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Created a new configuration file (myst.yml) to define project metadata, structure, and navigation per jupyter book 2.x
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_config.yml renamed to ._config.yml.bak

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_toc.yml renamed to ._toc.yml.bak

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‎myst.yml‎

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version: 1
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project:
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title: Neural Data Science in Python
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authors:
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- name: Aaron J Newman
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copyright: >-
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2020-23. This work is licensed under a Creative Commons
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Attribution-NonCommercial-ShareAlike 4.0 Unported License
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exclude:
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- _build
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- Thumbs.db
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- .DS_Store
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- '**.ipynb_checkpoints'
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github: neural-data-science/NESC_3505_textbook
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bibliography:
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- references.bib
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toc:
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- file: intro.md
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- title: About This Course
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children:
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- file: 1-intro/why.md
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- file: 1-intro/learning_objectives.md
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- file: syllabus.md
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- file: 1-intro/learning_approach.md
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children:
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- file: 1-intro/actually_write_code.md
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- file: 1-intro/mindset.md
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- file: 1-intro/flipped_classroom.md
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- file: 1-intro/errors_debugging.md
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- file: 1-intro/ai.md
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- file: 1-intro/teamwork.md
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- file: 1-intro/pedagogy.md
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children:
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- file: 1-intro/teaching_approach.md
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- file: 1-intro/authenticity.md
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- file: 1-intro/21st_cen_skills.md
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- file: 1-intro/constructivism.md
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- file: 1-intro/connectivism.md
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- file: 1-intro/open.md
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children:
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- file: 1-intro/software.md
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- file: 1-intro/free_licenses.md
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- file: 1-intro/open_science.md
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- file: 1-intro/peer_review.md
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- file: 1-intro/for_profit.md
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- file: 1-intro/impact_factors.md
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- file: 1-intro/novelty.md
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- file: 1-intro/open_publishing.md
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- file: 1-intro/preregistration.md
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- file: 1-intro/open_methods.md
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- file: 1-intro/oer.md
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- file: 1-intro/oer_this_course.md
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- file: 1-intro/licenses.md
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- title: Introduction to Data Science
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children:
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- file: 2-nds/introduction.md
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- file: 2-nds/learning_objectives.md
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- file: 2-nds/what_is_nds.md
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children:
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- file: 2-nds/data.md
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- file: 2-nds/where.md
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- file: 2-nds/data_science.md
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- file: 2-nds/data_cleaning.md
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- file: 2-nds/tools_for_nds.md
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children:
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- file: 2-nds/spreadsheets.md
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- file: 2-nds/spreadsheets_limits.md
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- file: 2-nds/reproducibility.md
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- file: 2-nds/sci_prog_lang.md
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- file: 2-nds/which_lang.md
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- file: 2-nds/libs.md
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- file: 2-nds/why_python.md
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- file: 2-nds/coding.md
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children:
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- file: 2-nds/python.md
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- file: 2-nds/terminal.md
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- file: 2-nds/jupyter.md
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- file: 2-nds/markdown.md
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- file: 2-nds/vscode.md
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- file: 2-nds/github.md
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- title: Set Up Your Computer for Data Science
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children:
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- file: 2b-setup/introduction.md
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- file: 2b-setup/learning_objectives.md
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- file: 2b-setup/first_steps.md
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children:
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- file: 2b-setup/github.md
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- file: 2b-setup/codespaces.md
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- file: 2b-setup/github_classroom.md
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- file: 2b-setup/install_tools.md
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children:
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- file: 2b-setup/anaconda.md
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- file: 2b-setup/miniconda.md
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- file: 2b-setup/vscode.md
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- file: 2b-setup/github_desktop.md
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- file: 2b-setup/first_repo.md
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children:
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- file: 2b-setup/clone.md
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- file: 2b-setup/github_repo.md
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- file: 2b-setup/repo_in_vscode.md
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- file: 2b-setup/edit_commit_push.md
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- file: 2b-setup/edit_readme.md
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- file: 2b-setup/new_markdown_file.md
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- file: 2b-setup/getting_help.md
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- file: 2b-setup/submitting_assignments.md
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- title: Introducing Python
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children:
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- file: 3-python/introduction.md
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- file: 3-python/learning_objectives.md
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- file: 3-python/preliminaries.md
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children:
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- file: 3-python/jupyter_intro.ipynb
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- file: 3-python/getting_help.md
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- file: 3-python/data_types.md
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children:
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- file: 3-python/variables_assignment.ipynb
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- file: 3-python/types_conversion.ipynb
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- file: 3-python/builtin.ipynb
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- file: 3-python/lists.ipynb
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- file: 3-python/dictionaries.ipynb
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- file: 3-python/flow_control.md
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children:
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- file: 3-python/for_loops.ipynb
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- file: 3-python/conditionals.ipynb
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- file: 3-python/working_w_data.md
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children:
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- file: 3-python/pandas_dataframes.ipynb
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- file: 3-python/looping_data_files.ipynb
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- title: AI-Assisted Coding
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children:
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- file: 3b-ai_assisted/introduction.md
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- file: 3b-ai_assisted/ai_assisted.ipynb
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- file: 3b-ai_assisted/rt_data.ipynb
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- file: 3b-ai_assisted/pandas_copilot.ipynb
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- file: 3b-ai_assisted/multi_data_files.ipynb
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children:
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- file: 3b-ai_assisted/multi_data_files_1.ipynb
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- file: 3b-ai_assisted/multi_data_files_2.ipynb
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- file: 3b-ai_assisted/multi_data_files_3.ipynb
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- title: Visualizing Data
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children:
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- file: 4-viz/introduction.md
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- file: 4-viz/learning_objectives.md
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- file: 4-viz/plotting.ipynb
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- file: 4-viz/proc_vs_oo.ipynb
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- file: 4-viz/subplots.ipynb
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- file: 4-viz/plotting_types.ipynb
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- file: 4-viz/seaborn.ipynb
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- file: 4-viz/human_factors.ipynb
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- title: Exploratory Data Analysis
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children:
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- file: 5-eda/introduction.md
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- file: 5-eda/learning_objectives.md
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- file: 5-eda/repeated_measures.ipynb
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- file: 5-eda/data_cleaning.ipynb
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- file: 5-eda/ttests.ipynb
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- title: Single Unit Data
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children:
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- file: 6-single_unit/introduction.md
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- file: 6-single_unit/learning_objectives.md
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- file: 6-single_unit/single_unit_intro.md
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children:
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- file: 6-single_unit/intro_spike_trains.ipynb
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- file: 6-single_unit/ten_intensities.ipynb
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- file: 6-single_unit/heat_maps.ipynb
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- file: 6-single_unit/intro_multielec_data.ipynb
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children:
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- file: 6-single_unit/pandas_multielec.ipynb
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- file: 6-single_unit/corr_spike_trains.ipynb
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- title: EEG Data
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children:
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- file: 7-eeg/introduction.md
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- file: 7-eeg/learning_objectives.md
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- file: 7-eeg/about_eeg.md
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- file: 7-eeg/approaches.md
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children:
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- file: 7-eeg/time_freq.md
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- file: 7-eeg/erps.md
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- file: 7-eeg/components.md
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- file: 7-eeg/mne_python.md
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children:
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- file: 7-eeg/mne_data_1.ipynb
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- file: 7-eeg/mne_data_2.ipynb
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- file: 7-eeg/erp_preprocessing.ipynb
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children:
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- file: 7-eeg/erp_filtering.ipynb
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- file: 7-eeg/erp_artifacts.ipynb
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- file: 7-eeg/erp_segmentation.ipynb
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- file: 7-eeg/erp_avg_reref.ipynb
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- file: 7-eeg/erp_group.md
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children:
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- file: 7-eeg/erp_group_viz.ipynb
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- file: 7-eeg/erp_group_stats.ipynb
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- title: MRI Data
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children:
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- file: 8-mri/introduction.md
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- file: 8-mri/learning_objectives.md
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- file: 8-mri/read_viz.ipynb
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- file: 8-mri/nifti.ipynb
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- file: 8-mri/fmri_glm.ipynb
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- title: Machine Learning
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children:
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- file: 9-machine_learning/introduction.md
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- title: References
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children:
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- file: zrefs.md
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site:
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options:
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logo: images/NESC3505_icon.png
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favicon: images/NESC3505_favicon.png
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analytics_google: G-1SNTM6T50K
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folders: true
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template: book-theme

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