leanpub/filenames.txt at master · genomicsclass/leanpub · GitHub

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## Chapter 0 - Introduction
intro introduction
intro getting_started
intro_exercises getting_started_exercises
intro dplyr_intro dplyr_introduction
intro_exercises dplyr_intro_exercises dplyr_introduction_exercises
intro math_notation Mathematical_notation

## Chapter 1 - Inference
inference random_variables
inference_exercises random_variables_exercises
inference populations_and_samples
inference_exercises populations_and_samples_exercises
inference clt_and_t-distribution CLT_and_t-distribution
inference_exercises clt_and_t-distribution_exercises CLT_and_t-distribution_exercises
inference clt_in_practice CLT_in_practice
inference_exercises clt_in_practice_exercises CLT_in_practice_exercises
inference t-tests_in_practice t-test_in_practice
inference confidence_intervals
inference power_calculations
inference_exercises power_calculations_exercises
inference monte_carlo
inference_exercises monte_carlo_exercises
inference permutation_tests
inference_exercises permutation_tests_exercises
inference association_tests
inference_exercises association_tests_exercises

## Chapter 2 - Exploratory Data Analysis
eda exploratory_data_analysis
eda plots_to_avoid
eda_exercises exploratory_data_analysis_exercises

## Chapter 3 - Robust Statistics
robust robust_summaries
robust ranktest Rank_tests
robust_exercises robust_summaries_exercises

## Chapter 4 - Matrix Algebra
matrixalg intro_using_regression Introduction_to_using_regression
matrixalg_exercises intro_using_regression_exercises Introduction_to_using_regression_exercises
matrixalg matrix_notation
matrixalg_exercises matrix_notation_exercises
matrixalg matrix_operations
matrixalg_exercises matrix_operations_exercises
matrixalg matrix_algebra_examples
matrixalg_exercises matrix_algebra_examples_exercises

## Chapter 5 - Linear Models
linear linear_models_intro Linear_models_introduction
linear_exercises linear_models_intro_exercises Linear_models_introduction_exercises
linear expressing_design_formula
linear_exercises expressing_design_formula_exercises
linear linear_models_in_practice
linear_exercises linear_models_in_practice_exercises
linear standard_errors
linear_exercises standard_errors_exercises
linear interactions_and_contrasts
linear_exercises interactions_and_contrasts_exercises
linear collinearity
linear_exercises collinearity_exercises
linear qr_and_regression QR_and_regression
linear linear_models_going_further

## Chapter 6 - Inference for High-Dimensional Data
advinference intro_to_highthroughput_data Introduction_to_high-throughput_data
advinference_exercises intro_to_highthroughput_data_exercises Introduction_to_high-throughput_data_exercises
advinference inference_for_highthroughput Inference_for_high-throughput_data
advinference_exercises inference_for_highthroughput_exercises Inference_for_high-throughput_data_exercises
advinference multiple_testing
advinference_exercises multiple_testing_exercises
advinference eda_for_highthroughput EDA_for_high-throughput_data
advinference_exercises eda_for_highthroughput_exercises EDA_for_high-throughput_data_exercises

## Chapter 7 - Statistical Modeling
modeling modeling
modeling_exercises modeling_exercises
modeling bayes Bayes_theorem
modeling_exercises bayes_exercises Bayes_theorem_exercises
modeling hierarchical_models
modeling_exercises hierarchical_models_exercises

## Chapter 8 - Distance and Dimension Reduction
highdim distance
highdim_exercises distance_exercises
highdim pca_motivation PCA_motivation
highdim svd SVD
highdim_exercises svd_exercises SVD_exercises
highdim projections
highdim rotations
highdim mds MDS
highdim_exercises mds_exercises MDS_exercises
highdim PCA

## Chapter 9 - Practical Machine Learning
ml clustering_and_heatmaps
ml_exercises clustering_and_heatmaps_exercises
ml conditional_expectation
ml_exercises conditional_expectation_exercises
ml smoothing
ml_exercises smoothing_exercises
ml machine_learning
ml crossvalidation
ml_exercises crossvalidation_exercises

## Chapter 10 - Batch Effects
batch intro_to_batch_effects Introduction_to_batch_effects
batch confounding
batch_exercises confounding_exercises
batch eda_with_pca EDA_with_PCA
batch_exercises eda_with_pca_exercises EDA_with_PCA_exercises
batch adjusting_with_linear_models
batch_exercises adjusting_with_linear_models_exercises
batch factor_analysis
batch_exercises factor_analysis_exercises
batch adjusting_with_factor_analysis
batch_exercises adjusting_with_factor_analysis_exercises