• beadarray

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

  • Referenced in 8 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 8873 articles [sw00771]
  • R is a language and environment for statistical...
  • SageMath

  • Referenced in 1778 articles [sw00825]
  • Sage (SageMath) is free, open-source math software...
  • TSPLIB

  • Referenced in 676 articles [sw00983]
  • TSPLIB is a library of sample instances for...
  • Bioconductor

  • Referenced in 308 articles [sw04205]
  • Bioconductor provides tools for the analysis and comprehension...
  • ape

  • Referenced in 57 articles [sw04569]
  • R package ape: Analyses of Phylogenetics and Evolution...
  • Genocop

  • Referenced in 1089 articles [sw04707]
  • Genocop, by Zbigniew Michalewicz, is a genetic algorithm...
  • BOBYQA

  • Referenced in 66 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 96 articles [sw06104]
  • Bioconductor/R package gcrma: Background Adjustment Using Sequence Information...
  • fastDNAml

  • Referenced in 91 articles [sw06651]
  • fastDNAml is a program for estimating maximum likelihood...
  • edgeR

  • Referenced in 49 articles [sw06936]
  • edgeR: a Bioconductor package for differential expression analysis...