User: Irsan

gravatar for Irsan
Irsan6.9k
Reputation:
6,920
Status:
Trusted
Location:
Amsterdam
Scholar ID:
Google Scholar Page
Last seen:
22 hours ago
Joined:
6 years, 9 months ago
Email:
i**********@gmail.com

PhD-student at Clinical Genetics, VU medical centre

Posts by Irsan

<prev • 496 results • page 2 of 50 • next >
2
votes
3
answers
2.3k
views
3
answers
Why does GISTIC require a markers file?
... In order to run [GISTIC(2.0)][1], you need at least: 1. Segmented copy numbers (.seg file, e.g. CBS output) 2. Gene annotation file in GISTIC format (refgene file) 3. A markers file that gives the genomic position of probes/windows that was used (before segmentation) I wonder what GISTIC does w ...
gistic copy number written 3.1 years ago by Irsan6.9k • updated 3.0 years ago by neelablore0
0
votes
2
answers
1.4k
views
2
answers
Comment: C: csv into genome browser
... Then make sure you have a VCF file, because that is the standard format for SNVs. IGV can import and visualize VCFs. ...
written 3.1 years ago by Irsan6.9k
1
vote
2
answers
1.4k
views
2
answers
Comment: C: csv into genome browser
... A csv file can contain anything. What kind of data are you talking about? single nucleotide variants/insertions & deletions, copy number, chipseq, methylation? ...
written 3.1 years ago by Irsan6.9k
0
votes
1
answer
1.1k
views
1
answers
Answer: A: CNV detection analysis using R or Matlab
... Use the off-target data to do copy number analysis, for example with CopyWriteR. Alo see this post: https://www.biostars.org/p/139385/ ...
written 3.1 years ago by Irsan6.9k
20
votes
0
answers
1.9k
views
0
answers
Blog: General recommendations for cancer genomics studies
... Dear fellow cancer researchers, In the last few years I have been working as a bio-informatician in a PhD-project aimed at improving retinoblastoma treatment and diagnosis through genomic characterization of human and murine tumor samples. Although retinoblastoma was my main project, I have been i ...
recommendations blog genomics cancer written 3.2 years ago by Irsan6.9k • updated 19 months ago by KevinL20
0
votes
0
answers
808
views
0
answers
Comment: C: Co-variants in differential expression analysis
... Do you know what you mean with co-variants? If you do, you should really be able to figure it out by reading the edgeR and/or limma vignettes like Devon said. ...
written 3.2 years ago by Irsan6.9k
1
vote
2
answers
2.7k
views
2
answers
Comment: C: mutation signature in cancer
... What people mean with a mutation signature varies a lot. I see that after you have explained that you mean the signatures defined by cosmic you got a useful answer. But still it is unclear for example whether you managed to process reads to variants, which is required input for the suggested prog ...
written 3.2 years ago by Irsan6.9k
0
votes
1
answer
766
views
1
answers
Comment: C: Can I identify differential expressing genes of 2 samples using only 4 chips?
... yes, that is possible. It is also very well possible that the power of your analysis is low. It also seems like you have 2 technical replicates per condition, which is a waste of money. If you have only one biological replicate, it is still possible to see what genes are differentially expressed bet ...
written 3.2 years ago by Irsan6.9k
0
votes
0
answers
2.4k
views
0
answers
Comment: C: Downregulated Genes with GFOLD
... If you have 34 cases and 34 controls, which are matched with each other, how come you say it is unreplicated? Are these 34 different experiments that have nothing to do with each other? ...
written 3.2 years ago by Irsan6.9k
1
vote
2
answers
2.7k
views
2
answers
Comment: C: mutation signature in cancer
... I don't think you will get any useful responses unless you explain a little bit more about your research rationale, study design, hypothesis etc. ...
written 3.2 years ago by Irsan6.9k

Latest awards to Irsan

Popular Question 3 months ago, created a question with more than 1,000 views. For Fastq Format Redundancy
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Titv Meaning
Good Answer 17 months ago, created an answer that was upvoted at least 5 times. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Good Answer 17 months ago, created an answer that was upvoted at least 5 times. For A: Random Genomic Regions Of A Given Length Distribution
Scholar 18 months ago, created an answer that has been accepted. For A: Bedtools Genomecoveragebed Usage : How To do per base coverage analysis for only
Popular Question 19 months ago, created a question with more than 1,000 views. For Cancer genomics journals
Popular Question 19 months ago, created a question with more than 1,000 views. For Fastq Format Redundancy
Appreciated 22 months ago, created a post with more than 5 votes. For C: Superimpose 2 Heatmaps
Popular Question 22 months ago, created a question with more than 1,000 views. For Revolution (?) in CNA detection using exome/targeted sequencing
Popular Question 22 months ago, created a question with more than 1,000 views. For Fastq Format Redundancy
Good Answer 22 months ago, created an answer that was upvoted at least 5 times. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Appreciated 22 months ago, created a post with more than 5 votes. For C: Conditional Coloring Of Heatmaps
Great Question 2.0 years ago, created a question with more than 5,000 views. For Why Is Stranded Rna Seq Better Than Unstranded?
Appreciated 2.0 years ago, created a post with more than 5 votes. For C: Superimpose 2 Heatmaps
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Does Bedops Have A Command Similar To The Bedtools Makewindows?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Revolution (?) in CNA detection using exome/targeted sequencing
Good Answer 2.3 years ago, created an answer that was upvoted at least 5 times. For A: Coverage Calculation
Epic Question 2.4 years ago, created a question with more than 10,000 views. For Why Is Stranded Rna Seq Better Than Unstranded?
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Monitor Hiseq Run Remotely Linux
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Titv Meaning
Epic Question 2.8 years ago, created a question with more than 10,000 views. For Why Is Stranded Rna Seq Better Than Unstranded?
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Mysql-Query On Go-Database Ucsc Server
Commentator 3.0 years ago, created a comment with at least 3 up-votes. For C: What Is The Difference Between Structural Variants (Svs) And Copy-Number Variant
Good Answer 3.1 years ago, created an answer that was upvoted at least 5 times. For A: Coverage Calculation

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1403 users visited in the last hour