• casper

  • Referenced in 5 articles [sw09370]
  • Quantifying alternative splicing from paired-end RNA-sequencing data. RNA-sequencing has revolutionized biomedical research ... particular, our ability to study gene alternative splicing. The problem has important implications for human ... health, as alternative splicing may be involved in malfunctions at the cellular level and multiple ... standard data summaries used to study alternative splicing are severely limited, as they ignore...
  • ECgene

  • Referenced in 4 articles [sw17328]
  • clustering and gene modeling for alternative splicing. With the availability of the human genome ... consistent fashion. Specifically, ECgene takes alternative splicing events into consideration. The position of splice sites ... whole procedure. Sequences that share any splice sites are grouped together to define ... possible gene models encompassing all alternative splicing events. EST sequences in each cluster are subclustered...
  • MapSplice

  • Referenced in 6 articles [sw31868]
  • datasets recapitulated the extensiveness of alternative splicing on a global level as well...
  • SpliceTrap

  • Referenced in 3 articles [sw29591]
  • SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Motivation: Alternative splicing ... SpliceTrap can identify major classes of alternative splicing events under a single cellular condition, without ... background set of reads to estimate relative splicing changes. We tested SpliceTrap both by simulation ... useful tool to study alternative splicing regulation, especially for accurate quantification of local exon-inclusion...
  • ASTALAVISTA

  • Referenced in 3 articles [sw17177]
  • ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets ... genomes, a constantly growing number of alternative splicing (AS) events has been reported over ... address ‘complex’ AS events. ASTALAVISTA (alternative splicing transcriptional landscape visualization tool) employs an intuitive...
  • Evigan

  • Referenced in 5 articles [sw14331]
  • gene finders, BLAST hits, EST matches, and splice site predictions; learned parameters encode the relative ... ability to produce a ranked list of alternative ... gene models may facilitate identification of alternatively spliced transcripts. Experimental application to ENCODE regions...
  • MADS

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

  • Referenced in 3 articles [sw17147]
  • splice sites. To avoid limitations of splice sites prediction (mainly, over-predictions) due to independent ... problem of predicting constitutive and alternative splicing as an optimization problem, where the optimal multiple ... algorithm in the software tool ASPIC (Alternative Splicing PredICtion). It is distinguished from other methods...
  • ASPicDB

  • Referenced in 2 articles [sw17172]
  • ASPicDB: a database resource for alternative splicing analysis. Motivation: Alternative splicing has recently emerged ... Although several online resources devoted to alternative splicing analysis are available they may suffer from ... access to reliable annotations of the alternative splicing pattern of human genes ... assessment of the functional implication of alternative splicing in the gene set under investigation. ASPicDB...
  • Puma

  • Referenced in 4 articles [sw19121]
  • produces gene and isoform expression for alternative splicing study. puma also offers improvements in terms...
  • ANOSVA

  • Referenced in 2 articles [sw35536]
  • Many or most mammalian genes undergo alternative splicing, generating a variety of transcripts from ... Splice VAriation (ANOSVA) to detect alternative splicing from expression data. Since ANOSVA requires no transcript ... with data from a prototype mouse alternative splicing array, run against normal adult tissues, yielding...
  • Oases

  • Referenced in 3 articles [sw17027]
  • noise, a robust resolution of alternative splicing events and the efficient merging of multiple assemblies...
  • QGRS mapper

  • Referenced in 2 articles [sw27630]
  • sequences, including that are alternatively processed (alternatively spliced or alternatively polyadenylated). QGRS Mapper is based...
  • AutoNet

  • Referenced in 1 article [sw30811]
  • Alternative splicing regulatory network reconstruction from exon array data. Pre-mRNA alternative splicing (AS) allows ... hypothesize the existence of an alternative splicing regulatory network (SRN). The SRN contains a list...
  • GENCODE

  • Referenced in 2 articles [sw22999]
  • been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE...
  • DRIMSeq

  • Referenced in 1 article [sw25781]
  • multivariate response. For example, alternative splicing can lead to multiple expressed isoforms from the same ... polymorphisms (SNPs) that affect splicing, so-called splicing quantitative trait loci (sQTL) will help ... attractive toolbox to carefully unravel alternative splicing outcomes and recently, fast and accurate methods...
  • 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...
  • EasyCluster2

  • Referenced in 1 article [sw28774]
  • refine exon-exon junctions and explore alternative splicing without known reference transcripts. Results in GFF3...
  • 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...
  • HMMSplicer

  • Referenced in 1 article [sw29568]
  • short read datasets. HMMSplicer identifies more splice junctions than currently available algorithms when tested ... genes with low expression levels, alternative splice isoforms, or non-canonical splice junctions. Because HHMSplicer...