coverpage
Title Page
About Packt
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Contributors
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Preface
Who this book is for
What this book covers
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Conventions used
Sections
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Python and the Surrounding Software Ecology
Introduction
Installing the required 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 Notebook
Getting ready
How to do it...
There's more...
See also
Next-Generation Sequencing
Introduction
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
Analyzing data in VCF
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...
Working with Genomes
Introduction
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
Population Genetics
Introduction
Managing datasets with PLINK
Getting ready
How to do it...
There's more...
See also
Introducing the Genepop format
Getting ready
How to do it...
See also
Exploring a dataset with Bio.PopGen
Getting ready
How to do it...
There's more...
See also
Computing F-statistics
Getting ready
How to do it...
See also
Performing Principal Components Analysis
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...
Population Genetics Simulation
Introduction
Introducing forward-time simulations
Getting ready
How to do it...
There's more...
Simulating selection
Getting ready
How to do it...
There's more...
Simulating population structure using island and stepping-stone models
Getting ready
How to do it...
Modeling complex demographic scenarios
Getting ready
How to do it...
Phylogenetics
Introduction
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...
Using the Protein Data Bank
Introduction
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...
Bioinformatics Pipelines
Introduction
Introducing Galaxy servers
Getting ready
How to do it…
There's more…
Accessing Galaxy using the API
Getting ready
How to do it…
Developing a Galaxy tool
Getting ready
How to do it…
There's more…
Using generic pipelines with bioinformatics data
Getting ready
How to do it…
Deploying a variant analysis pipeline with Airflow
Getting ready
How to do it…
There's more…
Python for Big Genomics Datasets
Introduction
Using high-performance data formats – HDF5
Getting ready
How to do it...
There's more...
Doing parallel computing with Dask
Getting ready
How to do it...
There's more...
Using high-performance data formats – Parquet
Getting ready
How to do it...
There's more...
Computing sequencing statistics using Spark
Getting ready
How to do it...
There's more...
Optimizing code with Cython and Numba
Getting ready
How to do it...
There's more...
Other Topics in Bioinformatics
Introduction
Doing metagenomics with the QIIME 2 Python API
Getting ready
How to do it...
There's more...
Inferring shared chromosomal segments with Germline
Getting ready
How to do it...
There's more...
Accessing the Global Biodiversity Information Facility via REST
How to do it...
There's more...
Georeferencing GBIF datasets
Getting ready
How to do it...
There's more...
Plotting protein interactions with Cytoscape the hard way
Getting ready
How to do it...
There's more...
Advanced NGS Processing
Introduction
Preparing the dataset for analysis
Getting ready
How to do it…
Using Mendelian error information for quality control
How to do it…
There's more…
Using decision trees to explore the data
How to do it…
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…
更新时间：2021-06-10 19:02:32
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