基礎生物資訊統計學
Fundamental Statistical Methods in Bioinformatics (S1)
| 節 | 週四 |
|---|---|
2 09:00–09:50 | 基礎生物資訊統計學 3 節連堂 |
3 10:10–11:00 | |
4 11:10–12:00 |
* 根據陽明交大上課時間表所列
Outline: This course covers the fundamentals of statistics and basic tools for bioinformatics analysis. In the first part students will learn basic statistical concepts and methods, including probability, random variables and distributions, parameter estimation, hypothesis testing, regression analysis, and categorical data analysis. In the second part several commonly used methods in bioinformatics will be introduced, including statistical meta analysis, survival analysis, clustering, classification, and nonparametric statistics. : For Non-BP student to register/sit-in any BP course, it is required to gain course chair's permission and follow the steps: (1) Submit the hard copy or PDF file of the completed TIGP Bioinformatics Course Registration Consent Form to the TIGP BP office (2) Provide the information via the google form at BP Class Enrollment Information. The deadline for above requirement is the 4th week of each semester. Signature of corresponding BP Course Chair should be collected and incomplete form will not be accepted. ※Course grade will NOT be given (even class enrollment is completed at school) if fail to follow the above procedures. For the most up-to-date syllabus, please visit https://tigpbp.iis.sinica.edu.tw/tigpbio/index.html
Midterm exam 50%. Final exam 50%
| 週次 | 主題 |
|---|---|
| 第 1 週 | 2021/9/16@Webex (1) Introduction to statistics (2) Descriptive statistics (3) Fundamental of molecular biology (4) Genomic data analysis |
| 第 2 週 | 2021/9/23@Webex (1) Applications in statistical genetics (2) Combinatorial analysis (3) Axioms of probabilities (4) Conditional probability and independence (5) Random variable and distribution function |
| 第 3 週 | 2021/9/30@Webex (1) An application in pharmacogenetic study (2) Discrete/continuous/mixed distributions (3) Joint/marginal/conditional distributions (4) Special discrete distributions (5) Introduction to contingency table |
| 第 4 週 | 2021/10/7@Webex (1) Continuous random variable (2) Expectation (3) Basic statistics (4) Limit theorems (optional) |
| 第 5 週 | 2021/10/14 (1) Unbiasedness (2) Point estimation (substitution principles, least square estimate, maximum likelihood estimate) (3) Interval estimation |
| 第 6 週 | 2021/10/21 (1) Hypothesis testing (2) Applications in cancer researches (3) Type I & type II errors and p-value (4) One-sample and two-sample z-tests (5) One-sample, two-sample, and paired t-tests (6) Bonferroni adjustment, false discovery rate, and q value |
| 第 7 週 | 2021/10/28 Review Week |
| 第 8 週 | 2021/11/4 Midterm Exam |
| 第 9 週 | 2021/11/11 (1) Applications to predictions of drug responses (2) Simple linear regression & inference (3) Diagnostic and remedial measures Dr. Grace Shieh (4) Matrix approach to simple linear regression (5) Multiple linear regression (6) Building the regression model |
| 第 10 週 | 2021/11/18 (1) Mantel-Haenszel test (2) Survival and hazard functions (3) Kaplan Meier estimate (4) Log-rank test (5) Proportional-hazards model (6) Lung cancer study |
| 第 11 週 | 2021/11/25 (1) Logistic regression (2) Meta analysis (effect size, precision, study weights, summary effect, heterogeneity, fixed-effect model, random-effect model, software) |
| 第 12 週 | 2021/12/2 (1) Clustering by geometry (K-means, EM algorithm, hierarchical clustering, self- organizing map, principal component analysis, independent component analysis) (2) Clustering on graphs (Basic concepts, max flow – min cut, normal cuts, spectral clustering, and community detection) (3) Advanced topics (Chinese restaurant process and affinity propagation) |
| 第 13 週 | 2021/12/9 (1) Bootstrap (2) One-sample sign test (3) One-sample Wilcoxon signed-rank test (4) Wilcoxon rank-sum test (Mann-Whitney U test) (5) Sign test for paired data (6) Wilcoxon signed-rank test for paired data |
| 第 14 週 | 2021/12/16 (1) Kruskal-Wallis test (2) Randomization/permutation test for two-way ANOVA (3) The product-moment correlation coefficient (4) Spearman rank correlation (5) Kendall’s coefficient of rank correlation |
| 第 15 週 | 2021/12/23 Review Week |
| 第 16 週 | 2021/12/30 Final Exam |
| 第 17 週 | |
| 第 18 週 |