User: poisonAlien

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Cancer genomics

Posts by poisonAlien

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Answer: A: Software to analyse mutational signatures other than DeconstructSigs R package
... There are few other tools. DeconstructSigs estimates loading of known signatures for every sample in the cohort. If you are interested in de-novo you could try [EMu](http://www.sanger.ac.uk/science/tools/emu) and [Mutational Signature framework](https://www.mathworks.com/matlabcentral/fileexchange/3 ...
written 9 days ago by poisonAlien2.5k
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Comment: C: Script for analyzing idat (illumina) microarray files with limma, any suggestion
... Try [Here](https://github.com/PoisonAlien/beadAnalyze) ...
written 12 days ago by poisonAlien2.5k
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Comment: C: Driver gene detection with SomInaClust
... Hi, You're passing MAF object as an input for `SomInaClust_det` function. My guess is it requires MAF file as an input. May be try this and see... ```r brca_Sominaclust <- SomInaClust_det(maf_brca, calculate_CDS = TRUE, convert_genenames_to_HGNC=FALSE) ``` ...
written 5 weeks ago by poisonAlien2.5k
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Answer: A: how to decide whether a mutation is driver for a specific cell line
... Hi, Whether a gene is a driver or not is usually done on large cohorts based on how frequently the gene is mutated. There are algorithms to identify such genes. How many cell lines do you have in your file ? In case if you're only interested in a particular mutation, - you will have to look at ...
written 3 months ago by poisonAlien2.5k
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Answer: A: Annotation of ID from TCGA gene expression data
... They are Ensemble Gene IDs. See [here][1] for converting them to Gene symbols. [1]: http://www.ensembl.org/Help/Faq?id=125 ...
written 3 months ago by poisonAlien2.5k
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Comment: C: Installing ensembl 86 VEP and vcf2maf and getting SNP MAFs
... > The "MAF" in vcf2maf refers to "Mutation Annotation Format", which was > something unncessarily invented and confusingly named for cancer > genetics. So true! This also conflicts with [Multiple Alignment Format][1] [1]: https://cgwb.nci.nih.gov/FAQ/FAQformat.html#format5 ...
written 4 months ago by poisonAlien2.5k
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Answer: A: Tools to identify the non-coding RNAs
... Try [lncRNA-screen][1] [1]: https://github.com/NYU-BFX/lncRNA-screen ...
written 4 months ago by poisonAlien2.5k
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Job: Bioinformatician - Cancer Genomics, Cancer Science Institute of Singapore, NUS, Singapore.
... We are seeking a bright, energetic individual with superior bioinformatic skills who can interact with approximately 10-15 post-docs/Ph.D. students; each of them are doing massively parallel sequencing of various tumors, RNA-Seq, ChIP-Seq, RNA array as well as combing the bioinformatics literature f ...
wxs R chip-seq job rna-seq written 4 months ago by poisonAlien2.5k
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Comment: C: Why copy number variations of TCGA is so high
... I believe that the papers that you're mentioning are looking at population based cnv's rather than sample wise. TCGA uses gistic to identify recurrent CN aberration in a cohort, which are potentially driver events. Above file is a CBS output and not all entries are copy number alterations. Last co ...
written 5 months ago by poisonAlien2.5k
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Comment: C: Why copy number variations of TCGA is so high
... how did you look at TCGA cnv data? Was it from GISTIC output ? ...
written 5 months ago by poisonAlien2.5k

Latest awards to poisonAlien

Scholar 23 days ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Benefits of 150 bp reads over 100 bp reads in RNA-seq
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How to use Samtools to remove reads whose mate does not map as expected
Scholar 3 months ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Popular Question 4 months ago, created a question with more than 1,000 views. For questions on rna-seq data analysis
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Next Generation Sequencing
Popular Question 10 months ago, created a question with more than 1,000 views. For questions on rna-seq data analysis
Appreciated 11 months ago, created a post with more than 5 votes. For A: Is there any better method to find significant SNVs ?
Scholar 11 months ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Popular Question 11 months ago, created a question with more than 1,000 views. For questions on rna-seq data analysis
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: Next Generation Sequencing
Appreciated 12 months ago, created a post with more than 5 votes. For A: Is there any better method to find significant SNVs ?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Scholar 12 months ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Would you buy a BGI/ CompleGenomics Revolocity (X10 competitor)?
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Would you buy a BGI/ CompleGenomics Revolocity (X10 competitor)?
Scholar 12 months ago, created an answer that has been accepted. For A: Is there a good manual/tutorial for TreeView?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Comparing vcf with dbSNP
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Next Generation Sequencing
Appreciated 16 months ago, created a post with more than 5 votes. For A: Is there any better method to find significant SNVs ?

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