Bioinformatics learning and data analysis tips and tricks. Please, contribute and get in touch!
- RNA-seq notes
- scRNA-seq notes
- ChIP-seq notes
- Methylation notes
- scATAC-seq notes
- SNP notes
- Hi-C tools
- Hi-C data
- scHi-C notes
- Cancer notes
- Immuno notes
See MDmisc notes for other programming and genomics-related notes.
The complete assembly of human genome (haploid CHM13 cell line). 3.055 billion base pairs, no gaps for all 22 chromosomes plus ChrX, new genes. Resolving ribosomal rDNA sequences. PacBio, Oxford Nanopore, other technologies. The Telomere-to-Telomere (T2T) consortium, UCSC, NCBI PRJNA559484, GitHub with download links to FASTA, gff3, liftover chains
- Nurk, Sergey, Sergey Koren, Arang Rhie, Mikko Rautiainen, Andrey V. Bzikadze, Alla Mikheenko, Mitchell R. Vollger et al. "The complete sequence of a human genome." bioRxiv (2021).
Milestones in Genomic Sequencing by Nature, 2000-2021 period, interactive infographics
Awesome-Bioinformatics - A curated list of awesome Bioinformatics libraries and software, by Daniel Cook and community-contributed
awosome-bioinformatics - A curated list of resources for learning bioinformatics
awesome-cancer-variant-databases - A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants, by Sean Davis and community-maintained
awesome-single-cell - List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc. By Sean Davis and community-maintained
awesome-alternative-splicing - Alternative splicing resources
awesome-10x-genomics - List of tools and resources related to the 10x genomics GEMCode/Chromium system, by Johan Dahlberg and community-contributed
awesome-multi-omics - List of software packages for multi-omics analysis, by Mike Love and community-maintained
awesome-bioinformatics-benchmarks - A curated list of bioinformatics bench-marking papers and resources
awesome_genome_browsers - genome browsers and genomic visualization tools. By David McGaughey
awesome-expression-browser - A curated list of software and resources for exploring and visualizing (browsing) expression data, and more. By Federico Marini and community-maintained
awesome-genome-visualization - A list of interesting genome browser or genome-browser-like implementations. By Colin Diesh
awesome-microbes - List of software packages (and the people developing these methods) for microbiome (16S), metagenomics (WGS, Shot-gun sequencing), and pathogen identification/detection/characterization. By Steve Tsang and community-contributed
sandbox.bio - an interactive bedtools tutorial developed by the Quinlan Lab
biotools - A massive collection of references on the topics of bioinformatics, sequencing technologies, programming, machine learning, and more. By John Didion
For all your seq... DNA & RNA - Illumina flyer with infographics of all sequencing-by-synthesis technologies. RNA and DNA versions
List of software/websites/databases/other stuff for genome engineering
multimodal-scRNA-seq - Figure depicting the breadth of multimodal scRNA-seq technologies. References to technology-specific papers
SequencEnG - Hierarchical summary of 66 sequencing technologies, computational algorithms, references to papers.
- Zhang, Y., Manjunath, M., Kim, Y., Heintz, J., and Song, J.S. (2019). SequencEnG: an interactive knowledge base of sequencing techniques. Bioinformatics 35, 1438–1440.
OmniPath: intra- & intercellular signaling knowledge - a database of molecular biology prior knowledge, combines data from more than 100 resources. Interface to R, Python, more.
The Leek group guide to genomics papers- Jeff Leek recommended list of genomics papers
Unix, R and python tools for genomics and data science - links and references to many computational biology resources, by Ming Tang
bioinformatics-one-liners - collection of bioinformatics-genomics bash one liners, using awk, sed etc., by Ming Tang
RNA-seq-analysis - RNAseq analysis notes, by Ming Tang
ChIP-seq-analysis - ChIP-seq analysis notes, by Ming Tang
DNA-seq-analysis - Notes on whole exome and whole genome sequencing analysis, by Ming Tang
DNA-methylation-analysis - DNA methylation analysis notes from Ming Tang
scATAC-seq-analysis-notes - single-cell ATAC-seq notes, by Ming Tang
List of bioinformatics tools developed by IHEC Int'l Human Epigenome Consortium researchers - tools for all types of genomic analyses
Learning Nextflow in 2020 - Materials to learn NextFlow
Nextflow Tower - management of Nextflow data pipelines. Video overview
nf-core - a framework for Nextflow-based pipeline creation, community-driven. Integrated with Conda, Docker, Biocontainers. Scalable to a cloud level. Pipeline assemblers: Flowcraft, Pipeliner. nf-core GitHub. All pipelines are on the nf-core hub.
- Ewels, Philip, Alexander Peltzer, Sven Fillinger, Johannes Alneberg, Harshil Patel, Andreas Wilm, Maxime Garcia, Paolo Di Tommaso, and Sven Nahnsen. “Nf-Core: Community Curated Bioinformatics Pipelines.” Preprint. Bioinformatics, April 16, 2019.
bcbio-nextgen - Validated, scalable, community developed variant calling and RNA-seq analysis. Documentation
RNA-seq theory and analysis - theory and practical guidelines for RNA-seq data analysis, by Skyler Kuhn
Data science for economists - from R, tidyverse to GitHub, web scraping, Docker, Google Cloud and more. By Grant McDermott
Reproducible research and data analysis with Linux containers and Nextflow pipelines, GitHub
Bioinformatics Coffee Hour - Short lessons from FAS Informatics coffee hour,data science, command line, R basics, Snakemake
The Biostar Handbook: 2nd Edition - Biostar Handbook - bioinformatics survival guide. A practical overview for the data analysis methods of bioinformatics. From Unix/command line to each type of sequencing data ana analysis
Beginner's Handbook to Next Generation Sequencing by GenoHub - omics technologies, experimental descriptions
Computational Genomics with R book by Altuna Akalin. From R basics to different types of bioinformatics analyses. GitHub
The Bioinformatics algorithms web site. Videos and Texts covering topics from biology to genome assembly algorithms, motif finding, sequence comparisons and more bioinformatics tasks and solutions. By Phillip Compeau and Pavel Pevzner
Algorithms for DNA Sequencing - Ben Langmead's course material. Slides on GitHub, Python/Colab code examples, Youtube videos
Applied Computational Genomics Course at UU by Aaron Quinlan. All slides on Google drive, Youtube videos for each lecture
Introduction to Computational Biology course by Mike Love. GitHub
Data Analysis in Genome Biology course by Thomas Girke. Bioinformatics of NGS data analysis GitHub
Bioconductor for Genomic Data Science course by Kasper Hansen. Includes videos, code examples and lecture material. GitHub
BPA-CSIRO Workshops - Cancer Genomics, Introduction to Next Generation Sequencing Hands-on Workshop. Links to topic-oriented GitHub repositories, PDF handouts. GitHub
The Bioconductor 2018 Workshop Compilation, editors - Levi Waldron, Sean Davis, Marcel Ramos, Lori Shepherd, Martin Morgan. Task-oriented workshops covering a range of genomics/Bioconductor analyses. GitHub
CSAMA - Course material for CSAMA: Statistical Data Analysis for Genome Scale Biology, by Bioconductor team. Lectures, Labs
JHU EN.601.749: Computational Genomics: Applied Comparative Genomics course, by Michael Schatz. Links to similar courses there. Other courses by Michael
JHU Data Science lab - several data science courses, links to topic-specific GitHub repositories, other resources
CSE 549 - Introduction to Computational Biology by Steven Skiena. Includes video lectures. Another course: CSE 519 - Data Science
DIYtranscriptomics.github.io - Course material for the "do-it-yourself" RNA-seq course, by Daniel Beiting. GitHub
Informatics for RNA-seq: A web resource for analysis on the cloud by Griffith lab. All aspects of RNA-seq analysis
RNA-seqlopedia - one long page of all steps of RNA-seq data analysis, from molecular biology to computational analysis, very detailed
BaRC Hot Topics - lecture slides and handouts on all genomics topics, from Unix to microarray, sequencing, genomics and statistics
Courses by Dr. Raghu Machiraju. Topics: data visualization, biomedical informatics, computer graphics, linked from the homepage. CSE5599-BMI7830 - biomedical informatics. CSE5544 – Introduction to Data Visualization
alignment-and-variant-calling-tutorial - basic walk-throughs for alignment and variant calling from NGS sequencing data, PDF lecture, by Erik Garrison.
Machine Learning in Genomics - Fall 2019 by Manolis Kellis. Course website
Free online training in bioinformatics and biostatistics! by David Tabb. Various topics beyond genomics
Bioconductor Workshop 2: RNA Seq and ChIP Seq Analysis - 6 hours workshop on RNA-seq and ChIP-seq technology and analysis by Levi Waldron and others
Differential Splicing Analysis with RNA-Seq: Current Applications, Approaches, & Limitations - 1 hour overview of differential splicing analysis
NHGRI_Genomics2016 - "Current Topics in Genome Analysis 2016" course - A lecture series covering contemporary areas in genomics and bioinformatics, slides
MIT_SysBiol2014 - "Foundations of Computational and Systems Biology", slides
Regulatory Genomics and Epigenomics - series of genomcs-oriented talks by Simons Institute. 26 videos, ~30min each.
Foundations of Data Science — Spring 2016 - course from UC Berkeley. Instructor: John DeNero. Video and slides. This course is accompanied by other "connector" courses from UC Berkeley
A Roadmap to the Living Genome by John Stamatoyannopoulos. An overview of cell type-specific (epi)genomic landscapes, visualization and analysis techniques, association and enrichment of disease-associated variants in regulatory regions.
RNA-Seq Methods and Algorithms - short video course by Harold Pimentel, pseudoalignment, kallisto, sleuth, practical
Integrating ENCODE Data With Your Research: An Interactive Survey of ENCODE Tools and Resources - set of short videos about ENCODE data and functionality