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Software Development Standards GitHub last commit

This project’s main contents are located in the project’s Wiki.

USCbiostats R packages

As of 2023-12-05, the packages listed here have been cited 135 times (source: Google Scholar).

Name Description Citations
AnnoQR R client wrap for AnnoQ API (https://github.com/blueOwl/AnnoQR)
aphylo Statistical inference of genetic functions in phylogenetic trees CRAN status CRAN downloads status 3
bayesnetworks C++ program to fit Bayesian networks, illustrated with simulated data
BinaryDosage Converts VCF files to a binary format CRAN status CRAN downloads status
causnet What the Package Does (One Line, Title Case)
cit Causal Inference Test CRAN status CRAN downloads status 26
fdrci Permutation-Based FDR Point and Confidence Interval Estimation CRAN status CRAN downloads status 28
fmcmc A friendly MCMC framework CRAN status CRAN downloads status 9
gesso Hierarchical GxE Interactions in a Regularized Regression Model CRAN status CRAN downloads status 3
GxEScanR R version of GxEScan CRAN status CRAN downloads status
HiLDA An R package for inferring the mutational exposures difference between groups 6
hJAM hJAM is a hierarchical model which unifies the framework of Mendelian Randomization and Transcriptome-wide association studies. CRAN status CRAN downloads status 4
iMutSig A web application to identify the most similar mutational signature using shiny 1
jsPhyloSVG htmlwidgets for the jsPhyloSVG JavaScript library
LUCIDus Latent and Unknown Cluster Analysis using Integrated Data CRAN status CRAN downloads status 19
MergeBinaryDosage R package for merging binary dosage files
methcon5 R package to identify and rank CpG DNA methylation conservation along the human genome CRAN status CRAN downloads status 3
partition A fast and flexible framework for agglomerative partitioning in R CRAN status CRAN downloads status 7
pfamscanr An R client for EMBL-EBI’s PfamScan API
polygons Flexible functions for computing polygons coordinates in R
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 CRAN status CRAN downloads status 5
xrnet R Package for Hierarchical Regularized Regression to Incorporate External Data CRAN status CRAN downloads status 1
xtune An R package for Lasso and Ridge Regression with differential penalization based on prior knowledge CRAN status CRAN downloads status 20

To update this list, modify the file packages.csv. The README.md file is updated automatically using GitHub Actions, so there’s no need to “manually” recompile the README file after updating the list.

Coding Standards

  1. Coding Standards
  2. Software Thinking
  3. Development Workflow
  4. Misc

We do have some direct guidelines developed as issue templates here.

Bioghost Server

  1. Introduction
  2. Setup
  3. Cheat Sheet

HPC in R

Happy Scientist Seminars

The Happy Scientist Seminars are educational seminars sponsored by Cores C and D of IMAGE, 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 ([email protected]). Our agenda will be driven by your specific interests as far as is possible.

List of past seminars with material can be found here.