This repository contain resources that I found useful on my path to mastering Bioinformatics. There are links to proper sites with proper documentation of concepts, books, and other sources of information.
- R markdown - A proper introduction to R markdown with examples
- DGE analysis - End to end analysis of Differentially expressed genes
- Rmd guide - Concepts of Git and Github
- Prevent the terminal from logging off the server - Practical solution
- Single cell RNA analysis - Single cell RNASeq analysis
- All about linux - wonderful linux resource
- Rmarkdown cheat sheet - A summary to how R markdown works
- GWENA:- An Awesome pipeline to construct a Biological network, Module construction and Enrichment analysis
- WCL - A guide for efficient pipeline writing and sharing
- How to use Sratoolkit - A guidance to effectively using SRAtool
- Using du and df - These are important commands to know disk utilization and storage space use. The commands are particularly important when using HPC resources
- Using R - A good R learning platform
- R for data sceince
- Differential gene expression - Analysis steps to counduct differential gene expression of RNA-Seq data
- Differential gene expression - A systematic guide to Differential gene expression
- Havard bioinformatics core - Bioinformatics training by harvard bioinformatics core
- Sample work of WGCNA - An example of analysis pipeline with code and results obtained.
- stable UCSC human reference genome - Download the stable reference hg38 genome here
- gene code reference genome - Get both hg18 and hg19 reference genomes here
- Next generation sequence analysis - A comprehensive NGS series analysis
- Hisat2 tutorial - A good tutorial of using hisat2
- DGE + Network analysis - This paper combines network analysis and differential gene expression. It includes actual codes used in analysis pipeline.
- WGCNA and DGE analysis- This paper has the pipeline to conduct DGE and network analysis.
- T-mux tutorial - An excellent guide to Tmux usage
- Network analysis paper - This is aa well curated paper that describes Gene co-expression analysis
- viGEN pipeline - An elaborate methodology used to conduct this study. All the code, tools and exaplanations are provided
- Decontaminer github - Analysis steps of decontaminer tool - Analysis steps of decontaminer tool - RNA-Seq contamination project
- Decontaminer publication - A new pipeline that detects viruses, bacteria and fungi contaminants