Basic introduction to common tools

RNA-seq

• RNA-Seq: a revolutionary tool for transcriptomics
• Advancing RNA-Seq analysis
• Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
• TopHat: discovering splice junctions with RNA-Seq
• TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
• Systematic evaluation of spliced alignment programs for RNA-seq data
• Assessment of transcript reconstruction methods for RNA-seq
• Transcriptome and genome sequencing uncovers functional variation in humans
• Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

DNAm

• Measuring cell-type specific differential methylation in human brain tissue
• From promises to practical strategies in epigenetic epidemiology
• A data-driven approach to preprocessing Illumina 450K methylation array data
• Epigenetic memory in induced pluripotent stem cells
• The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores
• Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies
• Analysing and interpreting DNA methylation data
• DNA methylation: roles in mammalian development
• The Key Role of Epigenetics in Human Disease Prevention and Mitigation
• Charting a dynamic DNA methylation landscape of the human genome
• Global Epigenomic Reconfiguration During Mammalian Brain Development
• Divergent neuronal DNA methylation patterns across human cortical development: Critical periods and a unique role of CpH methylation

bash and linux

• Linux essentials
• The Unix Workbench by Sean Kross.
• Rsync (Remote Sync): 10 Practical Examples of Rsync Command in Linux.
• Linux file permissions.
• How To Use Linux Screen – website 1 and How To Use Linux Screen – website 2.

R

• Download and install R from CRAN.
• R 101 LIBD rstats blog post by Carrie Wright.
• Download RStudio Desktop.
• Using the RStudio Terminal.
• RStudio cheatsheets for many things including regular expressions, purrr for functional programming, etc.
• Building Tidy Tools workshop materials by Charlotte Wickham and Hadley Wickham for the rstudio 2019 conference. Materials from other workshops is available here.
• R Markdown documentation website announced by Alison Hill.
• Cookbook for R graphs with useful ggplot2 code.
• Updating R blog post by Leo.
• Tutorial for building R websites by Emily C Zabor which is how this website was made. More on R Markdown websites here.

python

• TODO