• MADS

  • Referenced in 3 articles [sw35537]
  • improved method for analysis of differential alternative splicing by exon-tiling microarrays. We describe ... differential splicing (MADS), for discovery of differential alternative splicing from exon-tiling microarray data. MADS...
  • Yanagi

  • Referenced in 1 article [sw33123]
  • quantification. Analysis of differential alternative splicing from RNA-seq data is complicated by the fact ... given length (L) while distinguishing annotated alternative splicing events in the transcriptome. In this paper ... segment library based on an analysis of differential exon skipping in Drosophila melanogaster and Homo...
  • SNPinfo

  • Referenced in 3 articles [sw17360]
  • structure, gene regulation, splicing and miRNA binding, and consider whether the alternative alleles ... likely to have differential effects on function. Users can assign weights for different functional categories...
  • Puma

  • Referenced in 4 articles [sw19121]
  • produces gene and isoform expression for alternative splicing study. puma also offers improvements in terms ... available uncertainty propagation methods. Included are summarisation, differential expression detection, clustering and PCA methods, together...
  • DiffSplice

  • Referenced in 1 article [sw17051]
  • DiffSplice: The genome-wide detection of differential splicing events with RNA-seq. RNA sequencing ... novel tool for discovering and quantitating alternative splicing variants present in an RNA-seq dataset...
  • DRIMSeq

  • Referenced in 1 article [sw25781]
  • attractive toolbox to carefully unravel alternative splicing outcomes and recently, fast and accurate methods ... Dirichlet-multinomial model naturally accounts for the differential gene expression without losing information about overall...
  • Magma

  • Referenced in 2857 articles [sw00540]
  • Computer algebra system (CAS). Magma is a large...
  • Mathematica

  • Referenced in 5883 articles [sw00554]
  • Almost any workflow involves computing results, and that...
  • R

  • Referenced in 8359 articles [sw00771]
  • R is a language and environment for statistical...
  • SageMath

  • Referenced in 1620 articles [sw00825]
  • Sage (SageMath) is free, open-source math software...
  • STAR

  • Referenced in 12 articles [sw02515]
  • STAR: ultrafast universal RNA-seq aligner. Motivation: Accurate...
  • UCI-ml

  • Referenced in 3041 articles [sw04074]
  • UC Irvine Machine Learning Repository. We currently maintain...
  • Bioconductor

  • Referenced in 298 articles [sw04205]
  • Bioconductor provides tools for the analysis and comprehension...
  • CRAN

  • Referenced in 456 articles [sw04351]
  • R is ‘GNU S’, a freely available language...
  • LIBSVM

  • Referenced in 1088 articles [sw04879]
  • LIBSVM is a library for Support Vector Machines...
  • gcrma

  • Referenced in 95 articles [sw06104]
  • Bioconductor/R package gcrma: Background Adjustment Using Sequence Information...
  • OpenGL

  • Referenced in 131 articles [sw06740]
  • OpenGL (Open Graphics Library) is a cross-language...
  • edgeR

  • Referenced in 46 articles [sw06936]
  • edgeR: a Bioconductor package for differential expression analysis...
  • Soap

  • Referenced in 37 articles [sw08915]
  • SOAP: short oligonucleotide alignment program. We have developed...
  • casper

  • Referenced in 5 articles [sw09370]
  • Quantifying alternative splicing from paired-end RNA-sequencing...