- A Bioinformatician's UNIX Toolbox from Heng Li
- Linux command line exercises for NGS data processing
- bash one-liners for bioinformatics
- some of my bash one-liner collections
- Use the Unofficial Bash Strict Mode (Unless You Looove Debugging)
- Bash by example
There are many online web based tools for visualization of (cancer) genomic data. I put my collections here.
- UCSC cancer genome browser It has many data including TCGA data buit in, and can be very handy for both bench scientist and bioinformaticians.
- UCSC Xena. A new tool developed by UCSC team as well. Poteintially very useful, but need more tutorials to follow.
- UCSC genome browser. One of the most famous genome browser and my favoriate. Every person studying genetics, genomics and molecular biology needs to know how to use it. Tutorials from OpenHelix.
- Epiviz 3 is an interactive visualization tool for functional genomics data. It supports genome navigation like other genome browsers, but allows multiple visualizations of data within genomic regions using scatterplots, heatmaps and other user-supplied visualizations.
- DisGeNET is a discovery platform integrating information on gene-disease associations (GDAs) from several public data sources and the literature
- Cancer3D is a database that unites information on somatic missense mutations from TCGA and CCLE, allowing users to explore two different cancer-related problems at the same time: drug sensitivity/biomarker identification and prediction of cancer drivers
- clinical intepretations of variants in cancer
- BioGrid Welcome to the Biological General Repository for Interaction Datasets
- AnnotationHub bioconductor package for TCGA and epigenome roadmap, ENCODE project.
- TCGAbiolinks bioconductor package
- RTCGA bioconductor
- paper Data mining The Cancer Genome Atlas in the era of precision cancer medicine
- PH525x series - Biomedical Data Science. Learn R and bioconductor.
- PCA, MDS, k-means, Hierarchical clustering and heatmap. I wrote it.
- Survival analysis of TCGA patients integrating gene expression (RNASeq) data
- Tutorial: Machine Learning For Cancer Classification. It has four parts.
- Learning bash scripting for beginners
- Bedtools tutorial
- Gemini explores your vcf, and slides.
- GNU parallel