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r-bigqf
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public |
A computationally-efficient leading-eigenvalue approximation to tail probabilities and quantiles of large quadratic forms, in particular for the Sequence Kernel Association Test (SKAT) used in genomics <doi:10.1002/gepi.22136>. Also provides stochastic singular value decomposition for dense or sparse matrices.
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2026-03-18 |
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r-coxme
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public |
Fit Cox proportional hazards models containing both fixed and random effects. The random effects can have a general form, of which familial interactions (a "kinship" matrix) is a particular special case. Note that the simplest case of a mixed effects Cox model, i.e. a single random per-group intercept, is also called a "frailty" model. The approach is based on Ripatti and Palmgren, Biometrics 2002.
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2026-03-18 |
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hail
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public |
Hail is Python-based data analysis tool for working with genomic data.
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2026-03-16 |
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r-susier
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public |
Implements methods for variable selection in linear regression based on the "Sum of Single Effects" (SuSiE) model, as described in Wang et al (2020) <DOI:10.1101/501114>. These methods provide simple summaries, called "Credible Sets", for accurately quantifying uncertainty in which variables should be selected.
The methods are motivated by genetic fine-mapping applications, and are particularly well-suited to settings where variables are highly correlated and detectable effects are sparse. The fitting algorithm, a Bayesian analogue of stepwise selection methods called "Iterative Bayesian Stepwise Selection" (IBSS), is simple
and fast, allowing the SuSiE model be fit to large data sets (thousands of samples and hundreds of thousands of variables).
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2026-03-10 |
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r-pecotmr
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public |
pecotmr implements pair-wise enrichment, colocalization, TWAS and Mendelian Randomization to integrate QTL and GWAS analysis based on a fine-mapped single effects model.
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2026-03-04 |
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bioconductor-snpstats
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public |
SnpMatrix and XSnpMatrix classes and methods
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2026-03-04 |
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r-colocboost
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public |
Multi-context colocalization analysis tool for molecular QTL and GWAS studies
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2026-03-04 |
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r-mr.mashr
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public |
Provides an implementation of methods for multivariate
multiple regression with adaptive shrinkage priors.
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2026-03-04 |
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yabai
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public |
A tiling window manager for macOS based on binary space partitioning
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2026-03-02 |
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count_somatic
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public |
A Rust program for counting somatic variants from VCF/BCF files, with support for Illumina Dragen and Graphtyper BCF/VCFs.
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2026-02-18 |
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oncokb-annotator
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public |
Annotates variants in MAF with OncoKB annotation.
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2026-02-04 |
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r-udr
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public |
R package implementing empirical Bayes methods for multivariate normal means.
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2026-01-29 |
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r-l0learn
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public |
Highly optimized toolkit for approximately solving L0-regularized learning problems (a.k.a. best subset selection). The algorithms are based on coordinate descent and local combinatorial search.
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2026-01-27 |
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leafcutter2
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public |
LeafCutter2 is a tool for clustering, functional characterization and quantification of splice junction read counts.
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2026-01-27 |
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r-archr
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public |
Analysis of Regulatory Chromatin in R
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2026-01-06 |
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gfold
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public |
CLI tool to help keep track of your Git repositories, written in Rust
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2025-12-28 |
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tabiew
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public |
A lightweight TUI application to view and query tabular data files, such as CSV, TSV, and parquet.
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2025-12-28 |
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filessh
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public |
A fast and convenient TUI file browser for remote servers
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2025-12-26 |
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qsv
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public |
Ultra-fast CSV data-wrangling toolkit
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2025-12-26 |
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dxda
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public |
CLI tool to manage the download of large quantities of files from DNAnexus
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2025-12-13 |
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ssed
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public |
Super sed stream editor
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2025-12-12 |
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r-knockoff
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public |
The knockoff filter is a general procedure for controlling the false discovery rate::
(FDR) when performing variable selection. For more information, see the website
below and the accompanying paper: Candes et al., "Panning for gold: model-X knockoffs'
for high-dimensional controlled variable selection", J. R. Statist. Soc. B (2018)
80, 3, pp. 551-577.
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2025-12-08 |
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r-rdsdp
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public |
R interface to DSDP semidefinite programming library. The DSDP software is a free
open source implementation of an interior-point method for semidefinite programming.
It provides primal and dual solutions, exploits low-rank structure and sparsity
in the data, and has relatively low memory requirements for an interior-point method.
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2025-12-08 |
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r-mr.mash.alpha
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public |
Provides an implementation of methods for multivariate
multiple regression with adaptive shrinkage priors.
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2025-12-02 |
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r-mr.ash.alpha
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public |
Implements variational empirical Bayes methods for linear
regression. Coordinate-wise optimization algorithms for model fitting
are implemented in C++ for efficient handling of large-scale data
sets.
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2025-11-13 |
