README.Rmd

---
title: 'Software Development Standards'
output: rmarkdown::github_document
---

This project's main contents is located in the project's [Wiki](https://github.com/USCbiostats/CodingStandards/wiki):

## Coding Standards

1.  [Coding Standards](../../wiki/Home#coding-standards)
2.  [Software Thinking](../../wiki/Home#software-thinking)
3.  [Development Workflow](../../wiki/Home#development-workflow)
4.  [Misc](../../wiki/Home#misc)

We do have some direct guidelines developed as issue templates [here](templates). 

## Bioghost Server

1.  [Introduction](../../wiki/Biogohst-server#introduction)
2.  [Setup](../../wiki/Biogohst-server#setup)
3.  [Cheat Sheet](../../wiki/Biogohst-server#cheat-sheet)

## HPC in R
    
*   [Parallel computing in R](../../wiki/HPC-in-R#parallel-computing-in-r)  
*   [parallel](../../wiki/HPC-in-R#parallel)
*   [iterators+foreach](../../wiki/HPC-in-R#foreach)
*   [RcppArmadillo + OpenMP](../../wiki/HPC-in-R#rcpparmadillo-and-openmp)

# Happy Scientist Seminars

The Happy Scientist Seminars are educational seminars sponsored by Cores C and D of the Biostats Program Project award. This series, the "Happy Scientist" seminar series, is aimed at providing educational material for members of Biostats, both students and faculty, about a variety of tools and methods that might prove useful to them. If you have any suggestions for subjects that you would like to learn about in future, please send email to Paul Marjoram at (pmarjora@usc.edu). Our agenda will be driven by your specific interests as far as is possible. 

List of past seminars with material can be found [here](/happy_scientist/).

# USCbiostats R packages

```{r listing-pkgs, echo = FALSE}
pkgs <- c(
  "aphylo" = "Statistical inference of genetic functions in phylogenetic trees",
  "bayesnetworks" = "C++ program to fit Bayesian networks, illustrated with simulated data",
  "BinaryDosage" = "Converts VCF files to a binary format",
  "causnet" = "What the Package Does (One Line, Title Case)",
  "fdrci" = "Permutation-Based FDR Point and Confidence Interval Estimation",
  "fmcmc" = "A friendly MCMC framework",
  "GxEScanR" = "R version of GxEScan",
  "HiLDA" = "An R package for inferring the mutational exposures difference between groups",
  "iMutSig" = "A web application to identify the most similar mutational signature using shiny",
  "jsPhyloSVG" = "htmlwidgets for the jsPhyloSVG JavaScript library",
  "LUCIDus" = "Latent and Unknown Cluster Analysis using Integrated Data",
  "MergeBinaryDosage" = "R package for merging binary dosage files",
  "rphyloxml" = "Read and write phyloXML files in R",
  "selectKSigs" = "Selection of K in finding the number of mutational signatures",
  "slurmR" = "slurmR: A Lightweight Wrapper for Slurm",
  "partition" = "A fast and flexible framework for agglomerative partitioning in R ",
  "polygons" = "Flexible functions for computing polygons coordinates in R ",
  "xtune" = "An R package for Lasso and Ridge Regression with differential penalization based on prior knowledge ",
  "xrnet" = "R Package for Hierarchical Regularized Regression to Incorporate External Data",
  hJAM = "hJAM is a hierarchical model which unifies the framework of Mendelian Randomization and Transcriptome-wide association studies."
  )

# Alphabetically ordered
pkgs <- pkgs[order(names(pkgs))]

dat <- data.frame(
  Name        = names(pkgs),
  Description = paste(
    pkgs,
    sprintf(
      "[![CRAN status](https://www.r-pkg.org/badges/version/%s)](https://CRAN.R-project.org/package=%1$s)",
      names(pkgs)
    ),
    sprintf(
      "[![CRAN downloads](http://cranlogs.r-pkg.org/badges/grand-total/%s)](https://cran.r-project.org/package=%1$s)",
      names(pkgs)
    ),
    sprintf(
      "[![status](https://tinyverse.netlify.com/badge/%s)](https://CRAN.R-project.org/package=%1$s)",
      names(pkgs)
    )
), stringsAsFactors = FALSE)

dat[which(names(pkgs)=="HiLDA"), "Description"] <- paste(
  pkgs["HiLDA"],
  "[![](https://img.shields.io/badge/release%20version-1.0.0-green.svg)](https://www.bioconductor.org/packages/HiLDA)",
  "[![](https://img.shields.io/badge/download-718/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/HiLDA)"
)

dat[which(names(pkgs)=="selectKSigs"), "Description"] <- paste(
  pkgs["selectKSigs"],
  "[![](https://img.shields.io/badge/release%20version-1.0.0-green.svg)](https://www.bioconductor.org/packages/selectKSigs)",
  "[![](https://img.shields.io/badge/download-182/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/selectKSigs)"
)

knitr::kable(dat, row.names = FALSE)
```