Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
Top 1.5% downloads on cran.r-project.org
Top 0.3% dependent packages on cran.r-project.org
Top 0.4% dependent repos on cran.r-project.org
Top 5.9% forks on cran.r-project.org
cran.r-project.org : ape
Analyses of Phylogenetics and Evolution
Registry
-
Source
- Documentation
- JSON
purl: pkg:cran/ape
License: GPL-2.0+
Latest release: about 1 month ago
First release: over 21 years ago
Dependent packages: 394
Dependent repositories: 965
Downloads: 114,956 last month
Stars: 45 on GitHub
Forks: 12 on GitHub
Docker dependents: 325
Docker downloads: 894,238
Total Commits: 153
Committers: 11
Average commits per author: 13.909
Development Distribution Score (DDS): 0.471
More commit stats: commits.ecosyste.ms
See more repository details: repos.ecosyste.ms
Last synced: about 6 hours ago
microeco 1.7.0
Microbial Community Ecology Data Analysis34 versions - Latest release: about 22 hours ago - 3 dependent packages - 3 dependent repositories - 2.46 thousand downloads last month - 174 stars on GitHub - 1 maintainer
Seurat 5.1.0
Tools for Single Cell Genomics41 versions - Latest release: 6 days ago - 63 dependent packages - 433 dependent repositories - 51.7 thousand downloads last month - 2,133 stars on GitHub - 1 maintainer
strap 1.6-1
Stratigraphic Tree Analysis for Palaeontology7 versions - Latest release: 10 days ago - 2 dependent packages - 3 dependent repositories - 737 downloads last month - 1 stars on GitHub - 1 maintainer
MonoPhy 1.3.1
Explore Monophyly of Taxonomic Groups in a Phylogeny5 versions - Latest release: 11 days ago - 1 dependent repositories - 106 downloads last month - 1 maintainer
paleoDiv 0.3.0
Extracting and Visualizing Paleobiodiversity3 versions - Latest release: 14 days ago - 216 downloads last month - 1 maintainer
secsse 3.1.0
Several Examined and Concealed States-Dependent Speciation and Extinction11 versions - Latest release: 16 days ago - 308 downloads last month - 1 stars on GitHub - 1 maintainer
FossilSim 2.3.3
Simulation of Fossil and Taxonomy Data8 versions - Latest release: 17 days ago - 1 dependent package - 1 dependent repositories - 374 downloads last month - 1 maintainer
MiscMetabar 0.9.1
Miscellaneous Functions for Metabarcoding Analysis3 versions - Latest release: 18 days ago - 538 downloads last month - 7 stars on GitHub - 1 maintainer
windex 2.0.8
Analysing Convergent Evolution using the Wheatsheaf Index11 versions - Latest release: 20 days ago - 265 downloads last month - 1 maintainer
ips 0.0.12
Interfaces to Phylogenetic Software in R3 versions - Latest release: 23 days ago - 2 dependent packages - 12 dependent repositories - 595 downloads last month - 1 maintainer
rphylopic 1.4.0
Get Silhouettes of Organisms from PhyloPic10 versions - Latest release: 23 days ago - 2 dependent repositories - 612 downloads last month - 77 stars on GitHub - 1 maintainer
bioregion 1.1.1
Comparison of Bioregionalisation Methods3 versions - Latest release: 27 days ago - 481 downloads last month - 5 stars on GitHub - 1 maintainer
glinvci 1.2.4
Phylogenetic Comparative Methods with Uncertainty Estimates9 versions - Latest release: 28 days ago - 300 downloads last month - 0 stars on GitHub - 1 maintainer
aqp 2.0.3
Algorithms for Quantitative Pedology55 versions - Latest release: 28 days ago - 5 dependent packages - 17 dependent repositories - 2.68 thousand downloads last month - 47 stars on GitHub - 1 maintainer
ecoregime 0.2.0
Analysis of Ecological Dynamic Regimes3 versions - Latest release: 29 days ago - 248 downloads last month - 1 stars on GitHub - 1 maintainer
POSTm 1.4
Phylogeny-Guided OTU-Specific Association Test for Microbiome Data4 versions - Latest release: 29 days ago - 194 downloads last month - 1 maintainer
iNEXT.beta3D 1.0.2
Interpolation and Extrapolation with Beta Diversity for Three Dimensions of Biodiversity3 versions - Latest release: 29 days ago - 359 downloads last month - 1 maintainer
palaeoverse 1.3.0
Prepare and Explore Data for Palaeobiological Analyses6 versions - Latest release: 30 days ago - 2 dependent packages - 283 downloads last month - 1 maintainer
yatah 1.0.0
Yet Another TAxonomy Handler4 versions - Latest release: about 1 month ago - 302 downloads last month - 6 stars on GitHub - 1 maintainer
supportR 1.3.0
Support Functions for Wrangling and Visualization4 versions - Latest release: about 1 month ago - 358 downloads last month - 5 stars on GitHub - 1 maintainer
pctax 0.1.1
Professional Comprehensive Omics Data Analysis2 versions - Latest release: about 1 month ago - 216 downloads last month - 4 stars on GitHub - 1 maintainer
MultivariateAnalysis 0.5.0
Pacote Para Analise Multivariada10 versions - Latest release: about 1 month ago - 689 downloads last month - 1 maintainer
TreeSearch 1.5.0
Phylogenetic Analysis with Discrete Character Data24 versions - Latest release: about 1 month ago - 3 dependent packages - 4 dependent repositories - 659 downloads last month - 5 stars on GitHub - 1 maintainer
stylo 0.7.5
Stylometric Multivariate Analyses28 versions - Latest release: about 1 month ago - 1 dependent package - 2 dependent repositories - 1.32 thousand downloads last month - 159 stars on GitHub - 1 maintainer
DAISIEprep 0.4.0
Extracts Phylogenetic Island Community Data from Phylogenetic Trees2 versions - Latest release: about 1 month ago - 1 dependent repositories - 298 downloads last month - 6 stars on GitHub - 1 maintainer
phylosem 1.1.4
Phylogenetic Structural Equation Model8 versions - Latest release: about 1 month ago - 330 downloads last month - 1 stars on GitHub - 1 maintainer
beautier 2.6.12
'BEAUti' from R15 versions - Latest release: about 1 month ago - 6 dependent packages - 10 dependent repositories - 670 downloads last month - 13 stars on GitHub - 1 maintainer
meconetcomp 0.5.0
Compare Microbial Networks of 'trans_network' Class of 'microeco' Package6 versions - Latest release: about 2 months ago - 384 downloads last month - 4 stars on GitHub - 1 maintainer
metafor 4.6-0
Meta-Analysis Package for R34 versions - Latest release: about 2 months ago - 82 dependent packages - 160 dependent repositories - 33.5 thousand downloads last month - 208 stars on GitHub - 1 maintainer
iNEXT.3D 1.0.4
Interpolation and Extrapolation for Three Dimensions of Biodiversity5 versions - Latest release: about 2 months ago - 2 dependent packages - 442 downloads last month - 1 maintainer
o2geosocial 1.1.2
Reconstruction of Transmission Chains from Surveillance Data5 versions - Latest release: about 2 months ago - 380 downloads last month - 7 stars on GitHub - 1 maintainer
spANOVA 0.99.4
Analysis of Field Trials with Geostatistics & Spatial AR Models5 versions - Latest release: about 2 months ago - 257 downloads last month - 1 maintainer
brms 2.21.0 💰
Bayesian Regression Models using 'Stan'60 versions - Latest release: about 2 months ago - 53 dependent packages - 186 dependent repositories - 26.5 thousand downloads last month - 1,231 stars on GitHub - 1 maintainer
phyloraster 2.1.0
Evolutionary Diversity Metrics for Raster Data2 versions - Latest release: about 2 months ago - 273 downloads last month - 5 stars on GitHub - 1 maintainer
pcutils 0.2.5
Some Useful Functions for Statistics and Visualization5 versions - Latest release: about 2 months ago - 4 dependent packages - 416 downloads last month - 2 stars on GitHub - 1 maintainer
phylopath 1.2.1
Perform Phylogenetic Path Analysis15 versions - Latest release: about 2 months ago - 2 dependent packages - 507 downloads last month - 11 stars on GitHub - 1 maintainer
immunarch 0.9.1
Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires10 versions - Latest release: about 2 months ago - 1.26 thousand downloads last month - 282 stars on GitHub - 1 maintainer
PCMBase 1.2.14
Simulation and Likelihood Calculation of Phylogenetic Comparative Models7 versions - Latest release: 2 months ago - 2 dependent packages - 2 dependent repositories - 495 downloads last month - 6 stars on GitHub - 1 maintainer
FinePop 1.5.2
Fine-Scale Population Analysis10 versions - Latest release: 2 months ago - 381 downloads last month - 1 maintainer
poppr 2.9.6 💰
Genetic Analysis of Populations with Mixed Reproduction42 versions - Latest release: 2 months ago - 7 dependent packages - 13 dependent repositories - 6.16 thousand downloads last month - 67 stars on GitHub - 1 maintainer
StructFDR 1.4
False Discovery Control Procedure Integrating the Prior Structure Information5 versions - Latest release: 2 months ago - 302 downloads last month - 1 maintainer
igraph 2.0.3
Network Analysis and Visualization71 versions - Latest release: 2 months ago - 941 dependent packages - 3,446 dependent repositories - 486 thousand downloads last month - 1 maintainer
lingtypology 1.1.17
Linguistic Typology and Mapping33 versions - Latest release: 2 months ago - 1 dependent package - 1 dependent repositories - 534 downloads last month - 49 stars on GitHub - 1 maintainer
deeptime 1.1.1
Plotting Tools for Anyone Working in Deep Time10 versions - Latest release: 2 months ago - 4 dependent packages - 5 dependent repositories - 770 downloads last month - 79 stars on GitHub - 1 maintainer
file2meco 0.7.1
Transform Files to 'microtable' Object with 'microeco' Package12 versions - Latest release: 2 months ago - 1 dependent package - 1 dependent repositories - 17 stars on GitHub - 1 maintainer
shinyTempSignal 0.0.8
Explore Temporal and Other Phylogenetic Signals7 versions - Latest release: 2 months ago - 239 downloads last month - 9 stars on GitHub - 1 maintainer
geomorph 4.0.7
Geometric Morphometric Analyses of 2D and 3D Landmark Data44 versions - Latest release: 2 months ago - 11 dependent packages - 17 dependent repositories - 2.91 thousand downloads last month - 73 stars on GitHub - 1 maintainer
UniprotR 2.4.0
Retrieving Information of Proteins from Uniprot30 versions - Latest release: 2 months ago - 2 dependent repositories - 985 downloads last month - 55 stars on GitHub - 1 maintainer
RAINBOWR 0.1.35
Genome-Wide Association Study with SNP-Set Methods10 versions - Latest release: 2 months ago - 1 dependent repositories - 347 downloads last month - 1 maintainer
geneHapR 1.2.4
Gene Haplotype Statistics, Phenotype Association and Visualization8 versions - Latest release: 3 months ago - 674 downloads last month - 1 maintainer
admtools 0.2.0
Estimate and Manipulate Age-Depth Models3 versions - Latest release: 3 months ago - 272 downloads last month - 2 stars on GitHub - 1 maintainer
GIFT 1.3.2
Access to the Global Inventory of Floras and Traits (GIFT)6 versions - Latest release: 3 months ago - 374 downloads last month - 10 stars on GitHub - 1 maintainer
mFD 1.0.7
Compute and Illustrate the Multiple Facets of Functional Diversity8 versions - Latest release: 3 months ago - 489 downloads last month - 19 stars on GitHub - 1 maintainer
CongreveLamsdell2016 1.0.3
Distance Metrics for Trees Generated by Congreve and Lamsdell4 versions - Latest release: 3 months ago - 247 downloads last month - 0 stars on GitHub - 1 maintainer
numbat 1.4.0
Haplotype-Aware CNV Analysis from scRNA-Seq8 versions - Latest release: 3 months ago - 840 downloads last month - 150 stars on GitHub - 1 maintainer
RPANDA 2.3
Phylogenetic ANalyses of DiversificAtion14 versions - Latest release: 3 months ago - 2 dependent packages - 3 dependent repositories - 516 downloads last month - 22 stars on GitHub - 1 maintainer
slendr 0.9.1
A Simulation Framework for Spatiotemporal Population Genetics13 versions - Latest release: 3 months ago - 1 dependent repositories - 323 downloads last month - 52 stars on GitHub - 1 maintainer
Platypus 3.5.0
Single-Cell Immune Repertoire and Gene Expression Analysis5 versions - Latest release: 3 months ago - 312 downloads last month - 1 maintainer
metacoder 0.3.7
Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data13 versions - Latest release: 3 months ago - 2 dependent packages - 4 dependent repositories - 1.04 thousand downloads last month - 2 stars on GitHub - 1 maintainer
adiv 2.2.1
Analysis of Diversity12 versions - Latest release: 3 months ago - 1 dependent package - 1 dependent repositories - 563 downloads last month - 1 maintainer
BAT 2.9.6
Biodiversity Assessment Tools40 versions - Latest release: 3 months ago - 2 dependent packages - 1 dependent repositories - 1.45 thousand downloads last month - 1 maintainer
treebase 0.1.5
Discovery, Access and Manipulation of 'TreeBASE' Phylogenies11 versions - Latest release: 3 months ago - 2 dependent packages - 9 dependent repositories - 358 downloads last month - 9 stars on GitHub - 1 maintainer
slouch 2.1.5
Stochastic Linear Ornstein-Uhlenbeck Comparative Hypotheses5 versions - Latest release: 3 months ago - 1 dependent package - 2 dependent repositories - 187 downloads last month - 2 stars on GitHub - 1 maintainer
funspace 0.2.1
Creating and Representing Functional Trait Spaces3 versions - Latest release: 3 months ago - 368 downloads last month - 1 maintainer
Quartet 1.2.6
Comparison of Phylogenetic Trees Using Quartet and Split Measures10 versions - Latest release: 3 months ago - 3 dependent packages - 5 dependent repositories - 8 stars on GitHub - 1 maintainer
nosoi 1.1.2
A Forward Agent-Based Transmission Chain Simulator6 versions - Latest release: 3 months ago - 7 stars on GitHub - 1 maintainer
treesliceR 1.0.1
To Slice Phylogenetic Trees and Infer Evolutionary Patterns Over Time2 versions - Latest release: 3 months ago - 177 downloads last month - 0 stars on GitHub - 1 maintainer
RRPP 2.0.0
Linear Model Evaluation with Randomized Residuals in a Permutation Procedure24 versions - Latest release: 3 months ago - 3 dependent packages - 3 dependent repositories - 2.1 thousand downloads last month - 4 stars on GitHub - 1 maintainer
apex 1.0.6 removed
Phylogenetic Methods for Multiple Gene Data6 versions - Latest release: 4 months ago - 4 dependent repositories - 153 downloads last month - 5 stars on GitHub - 1 maintainer
PhylogeneticEM 1.7.0
Automatic Shift Detection using a Phylogenetic EM9 versions - Latest release: 4 months ago - 301 downloads last month - 15 stars on GitHub - 1 maintainer
treestats 1.0.5
Phylogenetic Tree Statistics2 versions - Latest release: 4 months ago - 263 downloads last month - 10 stars on GitHub - 1 maintainer
tidygraph 1.3.1
A Tidy API for Graph Manipulation10 versions - Latest release: 4 months ago - 58 dependent packages - 215 dependent repositories - 68 thousand downloads last month - 536 stars on GitHub - 1 maintainer
enveomics.R 1.9.1
Various Utilities for Microbial Genomics and Metagenomics23 versions - Latest release: 4 months ago - 462 downloads last month - 1 maintainer
phylobase 0.8.12 💰
Base Package for Phylogenetic Structures and Comparative Data16 versions - Latest release: 4 months ago - 19 dependent packages - 51 dependent repositories - 4.58 thousand downloads last month - 17 stars on GitHub - 1 maintainer
iCellR 1.6.7
Analyzing High-Throughput Single Cell Sequencing Data24 versions - Latest release: 4 months ago - 643 downloads last month - 116 stars on GitHub - 1 maintainer
warbleR 1.1.30
Streamline Bioacoustic Analysis32 versions - Latest release: 4 months ago - 3 dependent packages - 6 dependent repositories - 1.07 thousand downloads last month - 49 stars on GitHub - 1 maintainer
Rphylopars 0.3.10
Phylogenetic Comparative Tools for Missing Data and Within-Species Variation11 versions - Latest release: 4 months ago - 3 dependent packages - 4 dependent repositories - 405 downloads last month - 27 stars on GitHub - 1 maintainer
harmonicmeanp 3.0.1
Harmonic Mean p-Values and Model Averaging by Mean Maximum Likelihood5 versions - Latest release: 4 months ago - 4 dependent packages - 6 dependent repositories - 523 downloads last month - 1 maintainer
ENMTools 1.1.2 removed
Analysis of Niche Evolution using Niche and Distribution Models11 versions - Latest release: 4 months ago - 1 dependent repositories - 241 downloads last month - 1 maintainer
Apoderoides 1.0.1
Prioritize and Delete Erroneous Taxa in a Large Phylogenetic Tree2 versions - Latest release: 4 months ago - 216 downloads last month - 0 stars on GitHub - 1 maintainer
debar 0.1.1 removed
A Post-Clustering Denoiser for COI-5P Barcode Data2 versions - Latest release: 4 months ago - 57 downloads last month - 1 maintainer
GaMaBioMD 0.2.0
Diversity Analysis for Sequence Data2 versions - Latest release: 4 months ago - 205 downloads last month - 1 maintainer
coil 1.2.4 removed
Contextualization and Evaluation of COI-5P Barcode Data7 versions - Latest release: 4 months ago - 107 downloads last month - 1 maintainer
ontophylo 1.1.3
Ontology-Informed Phylogenetic Comparative Analyses2 versions - Latest release: 4 months ago - 184 downloads last month - 0 stars on GitHub - 1 maintainer
changeRangeR 1.1.0 removed
Change Metrics for Species Geographic Ranges4 versions - Latest release: 4 months ago - 26 downloads last month - 1 maintainer
phytools 2.1-1
Phylogenetic Tools for Comparative Biology (and Other Things)49 versions - Latest release: 4 months ago - 65 dependent packages - 156 dependent repositories - 11.6 thousand downloads last month - 189 stars on GitHub - 1 maintainer
mdendro 2.2.1
Extended Agglomerative Hierarchical Clustering6 versions - Latest release: 4 months ago - 1 dependent repositories - 360 downloads last month - 1 maintainer
castor 1.8.0
Efficient Phylogenetics on Large Trees41 versions - Latest release: 4 months ago - 5 dependent packages - 13 dependent repositories - 1.68 thousand downloads last month - 1 maintainer
scrm 1.7.5
Simulating the Evolution of Biological Sequences12 versions - Latest release: 4 months ago - 3 dependent packages - 5 dependent repositories - 459 downloads last month - 8 stars on GitHub - 1 maintainer
jaatha 3.2.5
Simulation-Based Maximum Likelihood Parameter Estimation20 versions - Latest release: 4 months ago - 1 dependent repositories - 411 downloads last month - 3 stars on GitHub - 1 maintainer
dowser 2.1.0
B Cell Receptor Phylogenetics Toolkit6 versions - Latest release: 5 months ago - 352 downloads last month - 1 maintainer
diversitree 0.10-0
Comparative 'Phylogenetic' Analyses of Diversification21 versions - Latest release: 5 months ago - 5 dependent packages - 16 dependent repositories - 1.06 thousand downloads last month - 1 maintainer
epm 1.1.2
EcoPhyloMapper6 versions - Latest release: 5 months ago - 353 downloads last month - 10 stars on GitHub - 1 maintainer
BAMMtools 2.1.11
Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees17 versions - Latest release: 5 months ago - 3 dependent packages - 5 dependent repositories - 1.69 thousand downloads last month - 1 maintainer
PhyInsight 0.1.0 removed
DNA Sequence Analysis & Generation Tree Creation1 version - Latest release: 5 months ago - 131 downloads last month - 1 stars on GitHub - 1 maintainer
treebalance 1.2.0
Computation of Tree (Im)Balance Indices3 versions - Latest release: 5 months ago - 1 dependent package - 1 dependent repositories - 211 downloads last month - 1 maintainer
TML 1.2.0
Tropical Geometry Tools for Machine Learning3 versions - Latest release: 5 months ago - 198 downloads last month - 2 stars on GitHub - 1 maintainer
pegas 1.3
Population and Evolutionary Genetics Analysis System31 versions - Latest release: 5 months ago - 20 dependent packages - 50 dependent repositories - 5.56 thousand downloads last month - 1 maintainer
tidytree 0.4.6
A Tidy Tool for Phylogenetic Tree Data Manipulation30 versions - Latest release: 5 months ago - 10 dependent packages - 37 dependent repositories - 26 thousand downloads last month - 1 maintainer
genBaRcode 1.2.7
Analysis and Visualization Tools for Genetic Barcode Data9 versions - Latest release: 5 months ago - 314 downloads last month - 1 maintainer