• affyPLM

  • Referenced in 6 articles [sw10464]
  • affyPLM: Methods for fitting probe-level models. A package that extends and improves the functionality ... implementation of methods for fitting probe-level models and tools using these models. PLM based...
  • dChip

  • Referenced in 3 articles [sw08350]
  • level analysis procedures. The model-based approach allows probe-level analysis on multiple arrays...
  • PLASQ

  • Referenced in 6 articles [sw18746]
  • PLASQ: A generalized linear model-based procedure to determine allelic dosage in cancer cells from ... chromosome per cell. We describe a probe-level allele-specific quantitation (PLASQ) procedure to determine ... generalized linear model that takes advantage of a novel classification of probes on the array...
  • BGX

  • Referenced in 15 articles [sw06935]
  • replicate summarisation in the spirit of the model outlined in [1]. It also provides ... take into account probe affinity effects from probe sequence information where available. The package employs ... results, such as ranking genes by expression level as well as statistically based methods...
  • cghseg

  • Referenced in 4 articles [sw06783]
  • copy number variations at the cohort level. Considering multiple profiles gives the opportunity to correct ... biases observed on single profiles, such as probe GC content or the so-called “wave ... this article, we extend the segmentation model developed in the univariate case to the joint...
  • PAGE

  • Referenced in 7 articles [sw23828]
  • method based on a parametric statistical analysis model. Compared with GSEA, the parametric analysis ... microarray data irrespective of different Affymetrix probe level analysis methods or different microarray platforms. Comparison...
  • GenXHC

  • Referenced in 2 articles [sw35559]
  • containing millions to hundreds of millions of probes that tile entire genomes are currently being ... hybridization noise. We present a probabilistic generative model for cross-hybridization in microarray data ... account multiple sources for each mRNA expression level measurement, as well as prior knowledge ... similarities between the nucleotide sequences of microarray probes and their target cDNAs. Results: The algorithm...
  • Z2pack

  • Referenced in 3 articles [sw20875]
  • levels of materials modeling: continuous k.p models, tight-binding models and ab initio calculations ... identify topological materials optimal for experimental probes, (b) classify existing compounds and (c) reveal materials...
  • pico ql

  • Referenced in 2 articles [sw13847]
  • provides both a /proc and a high-level web interface to be able to issue ... structures. Currently PiCO QL supports data structures modelling processes (such as the linked list ... structures. See Fast track roll your own probes tutorial in the PiCO QL LKM wiki...
  • TUNE

  • Referenced in 1 article [sw35757]
  • structure and often biological function of the probe. Here we present a new threading scoring ... sequence–structure compatibility. An artificial neural network model is trained to predict compatibility of amino ... model can then be used to construct protein sequence–structure alignments. Results: Our model ... decoy protein 3D structures. With a residue level structural description, its performance is comparable...
  • FEMVib

  • Referenced in 1 article [sw09266]
  • initio multi-dimensional solver for probing vibrational dynamics in polyatomic molecules and free radicals. Accurate ... oscillator provides the traditional first approximation for modeling molecular vibrational states. Rarely does a vibrational ... beyond this first approximation, and harmonic energy levels are routinely used to predict the infrared...
  • CGAL

  • Referenced in 372 articles [sw00118]
  • The goal of the CGAL Open Source Project...
  • LAPACK

  • Referenced in 1654 articles [sw00503]
  • LAPACK is written in Fortran 90 and provides...
  • Magma

  • Referenced in 3055 articles [sw00540]
  • Computer algebra system (CAS). Magma is a large...
  • Maple

  • Referenced in 5220 articles [sw00545]
  • The result of over 30 years of cutting...
  • Matlab

  • Referenced in 12721 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • R

  • Referenced in 8904 articles [sw00771]
  • R is a language and environment for statistical...
  • SageMath

  • Referenced in 1792 articles [sw00825]
  • Sage (SageMath) is free, open-source math software...