• BART-BMA

  • Referenced in 5 articles [sw23498]
  • posterior distribution more efficiently than BART for datasets with large p. BART-BMA incorporates elements ... simulated data and data from two real proteomic experiments, one to distinguish between patients with...
  • Decon2LS

  • Referenced in 3 articles [sw16610]
  • profiles. Application of Decon2LS to deisotope different datasets obtained across different instruments yielded a high ... package for discovering and visualizing features in proteomics studies that require automated interpretation of mass...
  • MS-BID

  • Referenced in 1 article [sw27622]
  • biomarker discovery using LC-MS-based comparative proteomic analysis. This platform consists of several computational ... peptides across a number of LC-MS datasets and (iii) selecting discriminatory peptides between classes...
  • DFLpred

  • Referenced in 0 articles [sw25081]
  • entire proteome on a single CPU. When assessed on an independent test dataset with ... these methods. Prediction on the complete human proteome reveals that about 10% of proteins have...
  • dmGWAS

  • Referenced in 3 articles [sw29291]
  • with that from prior-knowledge databases and proteome studies has recently gained attention. These methodologies ... integrating the association signal from GWAS datasets into the human protein-protein interaction (PPI) network...
  • PhosphoPredict

  • Referenced in 0 articles [sw25089]
  • phosphorylation substrates and sites in the human proteome by combining informative protein sequence and functional ... kinases, respectively when evaluated on independent test datasets. PhosphoPredict is further applied at the high ... specificity of 95% to the entire human proteome and identified a large number of potential...
  • PONDR-FIT

  • Referenced in 2 articles [sw16904]
  • useful strategy especially for many large-scale proteomic investigations. Here we introduced a consensus artificial ... single predictors, depending on the datasets being used. Analysis of the errors shows that...
  • OOgenesis_Pred

  • Referenced in 5 articles [sw25083]
  • yielded 91.62% and 85.38% prediction accuracy for datasets with 90% and 50% identity, respectively, which ... will become a powerful tool for future proteomic studies related to oogenesis...
  • PPI_SVM

  • Referenced in 2 articles [sw30744]
  • applied to the whole proteome in high-throughput studies. Our machine learning classifier, following ... combined with good selectivity on the benchmarking dataset. The PPI_SVM source code, train/test datasets...
  • RVMAB

  • Referenced in 1 article [sw24037]
  • yeast and human datasets respectively, which are significantly better than the method based ... SIPs. For facilitating extensive studies for future proteomics research, the RVMAB server is freely available...
  • Phage_Finder

  • Referenced in 1 article [sw25874]
  • completed bacterial genomes. Using a test dataset of 42 bacterial genomes whose prophages have been ... BLAST score ratio (BSR) of the phage/prophage proteomes. This method verified many known bacteriophage groups...
  • PPIs-WDSVM

  • Referenced in 1 article [sw34761]
  • important role in the field of proteomics research. In recent years, an increasing number ... extit{H. pylori}) and extit{Saccharomyces cerevisiae} datasets were 95.97% and 95.55% by 5-fold...
  • Matlab

  • Referenced in 13460 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • R

  • Referenced in 9810 articles [sw00771]
  • R is a language and environment for statistical...
  • STAR

  • Referenced in 15 articles [sw02515]
  • STAR: ultrafast universal RNA-seq aligner. Motivation: Accurate...
  • UCI-ml

  • Referenced in 3379 articles [sw04074]
  • UC Irvine Machine Learning Repository. We currently maintain...
  • Bioconductor

  • Referenced in 320 articles [sw04205]
  • Bioconductor provides tools for the analysis and comprehension...
  • fda (R)

  • Referenced in 1461 articles [sw04511]
  • fda: Functional Data Analysis , These functions were developed...
  • PLINK

  • Referenced in 66 articles [sw04581]
  • PLINK is a free, open-source whole genome...
  • KernSmooth

  • Referenced in 978 articles [sw04586]
  • Kernel smoothing refers to a general methodology for...