DNA Ghost:

This note based blog covers bioinformatics and cancer genomics 

July 30, 2020

  In PREVIOUS ARTICLE, we mentioned that Bayesian approach is being used for somatic variant detection. We will pick up this topic from here and spend two articles on building a site specific error model using MCMC for variant detection. Before walking into actual appl...

May 25, 2020

  In previous post, we mentioned that each locus across genome owns different noise rate due to variety of technical / biological factors. Bayesian method may better detect genuine variants by adding these factors into consideration. Before diving into more sophisticat...

May 25, 2020

 

  In previous POST, we discussed some basics of probability distribution and corresponding hypothesis testing. Here let's continue this topic and talk about the usage of probability distribution in NGS data analysis. More specifically, why do we choose what we choose...

February 7, 2020

  Bioinformatics is an interdisciplinary of biology (clinical medicine), computer science as well as statistics. To enable an in-depth biomedical / bioinformatics research, especially data driven research, researchers ought to have robust and intuitive understanding to...

January 20, 2020

In oncology research, it is a common goal to uncover specific molecular pattern of cancer. High-throughput sequencing has been become the routine approach to start with. However, sequencing technique such as RNA-Seq and bisulfite sequencing generates high dimension dat...

June 4, 2019

Survival analysis and logistic regression share certain similarities. The use of logistic regression for survival analysis, although not strictly correct due to data censoring in survival data, provides intuitive understanding. 

Logistic regression

Let's recall how...

January 30, 2019

When comes to a general bioinformatics task, there are always a bunch of tools on which we have to evaluate based on their underlying algorithm. Moreover, when we are about to build a model on our own, we again have to pick from a variety of ML model. How do we know wh...

December 27, 2018

Ghost recently did some research on cell type decomposition technique, specifically TIL decomposition in tumor sample. TIMER and CIBERSORT came across alone with their technical debates published on correspondence of Genome Biology. Li in Revisit linear regression-base...

December 3, 2018

Ghost came across this interesting figure on Cell Science and would like to take this opportunity to talk about tumor microenvironment. 

A route towards tumorigenesis

Tumor microenvironment is dynamic battlefield between tumor and immune system. This long-lasting ba...

November 30, 2018

Ghost encountered dimension reduction problem while designing a model aiming to describe patient's immuno-oncology (IO) status. The model is supposed to incorporate well-known immune related factors listed in the figure below (for factor selection details, please read...

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