دانلود کتاب Bioinformatics with Python Cookbook: Use modern Python libraries and applications to solve real-world computational biology problems

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Cover
Title Page
Copyright and Credits
Contributors
Table of Contents
Preface
Chapter 1: Python and the Surrounding Software Ecology
Installing the required basic software with Anaconda
Getting ready
How to do it...
There’s more...
Installing the required software with Docker
Getting ready
How to do it...
See also
Interfacing with R via rpy2
Getting ready
How to do it...
There’s more...
See also
Performing R magic with Jupyter
Getting ready
How to do it...
There’s more...
See also
Chapter 2: Getting to Know NumPy, pandas, Arrow, and Matplotlib
Using pandas to process vaccine-adverse events
Getting ready
How to do it...
There’s more...
See also
Dealing with the pitfalls of joining pandas DataFrames
Getting ready
How to do it...
There’s more...
Reducing the memory usage of pandas DataFrames
Getting ready
How to do it…
See also
Accelerating pandas processing with Apache Arrow
Getting ready
How to do it...
There’s more...
Understanding NumPy as the engine behind Python data science and bioinformatics
Getting ready
How to do it…
See also
Introducing Matplotlib for chart generation
Getting ready
How to do it...
There’s more...
See also
Chapter 3: Next-Generation Sequencing
Accessing GenBank and moving around NCBI databases
Getting ready
How to do it...
There’s more...
See also
Performing basic sequence analysis
Getting ready
How to do it...
There’s more...
See also
Working with modern sequence formats
Getting ready
How to do it...
There’s more...
See also
Working with alignment data
Getting ready
How to do it...
There’s more...
See also
Extracting data from VCF files
Getting ready
How to do it...
There’s more...
See also
Studying genome accessibility and filtering SNP data
Getting ready
How to do it...
There’s more...
See also
Processing NGS data with HTSeq
Getting ready
How to do it...
There’s more...
Chapter 4: Advanced NGS Data Processing
Preparing a dataset for analysis
Getting ready
How to do it…
Using Mendelian error information for quality control
How to do it…
There’s more…
Exploring the data with standard statistics
How to do it…
There’s more…
Finding genomic features from sequencing annotations
How to do it…
There’s more…
Doing metagenomics with QIIME 2 Python API
Getting ready
How to do it...
There’s more...
Chapter 5: Working with Genomes
Technical requirements
Working with high-quality reference genomes
Getting ready
How to do it...
There’s more...
See also
Dealing with low-quality genome references
Getting ready
How to do it...
There’s more...
See also
Traversing genome annotations
Getting ready
How to do it...
There’s more...
See also
Extracting genes from a reference using annotations
Getting ready
How to do it...
There’s more...
See also
Finding orthologues with the Ensembl REST API
Getting ready
How to do it...
There’s more...
Retrieving gene ontology information from Ensembl
Getting ready
How to do it...
There’s more...
See also
Chapter 6: Population Genetics
Managing datasets with PLINK
Getting ready
How to do it...
There’s more...
See also
Using sgkit for population genetics analysis with xarray
Getting ready
How to do it...
There’s more...
Exploring a dataset with sgkit
Getting ready
How to do it...
There’s more...
See also
Analyzing population structure
Getting ready
How to do it...
See also
Performing a PCA
Getting ready
How to do it...
There’s more...
See also
Investigating population structure with admixture
Getting ready
How to do it...
There’s more...
Chapter 7: Phylogenetics
Preparing a dataset for phylogenetic analysis
Getting ready
How to do it...
There’s more...
See also
Aligning genetic and genomic data
Getting ready
How to do it...
Comparing sequences
Getting ready
How to do it...
There’s more...
Reconstructing phylogenetic trees
Getting ready
How to do it...
There’s more...
Playing recursively with trees
Getting ready
How to do it...
There’s more...
Visualizing phylogenetic data
Getting ready
How to do it...
There’s more...
Chapter 8: Using the Protein Data Bank
Finding a protein in multiple databases
Getting ready
How to do it...
There’s more
Introducing Bio.PDB
Getting ready
How to do it...
There’s more
Extracting more information from a PDB file
Getting ready
How to do it...
Computing molecular distances on a PDB file
Getting ready
How to do it...
Performing geometric operations
Getting ready
How to do it...
There’s more
Animating with PyMOL
Getting ready
How to do it...
There’s more
Parsing mmCIF files using Biopython
Getting ready
How to do it...
There’s more
Chapter 9: Bioinformatics Pipelines
Introducing Galaxy servers
Getting ready
How to do it…
There’s more
Accessing Galaxy using the API
Getting ready
How to do it…
Deploying a variant analysis pipeline with Snakemake
Getting ready
How to do it…
There’s more
Deploying a variant analysis pipeline with Nextflow
Getting ready
How to do it…
There’s more
Chapter 10: Machine Learning for Bioinformatics
Introducing scikit-learn with a PCA example
Getting ready
How to do it...
There’s more...
Using clustering over PCA to classify samples
Getting ready
How to do it...
There’s more...
Exploring breast cancer traits using Decision Trees
Getting ready
How to do it...
Predicting breast cancer outcomes using Random Forests
Getting ready
How to do it…
There’s more...
Chapter 11: Parallel Processing with Dask and Zarr
Reading genomics data with Zarr
Getting ready
How to do it...
There’s more...
See also
Parallel processing of data using Python multiprocessing
Getting ready
How to do it...
There’s more...
See also
Using Dask to process genomic data based on NumPy arrays
Getting ready
How to do it...
There’s more...
See also
Scheduling tasks with dask.distributed
Getting ready
How to do it...
There’s more...
See also
Chapter 12: Functional Programming for Bioinformatics
Understanding pure functions
Getting ready
How to do it...
There’s more...
Understanding immutability
Getting ready
How to do it...
There’s more...
Avoiding mutability as a robust development pattern
Getting ready
How to do it...
There’s more...
Using lazy programming for pipelining
Getting ready
How to do it...
There’s more...
The limits of recursion with Python
Getting ready
How to do it...
There’s more...
A showcase of Python’s functools module
Getting ready
How to do it...
There’s more...
See also...
Index
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