question 7 months ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Popular Question 8 months ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Popular Question 8 months ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: What Regulates Alternative Splicing And Intergenic Trans Splicing?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 733 users visited in the last hour