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restrander
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public |
No Summary
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2024-09-16 |
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ldak6
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public |
No Summary
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2024-08-06 |
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tinytex
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public |
A lightweight LaTeX distribution based on TeX Live
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2024-04-29 |
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ngstools
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public |
Programs to analyse NGS data for population genetics purposes. (not to be confused with ngs-tools)
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2024-03-21 |
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r-corehunter
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public |
Core Hunter is a tool to sample diverse, representative subsets from large germplasm collections, with minimum redundancy. Such so-called core collections have applications in plant breeding and genetic resource management in general. Core Hunter can construct cores based on genetic marker data, phenotypic traits or precomputed distance matrices, optimizing one of many provided evaluation measures depending on the precise purpose of the core (e.g. high diversity, representativeness, or allelic richness). In addition, multiple measures can be simultaneously optimized as part of a weighted index to bring the different perspectives closer together. The Core Hunter library is implemented in Java 8 as an open source project (see <http://www.corehunter.org>).
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2024-03-07 |
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r-detectruns
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public |
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>).
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2024-02-29 |
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r-doubletfinder
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public |
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
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2024-02-29 |
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r-sccustomize
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public |
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.
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2024-02-29 |
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r-bbplot
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public |
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
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2024-01-23 |
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r-carma
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public |
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.
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2024-01-23 |
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r-ccgwas
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public |
More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description.
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2024-01-23 |
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r-genomicsem
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public |
Later
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2024-01-23 |
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r-sicegar
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public |
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".
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2024-01-17 |
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bolt-lmm-amd
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public |
Efficient large cohorts genome-wide Bayesian mixed-model association testing
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2024-01-08 |
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bolt-lmm
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public |
Efficient large cohorts genome-wide Bayesian mixed-model association testing
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2024-01-03 |
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r-tuneranger
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public |
Tuning random forest with one line. The package is mainly based on the packages 'ranger' and 'mlrMBO'.
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2023-12-01 |
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r-rubias
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public |
Implements Bayesian inference for the conditional genetic stock identification model. It allows inference of mixed fisheries and also simulation of mixtures to predict accuracy. A full description of the underlying methods is available in a recently published article in the Canadian Journal of Fisheries and Aquatic Sciences: <doi:10.1139/cjfas-2018-0016>.
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2023-10-31 |
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dogfinder
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public |
DoGFinder software is a package that identifies DoGs and quantifies their expression levels, from RNA-seq data.
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2023-10-13 |
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rstudio-desktop-rhel8-experimental
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public |
Experimental rstudio package to solve some local issues
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2023-09-07 |
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r-cytonorm
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public |
This package can be used to normalize cytometry samples when a control sample is taken along in each of the batches. This is done by first identifying multiple clusters/cell types, learning the batch effects from the control samples and applying quantile normalization on all markers of interest.
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2023-07-06 |
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r-hscovar
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public |
The theoretical covariance between pairs of markers is calculated from either paternal haplotypes and maternal linkage disequilibrium (LD) or vise versa. A genetic map is required. Grouping of markers is based on the correlation matrix and a representative marker is suggested for each group. Employing the correlation matrix, optimal sample size can be derived for association studies based on a SNP-BLUP approach. The implementation relies on paternal half-sib families and biallelic markers. If maternal half-sib families are used, the roles of sire/dam are swapped. Multiple families can be considered. Wittenburg, Bonk, Doschoris, Reyer (2020) "Design of Experiments for Fine-Mapping Quantitative Trait Loci in Livestock Populations" <doi:10.1186/s12863-020-00871-1>. Carlson, Eberle, Rieder, Yi, Kruglyak, Nickerson (2004) "Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium" <doi:10.1086/381000>.
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2023-06-18 |
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r-bedmatrix
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public |
A matrix-like data structure that allows for efficient, convenient, and scalable subsetting of binary genotype/phenotype files generated by PLINK (<https://www.cog-genomics.org/plink2>), the whole genome association analysis toolset, without loading the entire file into memory.
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2023-06-18 |
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r-crochet
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public |
Functions to help implement the extraction / subsetting / indexing function '[' and replacement function '[<-' of custom matrix-like types (based on S3, S4, etc.), modeled as closely to the base matrix class as possible (with tests to prove it).
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2023-06-18 |
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gz-sort
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public |
No Summary
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2023-06-18 |
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gmrm
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public |
A Bayesian grouped mixture of regressions model capable of estimating SNP marker effect sizes for multiple outcomes simultaneously
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2023-06-18 |
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r-ngslca
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public |
Provides functionality for processing lca files generated by the 'ngsLCA' main program <https://github.com/miwipe/ngsLCA> and visualizing taxonomic profiles.
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2023-06-18 |
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qmihr
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public |
No Summary
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2023-06-18 |
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r-bhr
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public |
More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description.
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2023-06-18 |
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r-sdmpredictors
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public |
Terrestrial and marine predictors for species distribution modelling from multiple sources, including WorldClim <https://www.worldclim.org/>,, ENVIREM <https://envirem.github.io/>, Bio-ORACLE <https://bio-oracle.org/> and MARSPEC <http://www.marspec.org/>.
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2023-06-18 |
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r-ldheatmap
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public |
Produces a graphical display, as a heat map, of measures of pairwise linkage disequilibria between single nucleotide polymorphisms (SNPs). Users may optionally include the physical locations or genetic map distances of each SNP on the plot. The methods are described in Shin et al. (2006) <doi:10.18637/jss.v016.c03>. Users should note that the imported package 'snpStats' and the suggested packages 'rtracklayer', 'GenomicRanges', 'GenomInfoDb' and 'IRanges' are all BioConductor packages <https://bioconductor.org>.
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2023-06-18 |
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r-terra
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public |
Methods for spatial data analysis with raster and vector data. Raster methods allow for low-level data manipulation as well as high-level global, local, zonal, and focal computation. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/terra/> to get started. 'terra' is very similar to the 'raster' package; but 'terra' can do more, is simpler to use, and it is faster.
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2023-06-18 |
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gdk-mvapich2
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public |
MPI implementation for GenomeDK
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2023-06-18 |
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somalier
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public |
No Summary
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2023-06-18 |
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gdk-mpich-mpifort
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public |
A high performance widely portable implementation of the MPI standard.
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2023-06-18 |
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gdk-mpich-mpicxx
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public |
A high performance widely portable implementation of the MPI standard.
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2023-06-18 |
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gdk-mpich-mpicc
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public |
A high performance widely portable implementation of the MPI standard.
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2023-06-18 |
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gdk-mpich
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public |
A high performance widely portable implementation of the MPI standard.
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2023-06-18 |
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py-mixer
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public |
No Summary
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2023-06-18 |
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msmc2
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public |
This program implements MSMC2, a method to infer population size history and population separation history from whole genome sequencing data.
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2023-06-18 |
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k-mers-gwas
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public |
No Summary
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2023-06-18 |
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maftools
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public |
mafTools is a collection of tools that operate on Multiple Alignment Format (maf) files.
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2023-06-18 |
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pinchesandcacti
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public |
This is a library for creating pinch graphs (generalised overlap graphs) and cactus graphs.
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2023-06-18 |
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asset-dfguan
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public |
Assembly evaluation tool
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2023-06-18 |
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gromacs
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public |
GROMACS is a versatile package to perform molecular dynamics.
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2023-06-18 |
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quicktest
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public |
Methods for testing association between uncertain genotypes and quantitative traits
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2023-06-18 |
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ohana
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public |
Ohana is a suite of software for analyzing population structure and admixture history using unsupervised learning methods.
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2023-06-18 |
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kplogo
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public |
k-mer probability logo (kpLogo) is a computational tool for sensitive discovery and visualization of position-specific ultra-short sequence motifs from a set of sequences with precisely defined positions.
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2023-06-18 |
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greedy-diffeomorphic
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public |
Very fast greedy diffeomorphic registration code.
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2023-06-18 |
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r-scenic
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public |
SCENIC (Single-Cell rEgulatory Network Inference and Clustering) is a computational method to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
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2023-06-18 |
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combined-pvalues-py37
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public |
A library to combine, analyze, group and correct p-values in BED files.
Unique tools involve correction for spatial autocorrelation.
This is useful for ChIP-Seq probes and Tiling arrays, or any data with spatial correlation.
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2023-06-18 |
