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Bioinformatics with Python Cookbook
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Bioinformaticsisanactiveresearchfieldthatusesarangeofsimple-to-advancedcomputationstoextractvaluableinformationfrombiologicaldata.Thisbookcoversnext-generationsequencing,genomics,metagenomics,populationgenetics,phylogenetics,andproteomics.You'lllearnmodernprogrammingtechniquestoanalyzelargeamountsofbiologicaldata.Withthehelpofreal-worldexamples,you'llconvert,analyze,andvisualizedatasetsusingvariousPythontoolsandlibraries.ThisbookwillhelpyougetabetterunderstandingofworkingwithaGalaxyserver,whichisthemostwidelyusedbioinformaticsweb-basedpipelinesystem.Thisupdatededitionalsoincludesadvancednext-generationsequencingfilteringtechniques.You'llalsoexploretopicssuchasSNPdiscoveryusingstatisticalapproachesunderhigh-performancecomputingframeworkssuchasDaskandSpark.Bytheendofthisbook,you'llbeabletouseandimplementmodernprogrammingtechniquesandframeworkstodealwiththeever-increasingdelugeofbioinformaticsdata.
目錄(289章)
倒序
- coverpage
- Title Page
- About Packt
- Why subscribe?
- Packt.com
- Contributors
- About the author
- About the reviewers
- Packt is searching for authors like you
- Preface
- Who this book is for
- What this book covers
- To get the most out of this book
- Download the example code files
- Download the color images
- Conventions used
- Sections
- Getting ready
- How to do it…
- How it works…
- There's more…
- See also
- Get in touch
- Reviews
- 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… 更新時間：2021-06-10 19:02:32
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