• RSEM

  • Referenced in 11 articles [sw17160]
  • issue is particularly important for quantification with de novo transcriptome assemblies in the absence ... with a de novo transcriptome assembler, RSEM enables accurate transcript quantification for species without sequenced ... particularly useful for quantification with de novo transcriptome assemblies. In addition, RSEM has enabled valuable...
  • CLIIQ

  • Referenced in 2 articles [sw34969]
  • CLIIQ: Accurate Comparative Detection and Quantification of Expressed Isoforms in a Population. The recently developed ... transcriptomic landscape of a tissue. Unfortunately, from a computational perspective, identification and quantification...
  • MITIE

  • Referenced in 1 article [sw34895]
  • Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples.Motivation: High-throughput sequencing ... transcriptional landscape, pose profound computational challenges for transcriptome reconstruction. Results: We present the novel framework ... Transcript IdEntification) for simultaneous transcript reconstruction and quantification. We define a likelihood function based ... designed for genome- and assembly-based transcriptome reconstruction. We present an extensive study based...
  • Yanagi

  • Referenced in 1 article [sw33123]
  • transcript segment library construction for RNA-seq quantification. Analysis of differential alternative splicing from ... describe Yanagi, a tool which segments a transcriptome into disjoint regions to create a segments ... transcriptomes of Drosophila melanogaster and Homo sapiens. Finally, we demonstrate the utility of quantification using...
  • Salmon

  • Referenced in 3 articles [sw31865]
  • produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Salmon achieves ... unsorted BAM file with alignments to the transcriptome produced with your favorite aligner...
  • Grouper

  • Referenced in 1 article [sw28783]
  • clustering and annotating contigs from de novo transcriptome assemblies. There are two main modules ... Salmon tools for rapid transcript-level quantification. It relies on the fragment equivalence classes, orphaned ... read mappings and quantification information computed by these tools in order to determine how contigs ... accurately cluster and annotate contigs from transcriptome assemblies...
  • SpliceTrap

  • Referenced in 3 articles [sw29591]
  • every exon is crucial for generating accurate transcriptomic maps and studying the regulation ... state-of-the-art tools for transcript quantification. SpliceTrap demonstrated improved accuracy, robustness and reliability...
  • R

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

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

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

  • Referenced in 335 articles [sw06029]
  • Stata is a complete, integrated statistical package that...
  • WEKA

  • Referenced in 287 articles [sw06435]
  • WEKA: Waikato Environment for Knowledge Analysis. WEKA is...
  • MPI

  • Referenced in 494 articles [sw06496]
  • Automatic differentiation through the use of hyper-dual...
  • Rcpp

  • Referenced in 192 articles [sw08385]
  • Rcpp: Seamless R and C++ Integration. The Rcpp...
  • mixOmics

  • Referenced in 28 articles [sw09508]
  • mixOmics: Omics Data Integration Project. The package provide...
  • BM-map

  • Referenced in 2 articles [sw10924]
  • BM-map: Bayesian mapping of multireads for next...
  • Voom

  • Referenced in 17 articles [sw14009]
  • Voom: precision weights unlock linear model analysis tools...
  • TopHat

  • Referenced in 22 articles [sw17157]
  • TopHat2: accurate alignment of transcriptomes in the presence...
  • Bowtie 2

  • Referenced in 20 articles [sw29190]
  • Bowtie 2 is an ultrafast and memory-efficient...