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# Stanford R packages

Stanford R packages Menu

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 |