While MacOS is already Unix-based, here are information on how to install Ubuntu on Win10. It is native to the Windows system but would need some extra work, e.g., installation of Ximg or VcXsrv, to get the native Ubuntu desktop. A current drawback with this Windows extension is its failure to exchange files between the two system, it is thus appealing to create and use virtual machines.
Linux distributions such as Fedora and Ubuntu offer their ways to set up and Oracle’s VirtualBox allows for canonical installations of Linux system installed as an application, or once the software is set up a pre-setup virtual disk attached to it. Later on when we remove files or create snapshot we can follow these steps to shrink it.
Now a variety of things can be done, for instance we can install Google-Chrome and sublime-text.
wget -q -O - https://dl-ssl.google.com/linux/linux_signing_key.pub | sudo apt-key add -
echo 'deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main' | sudo tee /etc/apt/sources.list.d/google-chrome.list
sudo apt-get update
sudo apt-get install google-chrome-stable
now you can start google-chrome.
wget -qO - https://download.sublimetext.com/sublimehq-pub.gpg | sudo apt-key add -
sudo apt-get install apt-transport-https
echo "deb https://download.sublimetext.com/ apt/stable/" | sudo tee /etc/apt/sources.list.d/sublime-text.list
sudo apt-get update
sudo apt-get install sublime-text
wget https://remarkableapp.github.io/files/remarkable_1.87_all.deb
sudo dpkg -i remarkable_1.87_all.deb
sudo apt-get install -f
git clone https://github.com/mathjax/MathJax.git MathJax
so that MathJax can be invoked from your Markdown document as follows,
<script type="text/javascript" src="/home/physalia/MathJax//MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
<script type="text/javascript" src="/home/physalia/MathJax/MathJax.js"></script>
An relatively easier option is Mango, also with the ability to generate HTML and PDF but does not require MathJax.
It is preferable to have within the Linux system R and RStudio. For instance in the case of Fedora, you can issue
dnf list R R-devel
dnf list rstudio
to check their availability and
sudo dnf install R R-devel
wget https://download1.rstudio.org/rstudio-1.0.153-x86_64.rpm
sudo rpm -i rstudio-1.0.153-x86_64.rpm
to install. For Ubuntu, simply replace dnf with apt, e.g.,
sudo apt install r-base r-base-dev r-mathlib
wget https://download1.rstudio.org/rstudio-xenial-1.0.153-amd64.deb
sudo dpkg -i rstudio-xenial-1.0.153-amd64.deb
It is more involved to download the source and compile, since it would involve installation of various componets (LaTeX, readline, TCL/Tk, etc.) as well.
In the order of relevance, if possible, they are:
Specific software for genetic data: fcgene, QCTOOL, PLINK, GCTA, BOLT-LMM, (locuszoom) MAGMA, depict, PASCAL finemap, TWAS, FUSION.
Rcmdr, devtools
dplyr, tidyr, tidyverse, ggplot2, metafor, NCBI2R, genetics, gap, HardyWeinberg, haplo.stats, kinship2, pedigreemm
snpStats, GenABEL
lme4, MCMCglmm, openxlsx, SKAT
R2BGLiMS, MendelianRandomization
| Software | URL | Notes |
|---|---|---|
| ANNOVAR | http://annovar.openbioinformatics.org/ (wANNOVAR) | Annotation |
| BEAGLE | https://faculty.washington.edu/browning/beagle/beagle.html | Genotype imputatoin |
| bedtools | http://bedtools.readthedocs.io/en/latest/ | Data manipulation |
| BOLT-LMM | https://data.broadinstitute.org/alkesgroup/BOLT-LMM/ | Mixed modeling |
| DEPICT | Broad, (GitHub) | Pathway analysis |
| EIGENSOFT | https://data.broadinstitute.org/alkesgroup/EIGENSOFT/ | PCA |
| finemap | http://www.christianbenner.com/# | fine-mapping on sumstats |
| FUSION | https://github.com/gusevlab/fusion_twas | TWAS |
| GARFIELD | http://www.ebi.ac.uk/birney-srv/GARFIELD/ | |
| GCTA | http://cnsgenomics.com/software/gcta/ | Mixed model |
| GenABEL | http://www.genabel.org/ | GWA analysis on chip data |
| GRAIL | http://software.broadinstitute.org/mpg/grail/ (VIZ-GRAIL) | Obsolete pathway analysis software |
| GTOOL | http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html | Data manipulation |
| IMPUTE2 | http://mathgen.stats.ox.ac.uk/impute/impute_v2.html | Genotype imputation |
| LDhub | http://ldsc.broadinstitute.org/ldhub/ | |
| LDSC | https://github.com/bulik/ldsc | Heritability from sumstats |
| LocusZoom | http://locuszoom.sph.umich.edu/ | Regional association plot |
| MaCH | http://csg.sph.umich.edu/abecasis/MACH/index.html | Genotype imputation |
| MAGENTA | https://software.broadinstitute.org/mpg/magenta/ | Pathway analysis |
| MAGMA | http://ctg.cncr.nl/software/magma | Pathway analysis |
| METAL | http://csg.sph.umich.edu/abecasis/metal/download/ | Metal-analysis |
| PASCAL | http://www2.unil.ch/cbg/images/3/3d/PASCAL.zip, (source) | Pathway analysis |
| PLINK2 | https://www.cog-genomics.org/plink2 | Efficient data analysis on directly genotyped data |
| PLINKSEQ | https://atgu.mgh.harvard.edu/plinkseq/ | |
| ProbABEL | https://github.com/GenABEL-Project/ProbABEL | GWA analysis for linear, logistic and survival models |
| QCTOOL | http://www.well.ox.ac.uk/~gav/qctool/#overview | QC summary statistics |
| QUICKTEST | https://wp.unil.ch/sgg/quicktest/ | Gene-environment interaction analysis |
| RV-TDT | http://bioinformatics.org/rv-tdt/ | |
| rvtests | http://genome.sph.umich.edu/wiki/Rvtests (GitHub) | Rare-variant analysis |
| samtools | https://github.com/samtools/ | Data manipulation |
| SEQPower | http://www.bioinformatics.org/spower/start | |
| SHAPIT | https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html | Haplotype phasing |
| SNPTEST | https://mathgen.stats.ox.ac.uk/genetics_software/snptest/snptest.html | Analysis of imputed genotype data |
| UNPHASED | https://sites.google.com/site/fdudbridge/software/unphased-3-1 | Haplotype analysisi |
| VAT | http://varianttools.sourceforge.net/Association/HomePage | |
| vcftools | https://vcftools.github.io/index.html | Data manipulation |
| VEGAS2 | online version, command-line version | Annotation |
| VEP | http://www.ensembl.org/info/docs/tools/vep/index.html | Annotation |
This is an extension of the Baylor list. The old Columbia/Rockefeller list may still contain useful links.
Institutional repositories are increasingly available, e.g. Eskin group, Broad Institute.
JAGS is Just Another Gibbs Sampler. It is a program for the statistical analysis of Bayesian hierarchical models by Markov Chain Monte Carlo.
R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS.
SAS (pronounced "sass") once stood for "statistical analysis system." It began at North Carolina State University as a project to analyze agricultural research. Demand for such software capabilities began to grow, and SAS was founded in 1976 to help customers in all sorts of industries – from pharmaceutical companies and banks to academic and governmental entities. SAS – both the software and the company – thrived throughout the next few decades. Development of the software attained new heights in the industry because it could run across all platforms, using the multivendor architecture for which it is known today. While the scope of the company has spread across the globe, the encouraging and innovative corporate culture has remained the same.
Stan (Thousands of users rely on Stan) for statistical modeling, data analysis, and prediction in the social, biological, and physical sciences, engineering, and business.
Stata is a complete, integrated statistical software package that provides everything you need for data analysis, data management, and graphics.