• PSPMCM

  • Referenced in 9 articles [sw27707]
  • proportional hazards mixture cure model. Indications and limitations of the proposed macro are discussed ... example in the field of cancer clinical trials is shown...
  • PCC_Mutations

  • Referenced in 1 article [sw42849]
  • Uncovering potential interventions for pancreatic cancer patients via mathematical modeling. Pancreatic ductal adenocarcinoma (PDAC ... because it is often diagnosed when the cancer is in a later stage ... built a Boolean model to analyze the microenvironment of pancreatic cancer in order to better ... pancreatic cancer, stellate cells, and their signaling cytokines. Specifically, we have used our model...
  • BayICE

  • Referenced in 1 article [sw40317]
  • BayICE: a Bayesian hierarchical model for semireference-based deconvolution of bulk transcriptomic data. Gene expression ... primary mission against diseases. For example, cancer immunology aims to clarify the role ... identified. This is particularly a problem in cancer studies. Hence, a preselection strategy that ... patients with nonsmall cell lung cancer. The model is implemented in the R package “BayICE...
  • horserule

  • Referenced in 5 articles [sw27913]
  • Random Forest on 16 datasets. The model and its interpretation is demonstrated on the well ... cancer classification. The posterior sampling, prediction and graphical tools for interpreting the model results...
  • ice

  • Referenced in 14 articles [sw24700]
  • becoming the standard route to estimating models with missing covariate data under a missing ... data from an observational study in ovarian cancer are used to illustrate the most important...
  • SPhyR

  • Referenced in 3 articles [sw34136]
  • CNAs in cancer, SPhyR employs the k-Dollo evolutionary model, where a mutation can only ... simulated data and on a metastatic colorectal cancer...
  • SNVMix

  • Referenced in 4 articles [sw29569]
  • transcriptome single nucleotide variant (SNV) discovery in cancer. NGS produces millions of short sequence reads ... three implementations of a probabilistic Binomial mixture model, called SNVMix, designed to infer SNVs from ... genomically unstable tumor genomes. The second models nucleotide and mapping qualities of the reads ... quantitatively evaluated these approaches on 16 ovarian cancer RNASeq datasets with matched genotyping arrays...
  • pRRophetic

  • Referenced in 1 article [sw42422]
  • very large panel of cancer cell lines, then applying these models to gene expression data ... prediction of clinical drug response for many cancer drugs in a user-friendly R environment ... multiple myeloma may be improved by training models on a large set of neoplastic hematological...
  • PINCAGE

  • Referenced in 1 article [sw35031]
  • sample classification. Model: Here, we present PINCAGE (Probabilistic INtegration of CAncer GEnomics data), a method ... that uses probabilistic integration of cancer genomics data for combined evaluation of RNA-seq gene ... promoters as well as gene bodies. It models the dependence between expression and methylation using...
  • nsiGGM

  • Referenced in 1 article [sw22173]
  • model guided by pathway information. Up to date, many biological pathways related to cancer have ... accommodating multiple studies, the joint Gaussian graphical model was previously proposed to incorporate nonzero edge ... rule employs the structured input-output lasso model, in order to estimate a sparse precision ... application to breast cancer data sets, we found that the proposed model is superior...
  • GBMCI

  • Referenced in 2 articles [sw11476]
  • against other popular survival models with a large-scale breast cancer prognosis dataset. Our experiment...
  • emba

  • Referenced in 1 article [sw35159]
  • ensemble of boolean models for biomarker discovery in cancer cell networks. The package allows ... pipeline which predicts synergistic drug combinations in cancer cell lines (developed by the DrugLogics research ... used to split a boolean model dataset to model groups with regards to the models...
  • BayesMendel

  • Referenced in 7 articles [sw11022]
  • called BayesMendel that allows implementation of Mendelian models in research and counseling settings. BayesMendel ... first release, it includes two major cancer syndromes: the breast-ovarian cancer syndrome ... hereditary non-polyposis colorectal cancer syndrome, along with up-to-date estimates of penetrance ... epidemiologists to flexibly implement their own Mendelian models for novel syndromes and local subpopulations, without...
  • ACSSCode

  • Referenced in 6 articles [sw26233]
  • front end via a Component Object Model interface passing an Extensible Markup Language string ... illustrated with an animal study in lung cancer prevention research...
  • BreastNet

  • Referenced in 1 article [sw41927]
  • neural network model through histopathological images for the diagnosis of breast cancer...
  • CASPAR

  • Referenced in 6 articles [sw12242]
  • shown to correlate with survival in several cancers, however, analysis of the data is difficult ... resulting in severely underdetermined regression or classification models. Several approaches exist to classify patients...
  • KEGGgraph

  • Referenced in 8 articles [sw06934]
  • interface between KEGG pathways and graph models as well as a collection of tools ... case study of analyzing human pancreatic cancer pathway...
  • HMM-DM

  • Referenced in 4 articles [sw23510]
  • approach first uses a hidden Markov model (HMM) to identify DM CG sites accounting ... using a real breast cancer dataset...
  • PBMDR

  • Referenced in 1 article [sw36892]
  • SNPs from eight breast-cancer-related gene. In simulated disease models, we demonstrated that PBMDR...
  • AugmentedPCA

  • Referenced in 1 article [sw40917]
  • these factor models on an open-source, RNA-seq cancer gene expression dataset, showing that...