Sequencing | DNA Ghost | United States

DNA Ghost:

This note based blog covers bioinformatics and cancer genomics

The power of biological replicates in statistical analysis

MCMC II: Applying MCMC in somatic variant calling

MCMC: Monte Carlo sampling and Markov Chain

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A glance into tumor microenvironment

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

Dimension reduction in RNA-Seq based model

Ghost encountered dimension reduction problem while designing a model aiming to describe patient's immuno-oncology (IO) status. The model...

Propose a new way of tumor classification for immuno-oncology

First things first, the proposed classification are immune suppressing and immune escaping. Now let's go back for some specifics. Immuno-...

Developing cancer vaccine: Neoantigen identification and beyond

Immunotherapy has been the hot spot in cancer treatment in recent years. As a key component, neoantigen identification is usually done bi...

Depicting tumor clonal evolution

Tumor clonal evolution Cancer is stubborn largely due to its nature of heterogeneity: they evolve to adjust the changes of surrounding en...

Calling somatic variants without matched normal

Identifying somatic mutation has always been challenging. Tumor heterogeneity The major challenge of calling somatic mutation is heteroge...

From variant calling approach: Frequentist vs Bayesian

Frequentist's approach: Assume sequencing error distribution. Frequentist's method makes the null hypothesis that non-reference allele is...

CNV detection II: Tumor CNV calling without matched normal

Ghost wrote a blog regarding tumor CNV calling with matched normal earlier. Here let's talk about what we can do when matched normal is n...

Neural network: Escaping from non-global minimum traps

Deep learning has been the hot spot in recent years and shown excellent performance in many applications. In bioinformatics, Google has d...

Matching cancer ontology with recurrent neural network

For people who have tried to build an oncology database or automated pipeline, one of the task is to define a standardized cancer type te...

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