Minor Allele Frequency Minor allele frequency (MAF) is the frequency at which the second most common allele occurs in a given population. They play a surprising role in heritability since MAF v...
Implementing DAG in Python
Workflow Oriented Why are DAGs good for task dependencies? The ‘G’ in DAG is ‘Graph’. A Graph is a collection of nodes and edges that connect the nodes. For our purposes, each node would be a t...
Topological Network Parameters
Connected components A component is a maximal connected subgraph. In undirected networks, two nodes are connected if there is a path of edges between them. All nodes that are pairwise connect...
Proteomics Informatics (Task 4)
Basic Information Doncheva NT, Assenov Y, Domingues FS, Albrecht M. Topological analysis and interactive visualization of biological networks and protein structures. Nat Protoc. 2012;7(4):670‐6...
Introduction to DESeq2
Goal Want their normalization to handle: Differences in library sizes Differences in library composition The goal is calculate a scaling factor for each factor. The scaling factor has to t...
Artificial Intelligence
Machine Learning Tom M. Mitchell Method 以认知科学为基础、数学方法为手段、可计算理论为标准、分析数据规律为目标、计算机技术为实现途径，沿着这样的路径，构建机器学习的理论、技术、方法、应用体系 (李凡长) 机器学习5原理 机器学习可解释原理 机器学习可学习原理 机器学习可泛化原理 机器学习自学习原理 机器学...
Experiment of Clinical Genomics Course
Basic Information This is a experiment guidence. Databases ClinVar annotate with existing data big (a large amount of data) ClinGen expert reviewed a...
Sequence Identity & Similarity & Homology
Introduction identity and similarity are very often used interchangeably (for nucleotide sequence or in the context of graph theory) Sequence Identity Sequence identity is the amount of c...
Weighted Gene Co-expression Network Analysis
Standard differential expression analyses seek to identify individual genes Each gene is treated as an individual entity Often misses the forest for the trees: Fails to recognize t...
Introduction to Gromacs
Steps to Run MD Simulation Prepare Your System Create Molecule: -avogadro Create Topology: -topologn gmx insert-molecules gmx solvate gmx grompp gmx gen...