• beadarray

  • Referenced in 10 articles [sw06092]
  • bead on the array carries copies of a single gene-specific probe with, on average...
  • ASTRAL-Pro

  • Referenced in 1 article [sw40987]
  • scalable inference of species trees from gene trees. However, most of these methods, including ... single-copy gene trees and do not attempt to model gene duplication and gene loss ... most phylogenomic studies have focused on single-copy genes and have discarded large parts ... measure of quartet similarity between single-copy and multicopy trees that accounts for orthology...
  • BUSCO

  • Referenced in 1 article [sw29505]
  • Single-Copy Orthologs. BUSCO v3 provides quantitative measures for the assessment of genome assembly, gene ... evolutionarily-informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB ... lineage-specific sets of Benchmarking Universal Single-Copy Orthologs. These conserved orthologs are ideal candidates ... scale phylogenomics studies, and the annotated BUSCO gene models built during genome assessments provide...
  • STAG

  • Referenced in 1 article [sw40984]
  • multi-copy gene families are comparable in accuracy to species trees inferred from single-copy ... ability to utilise data from multi-copy gene families increases the amount of data available...
  • StochPy

  • Referenced in 7 articles [sw27252]
  • Simulating Stochastic Biological Processes. Single-cell and single-molecule measurements indicate the importance of stochastic ... biology. Stochasticity creates spontaneous differences in the copy numbers of key macromolecules and the timing ... analyses of the probability distributions of molecule copy numbers and event waiting times, analyses ... with stochastic models of gene expression, cell division, and single-molecule enzyme kinetics. StochPy...
  • FISHtrees

  • Referenced in 1 article [sw29659]
  • model changes in ploidy and individual gene copy-number variations. We present FISHtrees 3.0, which ... merging trees for changes of a single gene into trees modeling changes in multiple genes...
  • ParticleMDI

  • Referenced in 1 article [sw35255]
  • Bayesian inference for mixture models with a single dataset. We apply our algorithm ... Genome Atlas, for which there are gene expression, copy number variation, DNA methylation, protein expression...
  • maskmeans

  • Referenced in 1 article [sw35561]
  • where multiple molecular profiles (gene expression, microRNA expression, methylation and copy number alterations) are used ... splitting and aggregation algorithms, as compared to single- and concatenated-view alternatives...
  • MLPAstats

  • Referenced in 1 article [sw18851]
  • method for candidate gene studies, aimed at the identification of copy number alterations. The analysis ... complexity and precision. However, there is no single framework from which the results of each ... cost-effective MLPA suitable for candidate gene studies. Its R implementation allows future methods...
  • abSNP

  • Referenced in 1 article [sw33988]
  • estimation. Variant calling, in particular, calling SNPs (single nucleotide polymorphisms) is a fundamental task ... data is primarily sampled from gene regions, this method is inexpensive. (b) abSNP is able ... successfully make calls on repetitive gene regions by exploiting the quality scores of multiply mapped ... abundance of different genes, in order to identify which repetitive copy a particular read...
  • R

  • Referenced in 10082 articles [sw00771]
  • R is a language and environment for statistical...
  • SageMath

  • Referenced in 2021 articles [sw00825]
  • Sage (SageMath) is free, open-source math software...
  • TSPLIB

  • Referenced in 699 articles [sw00983]
  • TSPLIB is a library of sample instances for...
  • Bioconductor

  • Referenced in 328 articles [sw04205]
  • Bioconductor provides tools for the analysis and comprehension...
  • ape

  • Referenced in 62 articles [sw04569]
  • R package ape: Analyses of Phylogenetics and Evolution...
  • Genocop

  • Referenced in 1103 articles [sw04707]
  • Genocop, by Zbigniew Michalewicz, is a genetic algorithm...
  • BOBYQA

  • Referenced in 80 articles [sw04769]
  • This Fortran software seeks the least value of...
  • oligo

  • Referenced in 9 articles [sw06102]
  • (R) A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon...
  • gcrma

  • Referenced in 101 articles [sw06104]
  • Bioconductor/R package gcrma: Background Adjustment Using Sequence Information...