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r-ggrasp
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public |
Given a group of genomes and their relationship with each other, the package clusters the genomes and selects the most representative members of each cluster. Additional data can be provided to the prioritize certain genomes. The results can be printed out as a list or a new phylogeny with graphs of the trees and distance distributions also available. For detailed introduction see: Thomas H Clarke, Lauren M Brinkac, Granger Sutton, and Derrick E Fouts (2018), GGRaSP: a R-package for selecting representative genomes using Gaussian mixture models, Bioinformatics, bty300, <doi:10.1093/bioinformatics/bty300>.
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2025-04-22 |
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msisensor
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public |
MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline.
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2025-04-22 |
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r-coenocliner
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public |
Simulate species occurrence and abundances (counts) along gradients.
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2025-04-22 |
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r-phylosignal
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public |
A collection of tools to explore the phylogenetic signal in univariate and multivariate data. The package provides functions to plot traits data against a phylogenetic tree, different measures and tests for the phylogenetic signal, methods to describe where the signal is located and a phylogenetic clustering method.
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2025-04-22 |
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r-phylomeasures
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public |
Given a phylogenetic tree T and an assemblage S of species represented as a subset of tips in T, we want to compute a measure of the diversity of the species in S with respect to T. The current package offers efficient algorithms that can process large phylogenetic data for several such measures. Most importantly, the package includes algorithms for computing efficiently the standardized versions of phylogenetic measures and their p-values, which are essential for null model comparisons. Among other functions, the package provides efficient computation of richness-standardized versions for indices such as the net relatedness index (NRI), nearest taxon index (NTI), phylogenetic diversity index (PDI), and the corresponding indices of two-sample measures. The package also introduces a new single-sample measure, the Core Ancestor Cost (CAC); the package provides functions for computing the value and the standardised index of the CAC and, more than that, there is an extra function available that can compute exactly any statistical moment of the measure. The package supports computations under different null models, including abundance-weighted models.
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2025-04-22 |
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r-bipartite
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public |
Functions to visualise webs and calculate a series of indices commonly used to describe pattern in (ecological) webs. It focuses on webs consisting of only two levels (bipartite), e.g. pollination webs or predator-prey-webs. Visualisation is important to get an idea of what we are actually looking at, while the indices summarise different aspects of the web's topology.
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2025-04-22 |
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gembs
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public |
gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (WGBS).
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2025-04-22 |
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convert_zero_one_based
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public |
Convert between zero and one based coordinate systems
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2025-04-22 |
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ribotish
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public |
Ribo TIS Hunter (Ribo-TISH) identifies translation activities using ribosome profiling data.
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2025-04-22 |
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deploid
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public |
A software that deconvolutes mixed genomes with unknown proportions.
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2025-04-22 |
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phame
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public |
A tool to derive SNP matrices and phylogenetic tree from raw reads, contigs, and full genomes.
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2025-04-22 |
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pblaa
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public |
PacBio tool to deconvolute mixtures of alleles and loci into phased consensus sequences.
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2025-04-22 |
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bs_call
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public |
DNA methylation and variant Caller for Bisulfite Sequencing Data.
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2025-04-22 |
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sourcetracker
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public |
Python implementation of the SourceTracker R package.
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2025-04-22 |
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squid
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public |
Detector for fusion-gene and non-fusion-gene transcriptomic structural variations from RNA-seq data
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2025-04-22 |
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pairtools
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public |
CLI tools to process mapped Hi-C data.
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2025-04-22 |
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barriers
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public |
Compute local minima and energy barriers of a landscape.
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2025-04-22 |
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vkmz
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public |
metabolomics formula prediction and van Krevelen diagram generation
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2025-04-22 |
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perl-test-without-module
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public |
Test fallback behaviour in absence of modules
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2025-04-22 |
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perl-class-singleton
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public |
Base class for creating singleton objects
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2025-04-22 |
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r-ichorcna
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public |
Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
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2025-04-22 |
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perl-package-stash-xs
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public |
faster and more correct implementation of the Package::Stash API
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2025-04-22 |
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gem3-mapper
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public |
The GEM read mapper (v3).
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2025-04-22 |
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pheniqs
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public |
Pheniqs is a flexible generic barcode classifier for high-throughput next-gen sequencing written in multi threaded C++11. It caters to a wide variety of experimental designs by addressing multiple combinatorial index tags in arbitrary locations along reads. Pheniqs implements a noise and quality aware probabilistic classifier with improved accuracy over standard edit distance methods and reports classification quality in standard SAM auxiliary tags. Please not configuation syntax has slightly changed for 2.1.x version.
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2025-04-22 |
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bamclipper
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public |
Remove primer sequence from BAM alignments by soft-clipping.
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2025-04-22 |
