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r-diversitree
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public |
Contains a number of comparative 'phylogenetic' methods, mostly focusing on analysing diversification and character evolution. Contains implementations of 'BiSSE' (Binary State 'Speciation' and Extinction) and its unresolved tree extensions, 'MuSSE' (Multiple State 'Speciation' and Extinction), 'QuaSSE', 'GeoSSE', and 'BiSSE-ness' Other included methods include Markov models of discrete and continuous trait evolution and constant rate 'speciation' and extinction.
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2025-03-25 |
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psmc
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public |
Pairwise Sequentially Markovian Coalescent
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2025-03-25 |
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snoreport
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public |
SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification
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2025-03-25 |
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stacks
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public |
Stacks is a software pipeline for building loci from RAD-seq
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2025-03-25 |
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r-lava-jw
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public |
Melds genome-wide association tests with structural equation modeling (SEM) using 'OpenMx'. This package contains low-level C/C++ code to rapidly read genetic data encoded in U.K. Biobank or 'plink' formats. Prebuilt modeling options include one and two factor models. Alternately, analyses may utilize arbitrary, user-provided SEMs. See Verhulst, Maes, & Neale (2017) <doi:10.1007/s10519-017-9842-6> for details. An updated manuscript is in preparation.
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2025-03-25 |
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r-matrixsampling
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public |
Provides samplers for various matrix variate distributions: Wishart, inverse-Wishart, normal, t, inverted-t, Beta type I, Beta type II, Gamma, confluent hypergeometric. Allows to simulate the noncentral Wishart distribution without the integer restriction on the degrees of freedom.
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2025-03-25 |
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r-superfreq
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public |
SuperFreq analyses SNVs and CNAs of multiple cancer exomes, sharing all information across samples and mutation types. The inputs are the bam-files and a preliminary SNV calling in .vcf format. SuperFreq filters and annotates the SNVs, calls CNAs and tracks clones over samples from the same individual. A matched normal improves results, but is not necessary. SuperFreq requireas at least two (preferably 5-10 or more) reference normal samples that do not have to be related to the studied cancer samples, but must be from the same sequencing platform and capture. These are used to improve results through variance of read depth and requrring false SNVs amongst other things. SuperFreq produces ample output in terms of plots and spread sheets, both for identifying properties of the cancer samples and for quality control.
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2025-03-25 |
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r-gwsem
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public |
Melds genome-wide association tests with structural equation modeling (SEM) using 'OpenMx'. This package contains low-level C/C++ code to rapidly read genetic data encoded in U.K. Biobank or 'plink' formats. Prebuilt modeling options include one and two factor models. Alternately, analyses may utilize arbitrary, user-provided SEMs. See Verhulst, Maes, & Neale (2017) <doi:10.1007/s10519-017-9842-6> for details. An updated manuscript is in preparation.
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2025-03-25 |
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seq-lang
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public |
A strongly-typed and statically-compiled high-performance Pythonic language!
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2025-03-25 |
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r-diem
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public |
Identification of debris-containing droplets from a droplet-based single cell/nucleus RNA-seq. 'diem' classifies droplets by modeling droplet expression with a multinomial mixture model. Droplets are assigned to debris or cell type clusters after estimating parameters with expectation maximization (EM). Provides quantifications of contamination in individual droplets for filtering and use as a covariate. See Alvarez M, Rahmani E, et al (2019) <doi:10.1101/786285> for details.
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2025-03-25 |
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tinytex
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public |
A lightweight LaTeX distribution based on TeX Live
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2025-03-25 |
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treepl
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public |
Phylogenetic penalized likelihood
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2025-03-25 |
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rnahybrid
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public |
RNAhybrid is a tool for finding the minimum free energy hybridization of a long and a short RNA.
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2025-03-25 |
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primer3
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public |
Design PCR primers from DNA sequence. From mispriming libraries to sequence quality data to the generation of internal oligos, primer3 does it.
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2025-03-25 |
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exabayes
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public |
ExaBayes is a software package for Bayesian tree inference. It is particularly suitable for large-scale analyses on computer clusters.
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2025-03-25 |
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fdstools
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public |
Forensic DNA Sequencing Tools
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2025-03-25 |
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phyx
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public |
No Summary
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2025-03-25 |
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epacts
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public |
No Summary
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2025-03-25 |
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regenie
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public |
whole genome regression modelling of large genome-wide association studies
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2025-03-25 |
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singularity
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public |
Singularity: Application containers for Linux
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2025-03-25 |
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grapes-static
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public |
Rate of Adaptive Protein Evolution Software
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2025-03-25 |
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argweaver
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public |
Sampling and manipulating genome-wide ancestral recombination graphs (ARGs)
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2025-03-25 |
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maffilter
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public |
The MafFilter genome alignment processor
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2025-03-25 |
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phusion2-crossgenome
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public |
No Summary
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2025-03-25 |
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redundans
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public |
No Summary
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2025-03-25 |
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r-ggimage
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public |
Supports image files and graphic objects to be visualized in 'ggplot2' graphic system.
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2025-03-25 |
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r-qgraph
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public |
Weighted network visualization and analysis, as well as Gaussian graphical model computation. See Epskamp et al. (2012) <doi:10.18637/jss.v048.i04>.
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2025-03-25 |
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rvtests
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public |
Rare variant test software for next generation sequencing data
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2025-03-25 |
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r-groupdata2
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public |
Methods for dividing data into groups. Create balanced partitions and cross-validation folds. Perform time series windowing and general grouping and splitting of data. Balance existing groups with up- and downsampling.
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2025-03-25 |
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hyphy
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public |
An open-source software package for comparative sequence analysis using stochastic evolutionary models.
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2025-03-25 |
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abra2
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public |
ABRA2 is an updated implementation of ABRA featuring
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2025-03-25 |
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r-bigutilsr
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public |
Utility functions for large-scale data. For now, package 'bigutilsr' mainly includes functions for outlier detection.
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2025-03-25 |
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r-hdpca
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public |
In high-dimensional settings: Estimate the number of distant spikes based on the Generalized Spiked Population (GSP) model. Estimate the population eigenvalues, angles between the sample and population eigenvectors, correlations between the sample and population PC scores, and the asymptotic shrinkage factors. Adjust the shrinkage bias in the predicted PC scores.
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2025-03-25 |
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ldak5-parallel
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public |
No Summary
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2025-03-25 |
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ldak5
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public |
No Summary
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2025-03-25 |
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raremetal
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public |
No Summary
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2025-03-25 |
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cget
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public |
Cmake package retrieval
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2025-03-25 |
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perl-digest-sha1
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public |
Perl interface to the SHA-1 algorithm
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2025-03-25 |
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perl-convert-uu
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public |
perl replacement for uudecode
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2025-03-25 |
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perl-file-map
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public |
Memory mapping made simple and safe.
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2025-03-25 |
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perl-perlio-layers
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public |
Querying your filehandle's capabilities
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2025-03-25 |
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perl
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public |
No Summary
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2025-03-25 |
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perl-extutils-cbuilder
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public |
Compile and link C code for Perl modules
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2025-03-25 |
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perl-devel-checklib
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public |
check that a library is available
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2025-03-25 |
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perl-io-captureoutput
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public |
capture STDOUT and STDERR from Perl code, subprocesses or XS
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2025-03-25 |
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perl-mock-config
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public |
temporarily set Config or XSConfig values
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2025-03-25 |
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r
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public |
No Summary
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2025-03-25 |
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gdk-ssl-cert
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public |
No Summary
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2025-03-25 |
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finestructure
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public |
No Summary
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2025-03-25 |
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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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2025-03-25 |
