User: Dawe

gravatar for Dawe
Dawe260
Reputation:
260
Status:
Trusted
Location:
Milan
Twitter:
daweonline
Last seen:
4 months, 1 week ago
Joined:
8 years, 4 months ago
Email:
d*********@gmail.com

Posts by Dawe

<prev • 16 results • page 1 of 2 • next >
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Answer: A: Why NMF for mutation signature analysis
... Basically any blind sourc separation method should work. The reason people use NMF is probably because it is simple and effective. BTW, you may find criticism and different flavors here https://www.biorxiv.org/content/early/2018/08/04/384834 d ...
written 4 months ago by Dawe260
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Answer: A: Reasons to refuse to give support
... Here’s what we do: in a true collaboration we take part to the conception of the experiment from the very beginning, we discuss which conditions should be met, which should be avoided. Of course there may be some borderline cases (e.g. unique samples in the sense they are extremely rare), we discuss ...
written 4 months ago by Dawe260
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Comment: C: 1000 Genomes exomes as controls
... I have now the very same problem. Did you find any valuable resource? I'm reading the original paper by Neale trying to implement c-alpha test based on allele counts found in ExAC data. In principle you won't need individual genotypes, only allele counts. Unfortunately the methodology described has ...
written 2.4 years ago by Dawe260
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Using offsets in edgeR to correct GC content
... Hi all, I'm performing some differential analysis with edgeR and I need to take into account GC content in my regions. From edgeR manual I see I should set GC percentage as "offset" in linear model. Unfortunately there is very little documentation about this, so I need some hint. Offsets can be pa ...
R gc linear models edger written 2.8 years ago by Dawe260 • updated 2.5 years ago by javiergutierreza30
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Job: Computational biologist @ Center for Translational Genomics and Bioinformatics (Milan)
... The Center of Translational Genomics and Bioinformatics (CTGB) is seeking a profile in collaboration with the Pathogenesis and Therapy of Primary Immunodeficiencies unit at SR-TIGET. The role will involve: - analysis of NGS data, with a focus on Exome Sequencing and Targeted Resequencing data for ...
immunodeficiency exome sequencing job gene therapy written 2.9 years ago by Dawe260
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Job: Computational biologist, analysis oriented, Center of Translational Genomics and Bioinformatics, Milan, Italy
... The Center of Translational Genomics and Bioinformatics (CTGB) is seeking a profile to reinforce the core team responsible for analysis of omics data generated by the Genomics Unit. The role will involve: analysis of NGS data, including the integration of different data sources, in collaboration ...
epigenome genomics rna-seq job written 3.8 years ago by Dawe260 • updated 3.8 years ago by Istvan Albert ♦♦ 79k
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Job: Computational biologist, programming oriented, Center of Translational Genomics and Bioinformatics, Milan, Italy
... The Center of Translational Genomics and Bioinformatics (CTGB) is seeking a motivated individual to reinforce the development team responsible for original analytical tools and platforms. The role will involve: development of libraries and tools for the analysis of sequencing data participat ...
core job genomics programming written 3.8 years ago by Dawe260 • updated 3.8 years ago by Istvan Albert ♦♦ 79k
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Filtering Pindel Results
... Dear all, I've been running pindel on a set of BAM files. I've then converted files to vcf using pindel2vcf utility. Which rules would apply to tell if a variant is likely to be present in a sample (or sample set)? I mean, if I have a variant with 10 reads in one sample and 2 reads in another (both ...
filter coverage pindel written 5.9 years ago by Dawe260 • updated 5.9 years ago by liangkaiye250
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Answer: A: Cross-Correlation On Chip-Seq Like Data?
... I'm kind of interested in this topic. I'm developer of a package for digital signal processing of quantitative genomic data (such as ChIP-seq). Cross-correlation is something I was implementing too, although I had some issues with the border effect, and also I was not sure xcorr is a proper measure ...
written 8.0 years ago by Dawe260
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Answer: A: Proteolysis Of A Protein Sequence
... There should be a plenty of such scripts. BTW, you can look at function "cleave" (line 764) in this source http://code.google.com/p/nsilk/source/browse/trunk/xllib/sequence.py?r=143 Nsilk is a python tool to spot protein-protein interactions, but that function will predict peptides from a sequence. ...
written 8.3 years ago by Dawe260

Latest awards to Dawe

Popular Question 2.3 years ago, created a question with more than 1,000 views. For Evidences For Choice Of Ngs Instrument
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Filtering Pindel Results
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Filtering Pindel Results
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Filtering Pindel Results
Teacher 5.9 years ago, created an answer with at least 3 up-votes. For A: Cross-Correlation On Chip-Seq Like Data?
Teacher 5.9 years ago, created an answer with at least 3 up-votes. For A: What Parameters Do You Use With Findpeaks For Chip Seq Peak Calling?
Teacher 5.9 years ago, created an answer with at least 3 up-votes. For A: How To Combine Multiple Wig/Bigwig Files Into One
Teacher 5.9 years ago, created an answer with at least 3 up-votes. For A: Open Source Mass Spec Search Engines?
Student 5.9 years ago, asked a question with at least 3 up-votes. For Filtering Pindel Results

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