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R packages maintained by Stanford R community members. These can be found on the Comprehensive R Archive Network (CRAN) or on Bioconductor.org. We are stlil working to complete this list. If you would like your package listed here please contact amyhodge@stanford.edu.
| Package Name | Description | Maintainer (Email link) |
| AIM | AIM: adaptive index model | Robert Tibshirani |
| akmeans | Adaptive Kmeans algorithm based on threshold | Jungsuk Kwac |
| allan | Automated Large Linear Analysis Node | Alan Lee |
| argparse | Command line optional and positional argument parser | Trevor L Davis |
| ASSISTant | Adaptive Subgroup Selection in Group Sequential Trials | |
| bigKRLS | bigKRLS: Optimized Kernel Regularized Least Squares | |
| biom | An interface package (beta) for the BIOM file format | Paul J. McMurdie |
| biomformat | An interface package for the BIOM file format | Paul J. McMurdie |
| BiSeq | Processing and analyzing bisulfite sequencing data | Katja Hebestreit |
| cate | High Dimensional Factor Analysis and Confounder Adjusted Testing and Estimation | Qingyuan Zhao |
| CBPS | Covariate Balancing Propensity Score | Christian Fong |
| DF.PSIdekick | CDF.PSIdekick: Evaluate Differentially Private Algorithms for Publishing Cumulative Distribution Functions | Daniel Muise |
| clogitL1 | Fitting exact conditional logistic regression with lasso and elastic net penalties | Stephen Reid |
| COCONUT | COmbat CO-Normalization Using conTrols (COCONUT) | Timothy E Sweeney |
| COMMUNAL | Robust Selection of Cluster Number K | Albert Chen |
| ConjointChecks | A package to check the cancellation axioms of conjoint measurement | Ben Domingue |
| covTest | Computes covariance test for adaptive linear modelling | Rob Tibshirani |
| cubature | Adaptive multivariate integration over Hypercubes | Balasubramanian Narasimhan |
| customizedTraining | Customized Training for Lasso and Elastic-Net Regularized Generalized Linear Models | Scott Powers |
| CVcalibration | Estimation of the Calibration Equation with Error-in Observations | Lu Tian |
| deconvolveR | Empirical Bayes Estimation Strategies | Balasubramanian Narasimhan |
| distcomp | Computations over Distributed Data without Aggregation | Balasubramanian Narasimhan |
| distory | Distance Between Phylogenetic Histories | Susan Holmes |
| ebal | Entropy reweighting to create balanced samples | Jens Hainmueller |
| ECOSolveR | Embedded Conic Solver in R | Balasubramanian Narasimhan |
| exactmeta | Exact fixed effect meta analysis | Lu Tian |
| findpython | Python tools to find an acceptable python binary | Trevor L Davis |
| freqdom | Frequency Domain Based Analysis: Dynamic PCA | Lukas Kidzinski |
| freqdom.fda | Functional Time Series: Dynamic Functional Principal Components | Lukas Kidzinski |
| gam | Generalized Additive Models | Trevor Hastie |
| gamsel | Fit Regularization Path for Generalized Additive Models | Trevor Hastie |
| gconcord | Concord method for Graphical Model Selection | Sang-Yun Oh |
| getopt | C-like getopt behavior | Trevor L Davis |
| glasso | Graphical lasso- estimation of Gaussian graphical models | Rob Tibshirani |
| glmnet | Lasso and Elastic-Net Regularized Generalized Linear Models | Trevor Hastie |
| grf | Generalized Random Forests (Beta) | Julie Tibshirani |
| GSA | Gene set analysis | Rob Tibshirani |
| happybiRthday | Calculate Upcoming Birthday Dates of Github Repos | Bohdan Khomtchouk |
| homomorpheR | Homomorphic Computations in R | Balasubramanian Narasimhan |
| igraphtosonia | Convert iGraph graps to SoNIA .son files | Sean J Westwood |
| impute | impute: Imputation for microarray data | Balasubramanian Narasimhan |
| ISLR | Data for An Introduction to Statistical Learning with Applications in R | Trevor Hastie |
| ivmodel | Statistical Inference and Sensitivity Analysis for Instrumental Variables Model | Hyunseung Kang |
| kerasformula | kerasformula: A High-Level R Interface for Neural Nets | Pete Mohanty |
| knockoff | Knockoff Filter for Controlling the False Discovery Rate | Evan Patterson |
| KRLS | Kernel-based Regularized Least squares (KRLS) | Jens Hainmueller |
| lars | Least Angle Regression, Lasso and Forward Stagewise | Trevor Hastie |
| locfdr | Computes Local False Discovery Rates | Balasubramanian Narasimhan |
| LocFDRPois | Functions for Performing Local FDR Estimation when Null and Alternative are Poisson | Kris Sankaran |
| lrgs | Linear Regression by Gibbs Sampling | Adam Mantz |
| mda | Mixture and Flexible Discriminant Analysis | Trevor Hastie |
| mdsdt | Functions for Analysis of Data with General Recognition Theory | Robert X.D. Hawkins |
| MetaIntegrator | Meta-Analysis of Gene Expression Data | Winston A. Haynes |
| MFKnockoffs | Model-Free Knockoff Filter for Controlled Variable Selection | Matteo Sesia |
| modeval | Evaluation of Classification Model Options | Younggun You |
| mRchmadness | Numerical Tools for Filling Out an NCAA Basketball Tournament Bracket | Eli Shayer |
| nearfar | Near-Far Matching | Joseph Rigdon |
| NetCluster | Clustering for networks | Sean J Westwood |
| npmr | Nuclear Penalized Multinomial Regression | Scott Powers |
| optismixture | Optimal Mixture Weights in Multiple Importance Sampling | Hera Y. He |
| optrdd | Optimized Regression Discontinuity Designs | Stefan Wager |
| orderedLasso | Ordered Lasso and Time-lag Sparse Regression | Xiaotong Suo |
| PAC | Partition-Assisted Clustering and Multiple Alignments of Networks | Ye Henry Li |
| pamr | Pam: prediction analysis for microarrays | Rob Tibshirani |
| pcdpca | Dynamic Principal Components for Periodically Correlated Functional Time Series | Lukasz Kidzinski |
| phyloseq | Handling and analysis of high-throughput microbiome census data | Paul J. McMurdie |
| popRange | popRange: A spatially and temporally explicit forward genetic simulator | Kimberly F. McManus |
| ProDenICA | Product Density Estimation for ICA using tilted Gaussian density estimates | Trevor Hastie |
| prototest | Inference on Prototypes from Clusters of Features | Stephen Reid |
| pscl | Political Science Computational Laboratory, Stanford University | Simon Jackman |
| ptycho | Bayesian Variable Selection with Hierarchical Priors | Laurel Stell |
| pweight | P-Value Weighting | Edgar Dobriban |
| QuantileGradeR | Quantile-Adjusted Restaurant Grading | Zoe Ashwood |
| RCA | Relational Class Analysis | Amir Goldberg |
| RandMeta | Efficient Numerical Algorithm for Exact Inference in Meta Analysis | Lu Tian |
| rda | Shrunken Centroids Regularized Discriminant Analysis | Rob Tibshirani |
| Rdsdp | R Interface to DSDP Semidefinite Programming Library | Zhisu Zhu |
| rgw | Goodman-Weare Affine-Invariant Sampling | Adam Mantz |
| RImmPort | RImmPort: Enabling Ready-for-analysis Immunology Research Data | Ravi Shankar |
| rolypoly | Identifying Trait-Relevant Functional Annotations | Diego Calderon |
| samr | SAM: Significance Analysis of Microarrays | Rob Tibshirani |
| sddpack | Semidiscrete Decomposition | Eric Sun |
| selectiveInference | Tools for Post-Selection Inference | Rob Tibshirani |
| SGL | Fit a GLM (or cox model) with a combination of lasso and group lasso regularization | Noah Simon |
| sglr | An R package for power and boundary calculations in pre-licensure vaccine trials using a sequential generalized likelihood ratio test | Balasubramanian Narasimhan |
| shuffle | The shuffle estimator for explainable variance | Yuval Benjamini |
| sisVIVE | Some Invalid Some Valid Instrumental Variables Estimator | Hyunseung Kang |
| SLOPE | Sorted L1 Penalized Estimation (SLOPE) | Evan Patterson |
| softImpute | Matrix Completion via Iterative Soft-Thresholded SVD | Trevor Hastie |
| sp23design | Design and Simulation of seamless Phase II-III Clinical Trials | Balasubramanian Narasimhan |
| spade | SPADE -- An analysis and visualization tool for Flow Cytometry | Zach Bjornson |
| sparsenet | Fit sparse linear regression models via nonconvex optimization | Trevor Hastie |
| structSSI | Multiple Testing for Hypotheses with Hierarchical or Group Structure | Kris Sankaran |
| superpc | Supervised principal components | Rob Tibshirani |
| Sushi | Tools for visualizing genomics data | Douglas H Phanstiel |
| svmpath | The SVM Path algorithm | Trevor Hastie |
| Synth | Synthetic Control Group Method for Comparative Case Studies | Jens Hainmueller |
| TANOVA | Time Course Analysis of Variance for Microarray | Weihong Xu |
| uniCox | Univarate shrinkage prediction in the Cox model | Rob Tibshirani |
| VDSPCalibration | Statistical Methods for Designing and Analyzing a Calibration Study | Lu Tian |