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pyensembl
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public |
Python interface to ensembl reference genome metadata
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2025-04-22 |
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bioconductor-experimenthub
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public |
Client to access ExperimentHub resources
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2025-04-22 |
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r-ecodist
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public |
Dissimilarity-based analysis functions including ordination and Mantel test functions, intended for use with spatial and community data.
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2025-04-22 |
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r-adephylo
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public |
Multivariate tools to analyze comparative data, i.e. a phylogeny and some traits measured for each taxa.
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2025-04-22 |
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r-phylobase
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public |
Provides a base S4 class for comparative methods, incorporating one or more trees and trait data.
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2025-04-22 |
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r-rnexml
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public |
Provides access to phyloinformatic data in 'NeXML' format. The package should add new functionality to R such as the possibility to manipulate 'NeXML' objects in more various and refined way and compatibility with 'ape' objects.
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2025-04-22 |
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bioconductor-flowsorted.blood.450k
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public |
Illumina HumanMethylation data on sorted blood cell populations
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2025-04-22 |
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asqcan
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public |
A combined pipeline for bacterial genome assembly, quality control and annotation
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2025-04-22 |
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drep
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public |
De-replication of microbial genomes assembled from multiple samples.
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2025-04-22 |
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mob_suite
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public |
MOB-suite is a set of tools for finding, typing and reconstruction of plasmids from draft and complete genome assemblies.
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2025-04-22 |
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real
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public |
REad ALigner for Next-Generation sequencing reads.
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2025-04-22 |
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bioconductor-pathprint
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public |
Pathway fingerprinting for analysis of gene expression arrays
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2025-04-22 |
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hic2cool
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public |
A converter between .hic files (from juicer) and single-resolution or multi-resolution .cool files (for cooler).
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2025-04-22 |
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swipe
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public |
Tool for performing rapid local alignment searches in amino acid or nucleotide sequence databases. It is a highly optimized implementation of the Smith-Waterman algoritm using SIMD parallel computing technology available on common CPUs.
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2025-04-22 |
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wisecondorx
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public |
WIthin-SamplE COpy Number aberration DetectOR, including sex chromosomes
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2025-04-22 |
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sbpipe
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public |
SBpipe is a collection of pipelines for systems modelling of biological networks. It allows mathematical modellers to automatically repeat the tasks of model simulation and parameter estimation, and extract robustness information from these repeat sequences in a solid and consistent manner, facilitating model development and analysis. SBpipe can run models implemented in COPASI, Python or coded in any other programming language using Python as a wrapper module. Pipelines can run on multicore computers, Sun Grid Engine (SGE), Load Sharing Facility (LSF) clusters, or via Snakemake.
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2025-04-22 |
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r-sbpiper
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public |
Provides an API for analysing repetitive parameter estimations and simulations of mathematical models. Examples of mathematical models are Ordinary Differential equations (ODEs) or Stochastic Differential Equations (SDEs) models. Among the analyses for parameter estimation 'sbpiper' calculates statistics and generates plots for parameter density, PCA of the best fits, parameter profile likelihood estimations (PLEs), and 2D parameter PLEs. These results can be generated using all or a subset of the best computed parameter sets. Among the analyses for model simulation 'sbpiper' calculates statistics and generates plots for deterministic and stochastic time courses via cartesian and heatmap plots. Plots for the scan of one or two model parameters can also be generated. This package is primarily used by the software 'SBpipe'. Citation: Dalle Pezze P, Le Novère N. SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks. BMC Systems Biology. 2017;11:46. <doi:10.1186/s12918-017-0423-3>.
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2025-04-22 |
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womtool
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public |
Command line utilities for interacting with WDL
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2025-04-22 |
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r-biodb
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public |
An R package for connecting to chemical and biological databases.
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2025-04-22 |
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migrate-n
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public |
Population Genetics - Panmixia and Migration detection
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2025-04-22 |
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fastspar
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public |
Rapid and scalable correlation estimation for compositional data
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2025-04-22 |
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r-rapidr
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public |
Package to perform non-invasive fetal testing for aneuploidies using sequencing count data from cell-free DNA
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2025-04-22 |
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r-propcis
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public |
Computes two-sample confidence intervals for single, paired and independent proportions.
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2025-04-22 |
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esimsa
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public |
Simple deconvolution of electrospray ionization peak lists
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2025-04-22 |
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ngmerge
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public |
Merging paired-end reads and removing sequencing adapters.
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2025-04-22 |
