• MAP-RSeq

  • Referenced in 1 article [sw34369]
  • gene expression, novel and fusion transcripts, alternative splice sites, long non-coding and circular RNAs...
  • PolyA_DB

  • Referenced in 2 articles [sw17173]
  • regulation of polyadenylation can be multifold. Alternative polyadenylation is controlled by cis elements and trans ... transcriptional initiation and splicing, systematic information on polyadenylation, including alternative polyadenylation and its regulation...
  • SNPinfo

  • Referenced in 3 articles [sw17360]
  • structure, gene regulation, splicing and miRNA binding, and consider whether the alternative alleles...
  • GeneSplicer

  • Referenced in 5 articles [sw17323]
  • compared to six programs representing the leading splice site detectors for each of these species ... case GeneSplicer performed comparably to the best alternative, in terms of both accuracy and computational...
  • GSNAP

  • Referenced in 1 article [sw17306]
  • standardization of indel positions, handling of ambiguous splicing, clipping and merging of overlapping paired ... reads, and alignments to circular chromosomes and alternate scaffolds. The programs have been adapted...
  • PALMapper

  • Referenced in 1 article [sw31862]
  • PALMapper: Fast and Accurate Spliced Alignments of Sequence Reads.Genome and transcriptome sequencing experience a challenging ... genes and the identification of alternative transcripts. One way to analyze this data is aligning ... data requires highly efficient methods for accurate spliced alignments, which is further challenged...
  • rnaSeqMap

  • Referenced in 1 article [sw18852]
  • with the use of gene annotations or alternatively, in an unsupervised mode, on any genomic ... regions of high expression, significance search and splicing analyses with nucleotide granularity. Conclusions: This software...
  • 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...
  • SVMlight

  • Referenced in 260 articles [sw04076]
  • Description (homepage): SVMlight is an implementation of Vapnik...
  • 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...
  • survival

  • Referenced in 157 articles [sw04364]
  • R package survival: Survival analysis, including penalised likelihood...
  • Rfam

  • Referenced in 33 articles [sw04637]
  • The Rfam database is a collection of RNA...
  • 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...