Bioinformatics resources provided by Michael Steinbaugh.
- R package for bcbio RNA-seq analysis.
- Toolkit for performing differential expression with DESeq2.
- Parameterized fast gene set enrichment analysis.
Single-cell RNA sequencing
- R package for bcbio single-cell RNA-seq analysis.
- Toolkit for 10X Genomics single-cell RNA-seq data.
- R package for for single-cell RNA-seq clustering analysis.
- Automated scoring for a C. elegans genome-wide RNAi screen.
- C. elegans genome annotations from WormBase.
- Base functions for bioinformatics and R package development.
- S4 generic functions for bioinformatics.
- Biological R input/output.
- Make syntactically valid names out of character vectors.
- Additional S3 and S4 coercion methods for easy interconversion between Bioconductor and tidyverse data classes.
- Trusty sidekick for R package development.
- Assertive check functions for defensive R programming.
- My dot files shared between machines.
- Shell bootloader for bioinformatics.
- Install conda
- . Quick installation guide for conda, along with tips for managing environments.
- Detect the Illumina sequencer model
- . Extract the Illumina sequencer instrument information from a FASTQ file.
- Cache R package library on Travis CI
- . How to cache an R/Bioconductor package with multiple dependencies.
- Vim quick reference
- . Reference commands for the vim text editor.
- Tmux quick reference
- . Reference commands for the tmux terminal multiplexer.
- Install a Raspberry Pi device
- . How to get a Pi up and running in less than 15 minutes.
- Git quick reference
- . Reference commands for the git version-control system.
- Install macOS
- . How to make that Mac feel new again.
- Install bcbio
- . bcbio is a python toolkit providing current best practice pipelines for next-generation sequencing data analysis.
- Make a private fork of a public git repository
- . GitHub currently only allows the creation of public forks. However, it is possible to sync code between a public repository and a private mirror.
- Install RDAVIDWebService
- . An R Package for retrieving data from DAVID into R objects using Web Services API.
- Automounts on macOS with NFS
- . The best method to automatically connect your Mac to network storage.
- C. elegans resources
- . Links to worm tools around the web.
- Programming style rules
- . Clean code, happy life.
- Install Ubuntu
- . Ubuntu Linux is a great programming environment but it’s more difficult to initially set up than macOS or Windows.