Package: pegas 1.3

pegas: Population and Evolutionary Genetics Analysis System

Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.

Authors:Emmanuel Paradis [aut, cre, cph], Thibaut Jombart [aut, cph], Zhian N. Kamvar [aut, cph], Brian Knaus [aut, cph], Klaus Schliep [aut, cph], Alastair Potts [aut, cph], David Winter [aut, cph]

pegas_1.3.tar.gz
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pegas_1.3.tgz(r-4.4-x86_64)pegas_1.3.tgz(r-4.4-arm64)pegas_1.3.tgz(r-4.3-x86_64)pegas_1.3.tgz(r-4.3-arm64)
pegas_1.3.tar.gz(r-4.5-noble)pegas_1.3.tar.gz(r-4.4-noble)
pegas_1.3.tgz(r-4.4-emscripten)pegas_1.3.tgz(r-4.3-emscripten)
pegas.pdf |pegas.html✨
pegas/json (API)
NEWS

Peer review:

Bug tracker:https://github.com/emmanuelparadis/pegas.html/issues

On CRAN:

80 exports 6.51 score 5 dependencies 18 dependents 117 mentions 460 scripts 6.1k downloads

Last updated 9 months agofrom:535a3ea809. Checks:OK: 9. Indexed: yes.

Exports:alleles2lociallelicrichnessamovaas.igraph.haploNetas.locias.network.haploNetdiffHaplodist.asddist.hammingdist.haplotype.lociexpand.genotypeF2F3F4Fstgenind2locigeodgeoTransgeoTrans2getAllelesgetGenotypesgetHaploNetOptionsgetINFOgetPhigetPloidyHhap.divhaploFreqhaploNethaplotypeheterozygosityhw.testis.phasedis.snpLDLD2LDmapLDscanloci2allelesloci2genindloci2SnpMatrixmjnMMDmsnmstmutationsnuc.divnullAlleles2NAplotNetMDSproba.genotypeR2.testrangePOSrarefactionplotread.gtxread.lociread.vcfreplotrhostrmstrr.testRstselectQUALsetHaploNetOptionssite.spectrumstairwayswtajima.testtheta.htheta.ktheta.msattheta.stheta.treetheta.tree.heterounphaseVCFheaderVCFlabelsVCFlociwrite.lociwrite.pegas.amovawrite.vcf

Dependencies:apedigestlatticenlmeRcpp