Embedded Files
Statistics in R
Statistics in R
r-statistics.co A modern, concise and useful guide to statistics and graphics with R
Reduced-Rank Regression (PCA etc)
Time-series analysis, especially how to detect outliers.
R/demography. Forecasting for mortality, fertility, migration and population Data
netma, Network and meta-analysis in R
MultiPhen: A Package to Test for Pleiotropic Effects ... in genome-wide association studies.
"Time-series analysis with R" pdf, demonstration in base R, with explanations. Includes monitoring the effect of interventions on health-care data.
Data processing and plotting in R
Data processing and plotting in R
Tidyverse A package of packages for big-data manipulations, and fancy graphics.
ggplot extensions Label, legend, and formula-positioning tools useful but buggy. Calender heatmaps great. ggQC control charts work well with facetting but the methods are a bit enigmatic. Looking-forward to using the control charts of ggQC, and the animated graphics.
Colour index Because the default colours aren't that great.
R Markdown
R Markdown
R markdown Dynamic doc, pdf or html generation.
R/knitr enabling production of markdown documents.
Web-sites with R markdown
Web-sites with R markdown
Brendan's blog : Markdown+Jekyll
Interactive graphics with R shiny
Interactive graphics with R shiny
World demographics interactive, example of a Shiny app.
Building a Shiny app with ggplot
RSudio connect Team R app development
Data and databases
Data and databases
NCBI 'National Center for Biotechnology Informatio', USA, medical and molecular biology database
Flybase Directory of Drosophila data
UCSC Genome browser .. Multi-layered, interactive maps of genomes. Awesome website.
Other really interesting stuff
Other really interesting stuff
GitHub Free software and code-sharing, as well as personal web-sites, demonstrations, blogs etc.
Kurtosis, The Length of Stay Conundrum Blog on applied statistics.
Making a website using github and markdown
Overleaf On-line report, poster and presentation generation and storage using Latex code.
Perl script to create a bed file from a vcf file
EvolDir Evolutionary biology network
Bioinformatics
Bioinformatics
Burrough-Wheeler Aligner Mapping next-generation sequencing reads to a reference genome.
SamTools Conversion, formatting and QC tool for read data.
Picard Conversion, formatting and QC tool for read data.
Integrated Genomics Viewer, visualisation of mapped read and genotype data.
Quick read quality control in R by Vince Buffalo
Biostars, bioinformatics forum
'Genome Analysis Tool-Kit', analysis of read-mapping, genotying and QC.
Google Sites
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