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1 | | -# Biomedical-Data-Science |
| 1 | +# Biomedical-Data-Science |
| 2 | +This is a graduate-level course covering the fundamentals of transparent and reproducible bioinformatics, targeted towards biomedical students. |
| 3 | + |
| 4 | +Lab01.ipynb: |
| 5 | +Introduces basic Unix commands commonly used in bioinformatics workflows. |
| 6 | +Covers commands like ls, cd, and file manipulation in a Unix environment. |
| 7 | + |
| 8 | +Lab02.ipynb: |
| 9 | +Focuses on Unix scripting to automate tasks in bioinformatics. |
| 10 | +Demonstrates how to create simple scripts using bash for handling repetitive tasks. |
| 11 | + |
| 12 | +Lab03.ipynb: |
| 13 | +Introduces Python programming for bioinformatics applications. |
| 14 | +Covers basic syntax, data types, and control structures relevant to biological data analysis. |
| 15 | + |
| 16 | +Lab04.ipynb: |
| 17 | +Provides a setup guide and initial steps for using bioinformatics tools. |
| 18 | +Guides users through configuring their environment for data analysis. |
| 19 | + |
| 20 | +Lab05.ipynb: |
| 21 | +Continues with setting up the computational environment for bioinformatics workflows. |
| 22 | +Covers additional configuration steps and essential bioinformatics software. |
| 23 | + |
| 24 | +Lab06.ipynb: |
| 25 | +Further explores bioinformatics tools and environment setup for analysis. |
| 26 | +Introduces key tools and libraries used in data handling and analysis. |
| 27 | + |
| 28 | +Lab07.ipynb: |
| 29 | +Introduces Git and GitHub for version control in bioinformatics projects. |
| 30 | +Guides users through repository creation, committing changes, and collaborating on code. |
| 31 | + |
| 32 | +Lab08.ipynb: |
| 33 | +Explores the use of R in bioinformatics through Google Colaboratory. |
| 34 | +Introduces basic R syntax and data manipulation techniques in a cloud environment. |
| 35 | + |
| 36 | +Lab09.ipynb: |
| 37 | +Introduces the use of Salmon for transcript quantification in RNA-seq data. |
| 38 | +Demonstrates how to align reads and interpret output files for gene expression analysis. |
| 39 | + |
| 40 | +Lab10.ipynb: |
| 41 | +Guides users through working with a reference genome and sequence data. |
| 42 | +Demonstrates file manipulation using commands like head and visualization of genomic data. |
| 43 | + |
| 44 | +Lab11.ipynb: |
| 45 | +Covers the setup of Miniconda and Mamba for managing bioinformatics environments. |
| 46 | +Introduces the use of Mamba for faster package management and environment handling. |
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