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r-structssi
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public |
Performs multiple testing corrections that take specific structure of hypotheses into account.
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2025-03-25 |
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r-aptreeshape
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public |
Simulation and analysis of phylogenetic tree topologies using statistical indices. It is a companion library of the 'ape' package. It provides additional functions for reading, plotting, manipulating phylogenetic trees. It also offers convenient web-access to public databases, and enables testing null models of macroevolution using corrected test statistics. Trees of class "phylo" (from 'ape' package) can be converted easily. Implements methods described in Bortolussi et al. (2005) and Maliet et al. (2017).
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2025-03-25 |
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goalign
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public |
goalign is a set of command line tools to manipulate multiple alignments
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2025-03-25 |
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gotree
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public |
gotree is a set of command line tools to manipulate phylogenetic trees
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2025-03-25 |
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iclipro
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public |
iCLIPro is a Python package that can be used to control for systematic misassignments in iCLIP data.
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2025-03-25 |
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r-spocc
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public |
A programmatic interface to many species occurrence data sources, including Global Biodiversity Information Facility ('GBIF'), 'USGSs' Biodiversity Information Serving Our Nation ('BISON'), 'iNaturalist', Berkeley 'Ecoinformatics' Engine, 'eBird', 'AntWeb', Integrated Digitized 'Biocollections' ('iDigBio'), 'VertNet', Ocean 'Biogeographic' Information System ('OBIS'), and Atlas of Living Australia ('ALA'). Includes functionality for retrieving species occurrence data, and combining those data.
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2025-03-25 |
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r-rgbif
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public |
A programmatic interface to the Web Service methods provided by the Global Biodiversity Information Facility ('GBIF'; <https://www.gbif.org/developer/summary>). 'GBIF' is a database of species occurrence records from sources all over the globe. 'rgbif' includes functions for searching for taxonomic names, retrieving information on data providers, getting species occurrence records, getting counts of occurrence records, and using the 'GBIF' tile map service to make 'rasters' summarizing huge amounts of data.
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2025-03-25 |
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isoseq3
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public |
Iso-Seq - Scalable De Novo Isoform Discovery
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2025-03-25 |
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lima
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public |
lima - The PacBio Barcode Demultiplexer
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2025-03-25 |
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r-rvertnet
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public |
Retrieve, map and summarize data from the 'VertNet.org' archives (<http://vertnet.org/>). Functions allow searching by many parameters, including 'taxonomic' names, places, and dates. In addition, there is an interface for conducting spatially delimited searches, and another for requesting large 'datasets' via email.
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2025-03-25 |
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r-geoaxe
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public |
Split 'geospatial' objects into pieces. Includes support for some spatial object inputs, 'Well-Known Text', and 'GeoJSON'.
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2025-03-25 |
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r-oai
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public |
A general purpose client to work with any 'OAI-PMH' (Open Archives Initiative Protocol for 'Metadata' Harvesting) service. The 'OAI-PMH' protocol is described at <http://www.openarchives.org/OAI/openarchivesprotocol.html>. Functions are provided to work with the 'OAI-PMH' verbs: 'GetRecord', 'Identify', 'ListIdentifiers', 'ListMetadataFormats', 'ListRecords', and 'ListSets'.
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2025-03-25 |
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r-rbison
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public |
Interface to the 'USGS' 'BISON' (<https://bison.usgs.gov/>) 'API', a 'database' for species occurrence data. Data comes from species in the United States from participating data providers. You can get data via 'taxonomic' and location based queries. A simple function is provided to help visualize data.
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2025-03-25 |
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r-rebird
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public |
A programmatic client for the eBird database, including functions for searching for bird observations by geographic location (latitude, longitude), eBird hotspots, location identifiers, by notable sightings, by region, and by taxonomic name.
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2025-03-25 |
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r-ridigbio
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public |
An interface to iDigBio's search API that allows downloading specimen records. Searches are returned as a data.frame. Other functions such as the metadata end points return lists of information. iDigBio is a US project focused on digitizing and serving museum specimen collections on the web. See <https://www.idigbio.org> for information on iDigBio.
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2025-03-25 |
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r-wicket
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public |
Utilities to generate bounding boxes from 'WKT' (Well-Known Text) objects and R data types, validate 'WKT' objects and convert object types from the 'sp' package into 'WKT' representations.
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2025-03-25 |
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illumiprocessor
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public |
illumiprocessor is a tool to batch process illumina sequencing reads using the excellent trimmomatic package.
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2025-03-25 |
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migraine
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public |
Implements coalescent algorithms for maximum likelihood analysis of population genetic data. The data currently handled are allelic counts but sequences will be handled in the forthcoming version.
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2025-03-25 |
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snpsplit
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public |
SNPsplit is an allele-specific alignment sorter which is designed to read in alignment files in SAM/BAM format and determine the allelic origin of reads that cover known SNP positions.
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2025-03-25 |
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bioconductor-microbiome
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public |
Microbiome Analytics
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2025-03-25 |
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perl-extutils-cppguess
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public |
guess C++ compiler and flags
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2025-03-25 |
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r-zerone
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public |
Zerone discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them.
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2025-03-25 |
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fermi-lite
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public |
Fermi-lite is a standalone C library as well as a command-line tool for assembling Illumina short reads in regions from 100bp to 10 million bp in size.
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2025-03-25 |
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satrap
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public |
A SOLiD assembly translation program.
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2025-03-25 |
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bioconductor-curatedmetagenomicdata
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public |
Curated Metagenomic Data of the Human Microbiome
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2025-03-25 |
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agfusion
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public |
Python package to annotate and visualize gene fusions.
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2025-03-25 |
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pyensembl
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public |
Python interface to ensembl reference genome metadata
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2025-03-25 |
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bioconductor-experimenthub
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public |
Client to access ExperimentHub resources
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2025-03-25 |
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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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2025-03-25 |
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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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2025-03-25 |
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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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2025-03-25 |
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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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2025-03-25 |
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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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2025-03-25 |
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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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2025-03-25 |
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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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2025-03-25 |
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real
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public |
REad ALigner for Next-Generation sequencing reads.
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2025-03-25 |
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bioconductor-pathprint
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public |
Pathway fingerprinting for analysis of gene expression arrays
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2025-03-25 |
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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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2025-03-25 |
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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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2025-03-25 |
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wisecondorx
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public |
WIthin-SamplE COpy Number aberration DetectOR, including sex chromosomes
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2025-03-25 |
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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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2025-03-25 |
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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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2025-03-25 |
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womtool
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public |
Command line utilities for interacting with WDL
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2025-03-25 |
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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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2025-03-25 |
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migrate-n
|
public |
Population Genetics - Panmixia and Migration detection
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2025-03-25 |
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fastspar
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public |
Rapid and scalable correlation estimation for compositional data
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2025-03-25 |
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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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2025-03-25 |
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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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2025-03-25 |
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esimsa
|
public |
Simple deconvolution of electrospray ionization peak lists
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2025-03-25 |
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bioconductor-mspuritydata
|
public |
Fragmentation spectral libraries and data to test the msPurity package
|
2025-03-25 |
