Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

Package Usage: cran: ape

Analyses of Phylogenetics and Evolution
102 versions
Latest release: about 1 year ago
377 dependent packages
58,959 downloads last month

View more package details: https://packages.ecosyste.ms/registries/cran.r-project.org/packages/ape

View more repository details: https://repos.ecosyste.ms/hosts/GitHub/repositories/emmanuelparadis%2Fape

Dependent Repos 965

rgyoung6/HACSim.R Fork of jphill01/HACSim.R
Iterative extrapolation of species haplotype accumulation curves for genetic diversity assessment.
  • >= 5.2 DESCRIPTION

Size: 1.24 MB - Last synced: 7 months ago - Pushed: over 4 years ago

hemstrow/snpR
  • * DESCRIPTION

Size: 14.8 MB - Last synced: 3 days ago - Pushed: 3 days ago

vibscc/DALI
R-package for the analysis of single-cell TCR/BCR data in the Seurat ecosystem
  • * DESCRIPTION

Size: 8.95 MB - Last synced: about 2 months ago - Pushed: about 1 year ago

GabrielNakamura/Herodotools
Herodotools: R package for analysis of historical biogeography
  • * DESCRIPTION

Size: 178 MB - Last synced: 3 months ago - Pushed: 3 months ago

MicrobiologyETHZ/phylloR
R package for phyllosphere analysis
  • * DESCRIPTION

Size: 162 KB - Last synced: 6 months ago - Pushed: 9 months ago

Hackout2/epiphylo
Epidemics and outbreak dynamics with phylogenetic trees
  • * DESCRIPTION

Size: 212 KB - Last synced: about 1 year ago - Pushed: about 9 years ago

helixcn/phylotools
Phylogenetic tools for Eco-phylogenetics
  • * DESCRIPTION

Size: 284 KB - Last synced: 6 months ago - Pushed: about 3 years ago

ericgoolsby/Rphylopars
Phylogenetic Comparative Tools for Missing Data and Within-Species Variation
  • * DESCRIPTION

Size: 893 KB - Last synced: 15 days ago - Pushed: over 1 year ago

gabferreira/phyloraster
  • * DESCRIPTION

Size: 21.6 MB - Last synced: 16 days ago - Pushed: about 2 months ago

darcyj/specificity
R package for calculating specificity in ecological data
  • * DESCRIPTION

Size: 17.9 MB - Last synced: 3 months ago - Pushed: 9 months ago

nrennie/aRt
R package to create generative art.
  • * DESCRIPTION

Size: 23.3 MB - Last synced: 6 months ago - Pushed: 6 months ago

microbiome/mia
Microbiome analysis
  • * DESCRIPTION

Size: 20.5 MB - Last synced: about 23 hours ago - Pushed: 1 day ago

cran/maticce
Mapping Transitions in Continuous Character Evolution
  • * DESCRIPTION

Size: 1.98 MB - Last synced: 9 months ago - Pushed: about 10 years ago

mattiaghilardi/FishCaCO3Model
  • >= 5.5 DESCRIPTION

Size: 15.5 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

ms609/TreeSearch
R package for phylogenetic tree search under custom optimality criteria
  • >= 5.6 DESCRIPTION

Size: 117 MB - Last synced: 1 day ago - Pushed: about 1 month ago

ropensci-archive/nbaR 📦
:warning: ARCHIVED :warning: R client library for the Netherlands Biodiversity Api (NBA)
  • * DESCRIPTION

Size: 5.99 MB - Last synced: 20 days ago - Pushed: 6 months ago

gschofl/genoslideR
Handle multiple genomic alignments with annotation in R
  • * DESCRIPTION

Size: 2.71 MB - Last synced: about 1 year ago - Pushed: about 10 years ago

sbotond/pcrcoal
pcrcoal is an R package implementing the coalescent approach to PCR simulation developed by Weiss and von Haeseler (NAR, 1997)
  • >= 2.3 pkg/DESCRIPTION

Size: 3.7 MB - Last synced: 7 months ago - Pushed: about 10 years ago

sbotond/phylosim
An R package for the Monte Carlo simulation of sequence evolution
  • >= 2.3 pkg/DESCRIPTION

Size: 8.02 MB - Last synced: 7 months ago - Pushed: about 10 years ago

grunwaldlab/metacoder
Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data
  • * DESCRIPTION

Size: 108 MB - Last synced: about 1 month ago - Pushed: 3 months ago

tfussell/rmetasim_gpu
A CUDA implementation of the R package, rmetasim, which simulates population dynamics, evolution, and demography.
  • * DESCRIPTION

Size: 223 KB - Last synced: about 1 year ago - Pushed: almost 12 years ago

cran/lefse
:exclamation: This is a read-only mirror of the CRAN R package repository. lefse — Phylogenetic and Functional Analyses for Ecology
  • * DESCRIPTION

Size: 102 KB - Last synced: 9 months ago - Pushed: over 9 years ago

florianhartig/DHARMa
Diagnostics for HierArchical Regession Models
  • * DHARMa/DESCRIPTION

Size: 7.49 MB - Last synced: 11 days ago - Pushed: 3 months ago

bwallace/OpenMeta-analyst-
intuitive software for advanced meta-analysis
  • * src/R/openmetar/DESCRIPTION

Size: 84.9 MB - Last synced: 7 months ago - Pushed: almost 4 years ago

YuLab-SMU/MicrobiotaProcess
:microbe: A comprehensive R package for deep mining microbiome
  • * DESCRIPTION

Size: 6.85 MB - Last synced: 25 days ago - Pushed: 25 days ago

waldronlab/MicrobiomeBenchmarkData
Data for benchmarking in microbiome research.
  • * DESCRIPTION

Size: 1.34 MB - Last synced: 5 days ago - Pushed: 5 days ago

marcocacciabue/infinity
Human Influenza classification web app
  • * DESCRIPTION

Size: 74.2 MB - Last synced: about 1 year ago - Pushed: about 1 year ago

raevskymichail/epi-impute
Epi-Impute: single-cell RNA-seq imputation via integration with single-cell ATAC-seq data
  • * DESCRIPTION

Size: 56.3 MB - Last synced: 7 months ago - Pushed: 10 months ago

ruffleymr/CAMI
Community Assembly Model Inference
  • * DESCRIPTION

Size: 191 MB - Last synced: 7 months ago - Pushed: over 4 years ago

broadinstitute/infercnv
Inferring CNV from Single-Cell RNA-Seq
  • * DESCRIPTION

Size: 22.6 MB - Last synced: about 1 month ago - Pushed: 2 months ago

brpetrucci/paleobuddy
paleobuddy: an R package for simulating diversification dynamics, fossil records and phylogenies in R.
  • * DESCRIPTION

Size: 56 MB - Last synced: 11 days ago - Pushed: 7 months ago

snaketron/scBubbletree
scBubbletree: quantitative tool for visual exploration of scRNA-seq data
  • >= 5.5 DESCRIPTION

Size: 57.2 MB - Last synced: 26 days ago - Pushed: 6 months ago

EpiModel/EpiModel
Mathematical Modeling of Infectious Disease Dynamics
  • * DESCRIPTION

Size: 18.1 MB - Last synced: 4 days ago - Pushed: 5 days ago

GregGuerin/biomapME
Functions for generating gridded biodiversity maps from point (incidence) data
  • * DESCRIPTION

Size: 2.92 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago

esnapd/DegeneratePrimerTools 📦
Utilities for Creating and Validating Degenerate primers
  • * DESCRIPTION

Size: 2.05 MB - Last synced: about 1 year ago - Pushed: over 5 years ago

maize-genetics/rTASSEL
R front-end for TASSEL
  • * DESCRIPTION

Size: 205 MB - Last synced: 3 months ago - Pushed: 6 months ago

hfgolino/EGAnet
  • * DESCRIPTION

Size: 108 MB - Last synced: about 19 hours ago - Pushed: about 20 hours ago

trollius/jive-package
jive-package
  • * DESCRIPTION

Size: 992 KB - Last synced: about 2 months ago - Pushed: almost 10 years ago

ncss-tech/sharpshootR
Miscellaneous soil data management, summary, visualization, and conversion utilities to support soil survey.
  • * DESCRIPTION

Size: 36.8 MB - Last synced: about 1 hour ago - Pushed: 28 days ago

joelnitta/gbfetch
Fetch! (GenBank sequences)
  • * DESCRIPTION

Size: 165 KB - Last synced: 2 months ago - Pushed: 2 months ago

bioRgeo/bioRgeo
An R package to compare several methods of bioregionalizations
  • * DESCRIPTION

Size: 86.4 MB - Last synced: about 1 year ago - Pushed: about 1 year ago

ropensci/taxize
A taxonomic toolbelt for R
  • * DESCRIPTION

Size: 31.5 MB - Last synced: 23 days ago - Pushed: 4 months ago

TGuillerme/dispRity
Measuring disparity with R
  • * DESCRIPTION

Size: 98.9 MB - Last synced: about 16 hours ago - Pushed: about 17 hours ago

darunabas/phyloregion
Biogeographic regionalization and spatial conservation
  • * DESCRIPTION

Size: 29.2 MB - Last synced: 7 days ago - Pushed: 3 months ago

sebastianduchene/NELSI
This is the repository for NELSI: Nucleotide Evolutionary rate Simulator
  • >= 3.0 DESCRIPTION

Size: 52.1 MB - Last synced: 7 months ago - Pushed: over 1 year ago

kullrich/MSA2dist
MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis
  • * DESCRIPTION

Size: 601 KB - Last synced: 12 days ago - Pushed: 13 days ago

r-forge/motmot
Read-only mirror of "motmot" from r-forge SVN.
  • * pkg/DESCRIPTION

Size: 109 KB - Last synced: 9 months ago - Pushed: about 2 years ago

eliotmiller/R2phylowood
Convert species centroids to phylowood input
  • * DESCRIPTION

Size: 141 KB - Last synced: 9 months ago - Pushed: almost 10 years ago

bodkan/slendr
Population genetic simulations in R 🌍
  • * DESCRIPTION

Size: 50 MB - Last synced: about 19 hours ago - Pushed: 1 day ago

ropensci/beautier
R package to generate the same BEAST2 XML parameter files as generated by BEAUti 2
  • * DESCRIPTION

Size: 11 MB - Last synced: 3 days ago - Pushed: about 1 month ago

r-forge/bmhyd
Read-only mirror of "bmhyd" from r-forge SVN.
  • * pkg/DESCRIPTION

Size: 185 KB - Last synced: 9 months ago - Pushed: about 2 years ago

YosefLab/VISION
Signature Analysis and Visualization for Single-Cell RNA-seq
  • * DESCRIPTION

Size: 94.6 MB - Last synced: 7 months ago - Pushed: about 1 year ago

ptitle/epm
An R package for the calculation of taxonomic, phenotypic and phylogenetic metrics across grid cells.
  • * DESCRIPTION

Size: 2.71 MB - Last synced: 11 days ago - Pushed: about 1 month ago

cran/PCPS
:exclamation: This is a read-only mirror of the CRAN R package repository. PCPS — Principal Coordinates of Phylogenetic Structure
  • * DESCRIPTION

Size: 83 KB - Last synced: 9 months ago - Pushed: over 4 years ago

KasperSkytte/ampvis2
Tools for visualising microbial community amplicon data
  • * DESCRIPTION

Size: 131 MB - Last synced: 4 months ago - Pushed: 4 months ago

andrew-hipp/RADami
RADseq helper R package
  • >= 4.0 DESCRIPTION

Size: 136 KB - Last synced: 6 months ago - Pushed: 6 months ago

jnpaulson/phyloseq Fork of joey711/phyloseq
phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
  • >= 3.1.1 DESCRIPTION

Size: 70 MB - Last synced: 11 months ago - Pushed: over 8 years ago

CHKim5/LMSstat
Package for automation of statistics that are widely used in metabolomics.
  • * DESCRIPTION

Size: 392 KB - Last synced: 7 months ago - Pushed: over 2 years ago

cjyetman/network.r2d3
  • * DESCRIPTION

Size: 6.74 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

rdinnager/LDA-metagenomics
R package containing code and data for LDA-metagenomics project --- a project exploring how Latent Dirichlet Allocation and other topic models can be applied to metagenomics data
  • * DESCRIPTION

Size: 1010 KB - Last synced: 8 months ago - Pushed: almost 10 years ago

rseng/rsepedia-analysis
Exploring clustering of research software encyclopedia entries
  • * _repos/github/GabrielNakamura/FishPhyloMaker/DESCRIPTION
  • * _repos/github/HajkD/LTRpred/DESCRIPTION
  • * _repos/github/ImperialCollegeLondon/safedata/DESCRIPTION
  • * _repos/github/YuLab-SMU/treeio/DESCRIPTION
  • >= 5.4 _repos/github/ramadatta/CPgeneProfiler/DESCRIPTION
  • >= 3.1 _repos/github/ropensci/RNeXML/DESCRIPTION
  • * _repos/github/ropensci/babette/DESCRIPTION
  • * _repos/github/ropensci/beastier/DESCRIPTION
  • * _repos/github/ropensci/beautier/DESCRIPTION
  • * _repos/github/ropensci/brranching/DESCRIPTION

Size: 433 MB - Last synced: 5 days ago - Pushed: 6 days ago

kharchenkolab/numbat
Haplotype-aware CNV analysis from single-cell RNA-seq
  • * DESCRIPTION

Size: 367 MB - Last synced: 4 days ago - Pushed: 4 days ago

leondap/recluster
  • * DESCRIPTION

Size: 256 KB - Last synced: 6 months ago - Pushed: 7 months ago

jeremycg/protractedbirthdeath
modelling speciation with incipient species
  • * protractedbirthdeath/DESCRIPTION

Size: 1.13 MB - Last synced: about 2 months ago - Pushed: over 6 years ago

mpeeples2008/ArchNetSci
Code repository and Bookdown project for Online Companion to Network Science in Archaeology by Tom Brughmans and Matthew A. Peeples (Cambridge Manuals in Archaeology)
  • * DESCRIPTION

Size: 191 MB - Last synced: about 2 months ago - Pushed: 2 months ago

r-forge/pan
Read-only mirror of "pan" from r-forge SVN.
  • * pkg/trunk/DESCRIPTION

Size: 4.88 KB - Last synced: 9 months ago - Pushed: about 2 years ago

dpasqualin/sfreemap
A Simulation Free approach for Stochastic Mapping
  • >= 5.3 DESCRIPTION

Size: 4.37 MB - Last synced: 7 months ago - Pushed: 10 months ago

cran/metagear
:exclamation: This is a read-only mirror of the CRAN R package repository. metagear — Comprehensive Research Synthesis Tools for Systematic Reviews and Meta-Analysis. Homepage: http://lajeunesse.myweb.usf.edu/ https://github.com/mjlajeunesse/ https://www.youtube.com/c/LajeunesseLab/
  • * DESCRIPTION

Size: 3.14 MB - Last synced: 7 months ago - Pushed: about 3 years ago

YuLab-SMU/treeio
:seedling: Base Classes and Functions for Phylogenetic Tree Input and Output
  • * DESCRIPTION

Size: 3 MB - Last synced: 28 days ago - Pushed: 29 days ago

daehwankim12/LMSstat Fork of CHKim5/LMSstat
Package for automation of statistics that are widely used in metabolomics.
  • * DESCRIPTION

Size: 313 KB - Last synced: about 2 months ago - Pushed: about 2 months ago

jspaezp/sctree
Tree based marker finding and gating visualization for single cell rna seq data
  • * DESCRIPTION

Size: 38 MB - Last synced: about 2 months ago - Pushed: about 2 years ago

cran/strataG
:exclamation: This is a read-only mirror of the CRAN R package repository. strataG — Summaries and Population Structure Analyses of Genetic Data. Homepage: https://github.com/EricArcher/strataG Report bugs for this package: https://github.com/EricArcher/strataG/issues
  • * DESCRIPTION

Size: 1.28 MB - Last synced: 7 months ago - Pushed: about 4 years ago

philliplab/MotifBinner
  • * DESCRIPTION

Size: 2.85 MB - Last synced: 9 months ago - Pushed: over 3 years ago

cran/readGenalex
:exclamation: This is a read-only mirror of the CRAN R package repository. readGenalex — Read, Write, Manipulate and Convert GenAlEx-Format Genotype Files. Homepage: https://github.com/douglasgscofield/readGenalex Report bugs for this package: https://github.com/douglasgscofield/readGenalex/issues
  • >= 2.4 DESCRIPTION

Size: 344 KB - Last synced: 9 months ago - Pushed: about 9 years ago

thibautjombart/treescape
Exploring tree diversity
  • * DESCRIPTION

Size: 20 MB - Last synced: 7 months ago - Pushed: about 7 years ago

jsigao/prioritree
  • * DESCRIPTION

Size: 49 MB - Last synced: about 2 months ago - Pushed: over 1 year ago

scrm/scrm-r
scrm, packaged for convenient usage in R
  • * DESCRIPTION

Size: 305 KB - Last synced: 10 days ago - Pushed: 4 months ago

lukejharmon/fossilMedusa
  • * DESCRIPTION

Size: 457 KB - Last synced: 8 months ago - Pushed: almost 9 years ago

alexharkess/tosr
An R interface to the Tree of Sex database (http://treeofsex.org/)
  • * DESCRIPTION

Size: 1.9 MB - Last synced: about 1 year ago - Pushed: about 9 years ago

fmichonneau/impatiens
  • * DESCRIPTION

Size: 16.3 MB - Last synced: 5 days ago - Pushed: over 8 years ago

djq99/receptormarker Fork of nsh87/receptormarker
Source for 'receptormarker' package for R: antibody receptor and phenotypic marker analysis
  • >= 3.2 DESCRIPTION

Size: 4.65 MB - Last synced: about 1 year ago - Pushed: over 8 years ago

EricArcher/strataG
strataG is a toolkit for haploid sequence and multilocus genetic data summaries, and analyses of population structure.
  • >= 5.4 DESCRIPTION

Size: 25.1 MB - Last synced: 7 months ago - Pushed: about 1 year ago

wanyuac/GeneMates
An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences
  • >= 4.1 DESCRIPTION

Size: 2.4 MB - Last synced: 7 months ago - Pushed: over 1 year ago

reconhub/outbreaker2
Disease outbreak reconstruction from epidemiological and genetic data
  • * DESCRIPTION

Size: 35.2 MB - Last synced: about 1 month ago - Pushed: over 1 year ago

rgyoung6/MACER
Molecular Acquisition, Cleaning, and Evaluation in R (MACER) is an R package to assist biological researchers in assembling taxonomically and marker focused molecular sequence data set. MACER accepts a list of genera as a user input and uses NCBI-GenBank and BOLD as resources to download and assemble molecular sequence datasets. These datasets are then assembled by marker, aligned, trimmed, and cleaned. The use of this package allows the publication of specific parameters to ensure reproducibility. The MACER package has four core functions.
  • * DESCRIPTION

Size: 1.32 MB - Last synced: about 2 months ago - Pushed: 6 months ago

fmichonneau/chopper
chopper -- an R package to manipulate DNA alignments and data preparation for phylogenetic analyses
  • >= 3.0 DESCRIPTION

Size: 97.7 KB - Last synced: 5 days ago - Pushed: over 6 years ago

alexology/biomonitoR
A package for calculating indices for biomonitoring of running waters with a focus on macroinvertebrate community. Still in development.
  • * DESCRIPTION

Size: 8.75 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

lvclark/polysat
polysat 1.7: tools for polyploid microsatellite analysis
  • * DESCRIPTION

Size: 2.71 MB - Last synced: 6 months ago - Pushed: over 1 year ago

cran/phylocurve
:exclamation: This is a read-only mirror of the CRAN R package repository. phylocurve — Phylogenetic Comparative Methods for High-Dimensional Traits. Homepage: http://www.phylocurve.org
  • * DESCRIPTION

Size: 132 KB - Last synced: 6 months ago - Pushed: almost 4 years ago

khalidtab/FALAPhyl
Pipeline aimed at microbial exploratory analysis. Based on snakemake, fastspar, and ggpubr, and custom R code for visualization.
  • * workflow/scripts/betapart/DESCRIPTION

Size: 6.84 MB - Last synced: 1 day ago - Pushed: 1 day ago

cran/rncl
:exclamation: This is a read-only mirror of the CRAN R package repository. rncl — An Interface to the Nexus Class Library. Homepage: https://github.com/fmichonneau/rncl Report bugs for this package: https://github.com/fmichonneau/rncl/issues
  • * DESCRIPTION

Size: 334 KB - Last synced: 9 months ago - Pushed: over 1 year ago