genomedk
by GenomeDK (Organization)
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Packages
| Name | Latest Version | Summary | Updated | License |
|---|
| r-doubletfinder | 2.0.4 | DoubletFinder identifies doublets by generating artificial doublets from existing scRNA-seq data and defining which real cells preferentially co-localize with artificial doublets in gene expression space. Other DoubletFinder package functions are used for fitting DoubletFinder to different scRNA-seq datasets. For example, ideal DoubletFinder performance in real-world contexts requires (I) Optimal pK selection and (2) Homotypic doublet proportion estimation. pK selection is achieved using pN-pK parameter sweeps and maxima identification in mean-variance-normalized bimodality coefficient distributions. Homotypic doublet proportion estimation is achieved by finding the sum of squared cell annotation frequencies. For more information, see our Cell Sysmtes paper https://www.cell.com/cell-systems/fulltext/S2405-4712(19)30073-0 and our github https://github.com/chris-mcginnis-ucsf/DoubletFinder | Mar 25, 2025 | CC-0 |
| r-sccustomize | 2.1.2 | Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430> RRID:SCR_024675. | Mar 25, 2025 | GPL-3 |
| ldak6 | 6.1 | — | Mar 25, 2025 | — |
| r-sicegar | 0.2.4 | Aims to quantify time intensity data by using sigmoidal and double sigmoidal curves. It fits straight lines, sigmoidal, and double sigmoidal curves on to time vs intensity data. Then all the fits are used to make decision on which model best describes the data. This method was first developed in the context of single-cell viral growth analysis (for details, see Caglar et al. (2018) <doi:10.7717/peerj.4251>), and the package name stands for "SIngle CEll Growth Analysis in R". | Mar 25, 2025 | GPL-2 | GPL-3 |
| restrander | 1.1.3 | — | Dec 23, 2025 | — |
| r-carma | 1.0 | Implementations for the Bayesian fine-mapping method CAusal Robust Mapping method with Annotations (CARMA). CARMA uses common GWAS data and linkage disequilibrium (LD) from external panels to predict causal variants. CARMA allows users to introduce functional annotations to jointly models summary statistics of GWAS and high-dimensional functional annotations. Also, CARMA provides a novel Bayesian hypothesis testing approach to account for discrepancies between summary statistics and LD from external reference panels in order to avoid an increase in false positives. | Mar 25, 2025 | GPL-2 |
| ngstools | 0.0.1 | Programs to analyse NGS data for population genetics purposes. (not to be confused with ngs-tools) | Mar 25, 2025 | GPL-3+ |
| r-spacemix | 0.13 | Runs SpaceMix: a method for inferring and visualizing patterns of population genetic structure | Jun 27, 2025 | BSD |
| r-detectruns | 0.9.6.9000 | Detection of runs of homozygosity and of heterozygosity in diploid genomes using two methods: sliding windows (Purcell et al (2007) <doi:10.1086/519795>) and consecutive runs (Marras et al (2015) <doi:10.1111/age.12259>). | Mar 25, 2025 | GPL-3 |
| r-ccgwas | 0.1.0 | More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description. | Mar 25, 2025 | What license is it under? |
| scdrs | 1.0.3b | Single-cell disease-relevance score | Feb 6, 2026 | MIT |
| bolt-lmm-amd | 2.4.1 | Efficient large cohorts genome-wide Bayesian mixed-model association testing | Mar 25, 2025 | GPL-3+ |
| r-hyprcoloc | 0.0.2 | Hypothesis Prioritisation in multi-trait Colocalization | Nov 17, 2025 | GPL-v3 |
| r-lfmm | 1.0 | Implements statistical methods for adjusting confounding factors in association studies. | Sep 9, 2025 | GPL-3 |
| r-rcpphungarian | 0.3 | Header library and R functions to solve minimum cost bipartite matching problem using Huhn-Munkres algorithm (Hungarian algorithm; <https://en.wikipedia.org/wiki/Hungarian_algorithm>; Kuhn (1955) <doi:10.1002/nav.3800020109>). This is a repackaging of code written by Cong Ma in the GitHub repo <https://github.com/mcximing/hungarian-algorithm-cpp>. | May 19, 2025 | GPL-2 |
| r-bbplot | 0.2 | Helps create and export ggplot2 charts in the style used by the BBC News data team thanks to two useful functions, one for styling and another for exporting ggplot graphics | Mar 25, 2025 | GPL-2 |
| r-covtools | 0.5.4 | Covariance is of universal prevalence across various disciplines within statistics. We provide a rich collection of geometric and inferential tools for convenient analysis of covariance structures, topics including distance measures, mean covariance estimator, covariance hypothesis test for one-sample and two-sample cases, and covariance estimation. For an introduction to covariance in multivariate statistical analysis, see Schervish (1987) <doi:10.1214/ss/1177013111>. | Jul 24, 2025 | GPL-3 |
| r-sht | 0.1.9 | We provide a collection of statistical hypothesis testing procedures ranging from classical to modern methods for non-trivial settings such as high-dimensional scenario. For the general treatment of statistical hypothesis testing, see the book by Lehmann and Romano (2005) <doi:10.1007/0-387-27605-X>. | Jul 24, 2025 | MIT |
| perl | 5.26.2 | — | Mar 25, 2025 | Perl Artistic |
| tinytex | 2026.02 | A lightweight LaTeX distribution based on TeX Live | Feb 10, 2026 | GPL2 |
| redundans | 2020.01.28 | — | Mar 25, 2025 | — |
| treepl | 2.6.3 | Phylogenetic penalized likelihood | Mar 25, 2025 | Unknown |
| rnahybrid | 2.1.2 | RNAhybrid is a tool for finding the minimum free energy hybridization of a long and a short RNA. | Mar 25, 2025 | GPLv2 |
| maffilter | 1.3.1 | The MafFilter genome alignment processor | Mar 25, 2025 | GPLv3 |
| hail | 2020.07.31 | Hail is an open-source, general-purpose, Python-based data analysis tool with additional data types and methods for working with genomic data. | Mar 25, 2025 | MIT |