https://github.com/asadprodhan/bioinformatics_core
Bioinf Tutorials
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
-
✓Academic publication links
Links to: scholar.google -
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (8.6%) to scientific vocabulary
Keywords
Repository
Bioinf Tutorials
Basic Info
Statistics
- Stars: 1
- Watchers: 1
- Forks: 1
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
Bioinformatics Core
CONTENT
Chapter 01. Bioinformatics Basics
Chapter 02. An Introduction to R Programming
Chapter 03. An Introduction to Bash Commands
Chapter 04. An Introduction to Remote Computing
Chapter 05. How to Retrieve Public Data
Chapter 06. DNA Data Wrangling
Chapter 07. Nanopore Sequencing Data Analysis
Chapter 08. Bioinformatics Tools for Pest and Pathogen Diagnosis
Chapter 09. Bioinformatics Workflow for Transcriptome Analysis Using Illumina Sequencing
Chapter 10. Bioinformatics Workflow for Microbiome Data Analysis
Chapter 11. Writing Manuscripts
Chapter 12. My Bioinformatics Presentations
CHAPTER 01. BIOINFORMATICS BASICS
01. How to set up Windows Subsystem for Linux (WSL)?
02. Navigating a Linux Computer
03. Getting started with bioinformatics coding
04. A beginner's guide to Bioinformatics
CHAPTER 02. R
01. Why graduate students should learn R?
03. An Introduction to R Coding
04. Data visualisation and analysis in R
CHAPTER 03. BASH
01. Navigating a Linux Computer
03. Bash Script to Extract Individual Entries from a Large fasta File
04. Bash Scrip To Show Directory Properties
CHAPTER 04. REMOTE COMPUTING
01. How to Connect to a Remote Linux Computer
02. How to Connect to Pawsey’s Nimbus Instance
03. How to Mount Cloud NAS Device to Linux Computer
CHAPTER 05. RETRIEVE PUBLIC DATA
01. Genome sequence metadata [manual]
02. Genome sequence metadata [command line]
04. Genome sequences using datasets [command line]
05. Genome sequences using wget [command line]
06. RefSeq genome sequences using wget [command line]
07. Downloading genomes using the accession number
08. Downloading genomes from RefSeq
CHAPTER 06. DNA DATA WRANGLING
01. How to Filter Out Contigs from a Genome Assembly
02. How to Extract Individual Entries from a Large fasta File
03. Hoq to Filtering out Invalid Characters from fastq Reads
04. How to Extract Individual Entries from a Large fasta File
05. How to Automate Gene Seq Extraction from Multiple Genomes
06. How to Split a Concatenated fasta File into Individual Files
CHAPTER 07. NANOPORE
01. An Introduction to Nanopore DNA Sequencing and Data Analysis
02. Automating Sample Labelling after Nanopore Sequencing
03. GPU-Accelerated Guppy Basecalling
05. Dorado Basecalled Reads Improve Old Bacterial Genome Assemblies
06. How to Channel Sequencing Reads from Multiple Subdirectories into Nextflow Pipeline
07. Miniasm (setting up and running miniasm assembler
08. Reducing Storage Space by Converting Nanopore fast5 Files to slow5
CHAPTER 08. PEST AND PATHOGEN DIAGNOSIS
01. Blastn (database download, execution, hit sequence extraction, and possible errors)
02. ANI (average nucleotide identity)
03. Bacterial ID (phylogenetic tree reconstruction using UBCG pipeline)
04. Kraken 2 (running on HPC using singularity container and nextflow?)
08. Diagnosing Bacteria Using Illumina Sequencing
CHAPTER 09. TRANSCRIPTOMICS
01. How to Analysis Transcriptome Illumina Sequencing Reads
02. How to Make Hierarchical Clustering Heatmap of the Target DEGs and Plot Individual Clusters
03. How to Do GO Term Enrichment Analysis using GOMCL
CHAPTER 10. MICROBIOME
01. Environmental Rhizosheath Microbiome Sampling Protocol
02. A Bioinformatics Pipeline for 16s Microbiome Data
CHAPTER 11. BUILDING CUSTOMISED DATABASE
01. How to Build a Customised Kraken2 Database
02. How to Build a Customised Bracken Database
CHAPTER 12. WRITING
01. Writing and Publishing Protocols using GitHub
02. Publishing a paper. Professor Hans Lambers
CHAPTER 13. PRESENTATIONS
Owner
- Name: Asad Prodhan
- Login: asadprodhan
- Kind: user
- Location: Perth, Australia
- Company: Department of Primary Industries and Regional Development
- Website: www.linkedin.com/in/asadprodhan
- Twitter: Asad_Prodhan
- Repositories: 2
- Profile: https://github.com/asadprodhan
Laboratory Scientist at DPIRD. My work involves Oxford Nanopore Sequencing and Bioinformatics for pest and pathogen diagnosis.
GitHub Events
Total
- Push event: 3
Last Year
- Push event: 3