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
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
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