Links

• ​Open sourcing bioinstruments (2019) (HN)

• ​goleft - Collection of bioinformatics tools distributed under MIT license in a single static binary.

• ​When the levee breaks: a practical guide to sketching algorithms for processing the flood of genomic data (2019)​

• ​Handbook of Statistical Genomics (2019)​

• ​Nature Reviews Genetics - Monthly review journal in genetics and covers the full breadth of modern genetics.

• ​Bioinformatics and Functional Genomics 3rd Edition by Jonathan Pevsner​

• ​Nucleus - Python and C++ code for reading and writing genomics data.

• ​Statistical Population Genomics​

• ​Genome Informatics 2019 Lightning Talk: A. Sina Booeshaghi​

• ​10x Genomics (Code)

• ​Neher Lab - Pathogen evolution, genomics, and biophysics lab in Switzerland.

• ​BEDOPS - High-performance genomic feature operations.

• ​Introduction to Genetics and Evolution​

• ​Open Targets - Partnership that uses human genetics and genomics data for systematic drug target identification and prioritisation.

• ​Next-Gen Sequence Analysis Workshop (2019)​

• ​Korkin Lab​

• ​Varlociraptor - Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.

• ​genetools - Single-cell analysis recipes. (Code)

• ​Learn Genetics (HN)

• ​fgsea - Fast Gene Set Enrichment Analysis.

• ​Awesome Genome Visualization​

• ​Computational Genomics Class Playlist at San Diego State University​

• ​Computational Genomics Manual (Code)

• ​A Theory of Natural Universal Computation Through RNA (2020) (Tweet)

• ​Hail - Open-source, general-purpose, Python-based data analysis tool with additional data types and methods for working with genomic data. (References)

• ​gnomAD - Genome aggregation database.

• ​We can now edit the human genome – how far should we go? (HN)

• ​Scientific Background: A tool for genome editing (2020)​

• ​Introduction to Social Science Genetics (2020)​

• ​gplearn - Implements Genetic Programming in Python, with a scikit-learn inspired and compatible API.

• ​Genetic List - Browsable genetic marker lists.

• ​Cutevariant - Standalone and free application to explore genetics variations from VCF file.

• ​A hypothesis is a liability (2020)​

• ​Awesome Imaging Genetics​

• ​There is little chance CRISPR will ever be widely used to directly treat disease (2020) (HN)

• ​misha - Genomic data analysis suite.

• ​MetaCell R - Single-cell mRNA Analysis.

• ​nf-core/eager - Bioinformatics best-practice analysis pipeline for NGS sequencing based ancient DNA (aDNA) data analysis.

• ​GenomicSQLite - Genomics Extension for SQLite.

• ​gfabase - Command-line utility for random-access storage of Graphical Fragment Assembly (GFA) data.

• ​GenomeSpy - Genome visualization tool with a grammar of graphics and WebGL-powered fluid interactions. (Code)

• ​Decoding the Language of Genomes (2020) (HN)

• ​GREIN - GEO RNA-seq Experiments Interactive Navigator. (Code)

• ​FUMA: Functional mapping and annotation of genetic associations (Code)

• ​GenePattern Notebook - Platform for integrating genomic analysis with Jupyter Notebooks.

• ​SCDE - R package for analyzing single-cell RNA-seq data.

• ​Human Genome Idiogram Vector Art Library - Contains image files for each of the 24 primary human chromosomes, as well as one for the entire genome lined up.

• ​RNA Memory Hypothesis (2021) (HN)

• ​ELI5 Epigenetics​

• ​Bioconductor - Provides tools for the analysis and comprehension of high-throughput genomic data. (GitHub)

• ​Orchestrating Single-Cell Analysis with Bioconductor (Code)

• ​Awesome CRISPR - List of software/websites/databases/papers for genome engineering.

• ​Genomics Workflows on AWS (Web)

• ​Pyne Lab - Single molecule biophysics of DNA interactions.

• ​Nextclade - Viral genome alignment, clade assignment, mutation calling, and quality checks. (Code)

• ​Shooting out the messenger—mRNA and how the pandemic advanced biotechnologies (2021) (Tweet)

• ​Cirrocumulus for Single-Cell Data Visualization (Code)

• ​On detecting gene-gene interactions (2020)​