This tool provides an algorithm to identify rare cell types in single-cell data. It also identifies abundant cell types. The method is based on transcript counts obtained with unique molecular identifies.

This package is a port of sofia-ml to R. Sofia-ml is a suite of fast incremental algorithms for machine learning that can be used for training models for classification or ranking.

This package provides an interface for the Basic Local Alignment Search Tool (BLAST) to search genetic sequence data bases. This includes interfaces to blastn, blastp, blastx, and makeblastdb.

This is a package for biclustering analysis and exploration of results.

This R package provides additional capabilities and speed for GenomicRanges operations.

This package can be used to compute local false discovery rates.

This package provides a collection of miscellaneous 3d plots, including isosurfaces.

This package allows users to test characteristics of common R objects.

This package provides a fast and scalable test runner for Ruby.

This package provides a rofi frontend for the buku bookmark manager.

Predicts the sex of samples in gene expression microarray datasets.

This package provides an R wrapper around the argon library.

LIGER is a package for integrating and analyzing multiple single-cell datasets, developed and maintained by the Macosko lab. It relies on integrative non-negative matrix factorization to identify shared and dataset-specific factors.

Seamlessly interfaces the Basic Local Alignment Search Tool (BLAST) running locally to search genetic sequence data bases. This work was partially supported by grant no. R21HG005912 from the National Human Genome Research Institute.

This package performs optimization in R using C++. A unified wrapper interface is provided to call C functions of the five optimization algorithms (Nelder-Mead, BFGS, CG, L-BFGS-B and SANN) underlying optim().

This package provides a toolkit of functions for nonlinear regression and repeated measurements. It was designated to be imported by other packages such as gnlm, stable, growth, repeated, and event.

This is the core package for the automated analysis of Affymetrix arrays.

This package provides a pipeline for the analysis of GRO-seq data.

This package provides basic features for the automated analysis of Affymetrix arrays.

This package performs a fast Wilcoxon rank sum test and auROC analysis.

This package provides functions used for local regression, likelihood and density estimation.

This package provides a utility for R to parse a bibtex file.

This package provides tools to calculate the Earth Mover's Distance (EMD).

This package provides miscellaneous helper functions for the development of R packages.