BOL: Related items

DIY Transcriptomics

Abhi — Wed, 31 Jul 2024 01:19:26 -0500

A semester-long course covering best practices for the analysis of high-throughput sequencing data from gene expression (RNA-seq) studies, with a primary focus on empowering students to be independent in the use of lightweight and open-source software using the R programming language and the Bioconductor suite of packages. This course follows a hybrid format in which online lectures are paired with in-person labs where students participate in hands-on, live coding exercises using real ‘omic datasets. The course is focused on datasets and topics central to infectious disease research, immunology, and One-Health, but the concepts and approaches covered are applicable to any genomic study.

https://diytranscriptomics.com

Address of the bookmark: https://diytranscriptomics.com

Python learning resources for bioinformatics and computational biologist !

Jit — Fri, 02 Mar 2018 06:54:15 -0600

Python is a general-purpose language, which means it can be used to build just about anything, which will be made easy with the right tools/libraries.

Professionally, Python is great for backend web development, data analysis, artificial intelligence, and scientific computing. Many developers have also used Python to build productivity tools, games, and desktop apps, so there are plenty of resources to help you learn how to do those as well.

For pros and cons visit http://www.bestprogramminglanguagefor.me/why-learn-python and http://bioinformaticsonline.com/discussion/view/459/python-vs-perl

More resources at https://github.com/CodementorIO/Python-Learning-Resources

Following are the list of useful python programming resources:

20 Python Libraries You Aren't Using (But Should) (Just fill the fields with any values)
A Beginner's Python Tutorial
A Byte of Python (3.x) (HTML, PDF, EPUB, Mobi)
A Guide to Python's Magic Methods - Rafe Kettler
A Whirlwind Tour of Python - Jake VanderPlas (PDF) (EPUB, MOBI)
Automate the Boring Stuff - Al Sweigart
Biopython (PDF)
Build applications in Python the antitextbook (3.x) (HTML, PDF, EPUB, Mobi)
Building Machine Learning Systems with Python - Willi Richert & Luis Pedro Coelho, Packt. (Just fill the fields with any values)
Building Skills in Object-Oriented Design (Python) (PDF) (2.1.1)
Building Skills in Python (PDF) (2.6)
Code Like a Pythonista: Idiomatic Python
CodeCademy Python
Composing Programs (3.x)
Data Structures and Algorithms in Python - B. R. Preiss (PDF)
Dive into Python 3 - Mark Pilgrim (3.0)
- Dive into Python - Mark Pilgrim (2.3)
From Python to NumPy
Full Stack Python
Functional Programming in Python (Just fill the fields with any values)
Fundamentals of Python Programming - Richard L. Halterman (PDF) (3.2)
Google's Python Class (2.4 - 2.x)
Google's Python Style Guide
Hacking Secret Cyphers with Python - Al Sweigart (3.3)
Hadoop with Python (Just fill the fields with any values)
High Performance Python (PDF)
Hitchhiker's Guide to Python! (2.6)
How to Make Mistakes in Python - Mike Pirnat (PDF) (1st edition)
How to Think Like a Computer Scientist: Learning with Python, Interactive Edition (3.2)
- How to Think Like a Computer Scientist: Learning with Python - Allen B. Downey, Jeff Elkner and Chris Meyers (2.4)
- Think Python - Allen B. Downey (2.x & 3.0)
Intermediate Python - Muhammad Yasoob Ullah Khalid (1st edition)
Introduction to Programming with Python (3.3)
- Introduction to Programming Using Python - Cody Jackson (1st edition) (2.3)
Introduction to Python - Kracekumar (2.7.3)
Invent Your Own Computer Games With Python - Al Sweigart (3.1)
Learn Python, Break Python
Learn Python in Y minutes
Learn Python The Hard Way (2.5 - 2.6)
Learn to Program Using Python - Cody Jackson (PDF)
Learning Python - Fabrizio Romano, Packt. (Just fill the fields with any values)
Learning to Program
Lectures on scientific computing with python - J.R. Johansson (2.7)
Making Games with Python & Pygame - Al Sweigart (2.7)
Modeling Creativity: Case Studies in Python - Tom D. De Smedt (PDF)
Natural Language Processing with Python (3.x)
Non-Programmer's Tutorial for Python 3 (3.3)
- Non-Programmer's Tutorial for Python 2.6 (2.6)
Picking a Python Version: A Manifesto (Just fill the fields with any values)
Porting to Python 3: An In-Depth Guide (2.6 - 2.x & 3.1 - 3.x)
Practical Programming in Python - Jeffrey Elkner (PDF)
Problem Solving with Algorithms and Data Structures using Python - Bradley N. Miller and David L. Ranum
Program Arcade Games With Python And Pygame (3.3)
Programming Computer Vision with Python (PDF)
Python 2 Official Documentation (PDF, HTML, TEXT) (2.x)
Python 2.7 quick reference - New Mexico Tech (2.7)
Python 3 Official Documentation (PDF, EPUB, HTML, TEXT) (3.x)
Python Cookbook - David Beazley
Python Data Science Handbook - Jake VanderPlas (HTML, Jupyter Notebooks)
Python for Econometrics - Kevin Sheppard (PDF) (2.7.5)
Python for Everybody Exploring Data Using Python 3 - Charles Severance (PDF, EPUB, HTML)
- Python for Informatics: Exploring Information (2.7.5)
Python for you and me (2.7.3)
Python for you and me (3.x)
Python Idioms (PDF)
Python in Education (Just fill the fields with any values)
Python in Hydrology - Sat Kumar Tomer
Python Koans (2.7 or 3.x)
Python Module of the Week (3.x)
- Python Module of the Week (2.x)
Python Notes for Professionals - Compiled from StackOverflow documentation (3.x)
Python Practice Book (2.7.1)
Python Practice Projects
Python Programming (PDF) (2.6)
Scipy Lecture Notes
SICP in Python (3.2)
Snake Wrangling For Kids (3.x)
Suporting Python 3: An In-Depth Guide (2.6 - 2.x & 3.1 - 3.x)
Test-Driven Web Development with Python (3.3 - 3.x)
Text Processing in Python - David Mertz (2.3 - 2.x)
The Coder's Apprentice: Learning Programming with Python 3 - Pieter Spronck (PDF) (3.x)
The Definitive Guide to Jython, Python for the Java Platform - Josh Juneau, Jim Baker, Victor Ng, Leo Soto, Frank Wierzbicki (2.5)
The Little Book of Python Anti-Patterns (Source)
The Programming Historian - William J. Turkel, Adam Crymble and Alan MacEachern
The Python Ecosystem: An Introduction
The Python GTK+ 3 Tutorial
The Standard Python Library - Fredrik Lundh
Think Complexity - Allen B. Downey (2nd Edition) (PDF, HTML)
Web2py: Complete Reference Manual, 6th Edition (pre-release) (2.5 - 2.x)
Wikibooks: Python Programming (2.7)

Bioinformatics in Thailand !

Shruti Paniwala — Wed, 28 Apr 2021 02:04:56 -0500

Our international PhD and master programs are designed for students who desire focused training in the elements of biology, computer science, and information technology needed for a successful career in the exciting new discipline of Bioinformatics & Systems Biology. Students in our program will receive comprehensive training in omics analysis, database design and management, software engineering and programming (including web-based development), simulation techniques and modeling, and data integration. Each student will apply their skills to a practical project, where they will design and implement a solution to a real-world problem under the guidance of an experienced mentor in industry or academia.

https://bioinformatics.kmutt.ac.th/about.html

Duangrudee Tanramluk (Ajarn Wi) uses computational biology and machine learning to tackle the key to drug design problems via MANORAA webserver.

https://mb.mahidol.ac.th/en/bioinformatics/

https://graduate.mahidol.ac.th/inter/

This international Doctorate programme is designed to further broaden students’ knowledge in Bioinformatics and Molecular Biology to their maximum capability.

http://www.mbb.psu.ac.th/programmes/phd

Ph.D. program in Bioinformatics and Computational Biology is a joint effort of the Faculty of Science and Faculty of Medicine, Chulalongkorn University. The program has study plans for both applicants who hold a bachelor’s degree and applicants who hold a master’s degree in any related fields of study.

http://www.bioinfo.sc.chula.ac.th/ph-d-program-specialization/

Additional detail

https://www.biotec.or.th/en/index.php/research/research-units/genome-technology-research-unit

https://tbrcnetwork.org/labtbrc/index.php/bioinformatics-and-chemoinformatics/

https://genomicsthailand.com/Genomic/home

Address of the bookmark: https://bioinformatics.kmutt.ac.th/

Pangolin tutorial !

Abhi — Fri, 10 Dec 2021 05:58:59 -0600

This is a tutorial for using the Pangolin Web Application. For information on using the command line tool, please visit the command line tool usage page.

https://cov-lineages.org/resources/pangolin/tutorial.html

Address of the bookmark: https://cov-lineages.org/resources/pangolin/tutorial.html

Free resources to learn statistics

BioStar — Sat, 06 Jul 2024 10:30:50 -0500

Welcome to the course notes for STAT 414: Introduction to Probability Theory. These notes are designed and developed by Penn State's Department of Statistics and offered as open educational resources. These notes are free to use under Creative Commons license CC BY-NC 4.0.

A free online version of the second edition of the book based on Stat 110, Introduction to Probability by Joe Blitzstein and Jessica Hwang, is now available at http://probabilitybook.net

Print copies are available via CRC Press, Amazon, and elsewhere.

Stat110x is also available as an edX course. Free signup at https://www.edx.org/course/introduction-to-probability-0

The edX course focuses on animations, interactive features, readings, and problem-solving, and is complementary to the Stat 110 lecture videos on YouTube, which are available at https://goo.gl/i7njSb

The Stat110x animations are available within the course and at https://goo.gl/g7pqTo

https://projects.iq.harvard.edu/stat110/home

Address of the bookmark: https://online.stat.psu.edu/stat414/

INC-Seq: accurate single molecule reads using nanopore sequencing

Jit — Mon, 27 Nov 2017 10:38:56 -0600

INC-Seq reads enabled accurate species-level classification, identification of species at 0.1 % abundance and robust quantification of relative abundances, providing a cheap and effective approach for pathogen detection and microbiome profiling on the MinION system.

Address of the bookmark: https://github.com/CSB5/INC-Seq

ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.

Seema Singh — Mon, 30 Apr 2018 04:38:40 -0500

ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set.

Detail paper at https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3927-8

Address of the bookmark: https://github.com/VicugnaPacos/ALPACA

Frequent Paired-end reads (PE 2x100) mapping command lines

Jit — Tue, 15 May 2018 08:59:29 -0500

bowtie2 -x hs37m -X 650 -q -1 r1.fq -2 r2.fq -S r12.bowtie2.sam

bwa aln hs37m.fa r1.fq > r1.sai && bwa aln hs37m.fa r2.fq > r2.sai \
&& bwa sampe hs37m r1.sai r2.sai r1.fq r2.fq > r12.bwa.sam

bwa bwasw ../index/bwa/hs37m.fa r12.fq > r12.bwasw.sam

gsnap -A sam -d hs37m r1.fq r2.fq > r12.gsnap.sam

novoalign -r Random -o SAM -f r1.fq r2.fq -i 500 50 -d hs37m-k14s3.novo > r12.novo.sam

smalt map -f samsoft -i 650 -o r12.smalt-k20s13.sam hs37m-k20s13 r1.fq r2.fq

stampy.py -g hs37m -h hs37m -o r12.stampy.sam -M r1.fq,r2.fq

soap -D hs37m.fa.index -a r1.fq -b r2.fq -l 32 -g 3 -u dummy -2 dummy -o r12.soap

GenomeMapper: Simultaneous alignment of short reads against multiple genomes

Jit — Fri, 25 May 2018 09:29:44 -0500

GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a single reference. If you are unsure which one is the appropriate GenomeMapper, you might want to use the latter https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768987/

Address of the bookmark: http://1001genomes.org/software/genomemapper.html

Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads

Jit — Tue, 12 Jun 2018 12:41:10 -0500

Breakpointer is a fast tool for locating sequence breakpoints from the alignment of single end reads (SE) produced by next generation sequencing (NGS). It adopts a heuristic method in searching for local mapping signatures created by insertion/deletions (indels) or more complex structural variants(SVs).

Address of the bookmark: https://github.com/ruping/Breakpointer