• Voom

  • Referenced in 17 articles [sw14009]
  • Voom: precision weights unlock linear model analysis tools for RNA-seq read counts. New normal ... linear modeling strategies are presented for analyzing read counts from RNA-seq experiments. The voom ... variance relationship of the log-counts, generates a precision weight for each observation and enters ... voom performs as well or better than count-based RNA-seq methods even when...
  • spdep

  • Referenced in 33 articles [sw04578]
  • schemes, statistics and models , A collection of functions to create spatial weights matrix objects from ... Assuncao/Reis Index, Getis/Ord G and multicoloured join count statistics, local Moran’s I and Getis/Ord ... error models, impact measures for lag models, weighted and unweighted SAR and CAR spatial regression...
  • PISA

  • Referenced in 1 article [sw20692]
  • complete, establishing its equivalence with the weighted model counting problems. We present two approaches...
  • SNVMix

  • Referenced in 4 articles [sw29569]
  • first models allelic counts as observations and infers SNVs and model parameters using an expectation ... second models nucleotide and mapping qualities of the reads by probabilistically weighting the contribution...
  • SimSeq

  • Referenced in 3 articles [sw34306]
  • have been simulated according to the assumed model. This testing strategy can result ... data. The vector of read counts simulated for a given experimental unit has a joint ... provide a vector of weights to control the distribution of effect sizes. The algorithm requires...
  • Whittle Surrogate

  • Referenced in 1 article [sw22532]
  • create a Markov model from data one counts the occurrence of symbols and their transitions ... transition probabilities in matrix form. Given the model one may wish to compute the likelihood ... each step a symbol is chosen randomly, weighted by the number of remaining sequences given...
  • PaxDb

  • Referenced in 1 article [sw29371]
  • data, re-processed using a standardized spectral counting pipeline. By aggregating and averaging over ... protein-network information, and demonstrate that our weighted integration exhibits more consistency than the data ... covers 85,000 proteins in 12 model organisms. All values can be seamlessly compared across...
  • ATLAS

  • Referenced in 197 articles [sw00056]
  • This paper describes the Automatically Tuned Linear Algebra...
  • cdd

  • Referenced in 112 articles [sw00114]
  • The program cdd+ (cdd, respectively) is a C...
  • CoCoA

  • Referenced in 634 articles [sw00143]
  • CoCoA is a system for Computations in Commutative...
  • Coq

  • Referenced in 1818 articles [sw00161]
  • Coq is a formal proof management system. It...
  • GAP

  • Referenced in 2948 articles [sw00320]
  • GAP is a system for computational discrete algebra...
  • GAUSS

  • Referenced in 119 articles [sw00322]
  • The GAUSS Mathematical and Statistical System is a...
  • gmp

  • Referenced in 272 articles [sw00363]
  • GMP is a free library for arbitrary precision...
  • Isabelle

  • Referenced in 617 articles [sw00454]
  • Isabelle is a generic proof assistant. It allows...
  • LAPACK

  • Referenced in 1647 articles [sw00503]
  • LAPACK is written in Fortran 90 and provides...
  • LSQR

  • Referenced in 368 articles [sw00530]
  • Algorithm 583: LSQR: Sparse Linear Equations and Least...
  • Macaulay2

  • Referenced in 1721 articles [sw00537]
  • Macaulay2 is a software system devoted to supporting...