• DEXUS

  • Referenced in 2 articles [sw23833]
  • condtions. Detection of differential expression in RNA-Seq data is currently limited to studies ... DEXUS for detecting differential expression in RNA-Seq data for which the sample conditions...
  • Oases

  • Referenced in 3 articles [sw17027]
  • tested on human and mouse RNA-seq data and is shown to improve significantly...
  • Salmon

  • Referenced in 3 articles [sw31865]
  • accurate, transcript-level quantification estimates from RNA-seq data. Salmon achieves its accuracy and speed...
  • GSAASeqSP

  • Referenced in 1 article [sw25397]
  • gene set association analysis of RNA-Seq data. RNA-Seq is quickly becoming the preferred ... analysis of count data from RNA-Seq requires new computational tools. We developed GSAASeqSP ... gene set association analysis of sequence count data. This toolset offers a variety of statistical ... show that GSAASeqSP analyses of RNA-Seq data from diverse tissue samples provide meaningful insights...
  • Wileup

  • Referenced in 1 article [sw31858]
  • tool for variant detection & annotation utilizing RNA-Seq data For calling RNA-Seq specific mutations ... case all possible mutation in the RNA-Seq data should be checked, a mpileup ... base positions in the RNA-Seq data is performed. Afterwards the distribution of bases ... your work please cite Using RNA-Seq data for the detection of a panel...
  • abSNP

  • Referenced in 1 article [sw33988]
  • innovations. (a) abSNP calls SNPs from RNA-Seq data. Since RNA-Seq data is primarily ... abSNP exploits a specific feature of RNA-Seq data, namely the varying abundance of different...
  • sydSeq

  • Referenced in 1 article [sw25399]
  • data-specific constitutive exons with RNA-Seq data. RNA-Seq has the potential to answer ... consistently conserved after splicing in a given data set. These are considered as the exons...
  • NGS-Trex

  • Referenced in 1 article [sw17151]
  • Trex: An Automatic Analysis Workflow for RNA-Seq Data. RNA-Seq technology allows the rapid ... analysis RNA-Seq is becoming very popular and widespread. Unfortunately data analysis is quite demanding...
  • rSeqDiff

  • Referenced in 2 articles [sw27647]
  • rSeqDiff: Detecting Differential Isoform Expression from RNA-Seq Data Using Hierarchical Likelihood Ratio Test. High...
  • HmmSeq

  • Referenced in 1 article [sw13742]
  • detecting differentially expressed genes from RNA-seq data. We introduce hmmSeq, a model-based hierarchical ... detecting differentially expressed genes from RNA-seq data. Our novel hmmSeq methodology uses hidden Markov ... Poisson variability. Moreover, for cases when paired data are available, hmmSeq includes a paired structure ... analyses of three publicly available RNA-seq data sets demonstrate the power and flexibility...
  • MAP-RSeq

  • Referenced in 1 article [sw34369]
  • system for RNA-Sequencing data analysis. RNA-Sequencing (RNA-Seq) technology is information-rich ... nucleotide variants (SNVs). By efficiently analyzing RNA-Seq data, we can query and obtain ... obtain a number of features from RNA-Seq data. To address this shortfall, Mayo Clinic ... computational workflow that leverages data from an RNA-Seq experiment to provide comprehensive reports...
  • PROPER

  • Referenced in 2 articles [sw17314]
  • power in differential expression analysis from RNA-seq data...
  • CLIIQ

  • Referenced in 2 articles [sw34969]
  • gene’s isoforms from RNA-Seq data remains to be a non-trivial problem...
  • GENCODE

  • Referenced in 2 articles [sw22999]
  • first public release of this annotation data set, few new protein-coding loci have been ... protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts ... most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript ... from the Illumina Body Map 2.0 RNA-seq data identify 3689 new loci not currently...
  • TRINITY

  • Referenced in 1 article [sw06130]
  • novo reconstruction of transcriptomes from RNA-Seq data. Trinity, developed at the Broad Institute, represents ... novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm ... large volumes of RNA-Seq reads. Trinity partitions the sequence data into many individual...
  • WemIQ

  • Referenced in 1 article [sw34552]
  • robust isoform quantification method for RNA-seq data. Motivation: The deconvolution of isoform expression from ... recent single-cell RNA-seq data, WemIQ also provides the opportunity to distinguish bias heterogeneity...
  • LSC

  • Referenced in 1 article [sw28781]
  • long reads from human brain cerebellum RNA-seq data and 64 million single ... reads from human brain RNA-seq data. The results show LSC can correct PacBio long ... directional gene isoform detection in RNA-seq study. Compared with another hybrid correction tool...
  • PUseqClust

  • Referenced in 1 article [sw31589]
  • PUseqClust: a clustering analysis method for RNA-seq data. Clustering analysis is an important technique ... unknown gene functions. In recent years, RNA-seq technology has been widely adopted to measure ... study proposes PUseqClust (propagating uncertainty into RNA-Seq ... clustering) framework for clustering of RNA-seq data. This framework first uses PGSeq to model...
  • scran

  • Referenced in 1 article [sw19472]
  • package scran. Methods for Single-Cell RNA-Seq Data Analysis. Implements a variety ... level analyses of single-cell RNA-seq data. Methods are provided for normalization of cell...
  • DoubleExpSeq

  • Referenced in 1 article [sw17050]
  • DoubleExpSeq: Differential Exon Usage Test for RNA-Seq Data via Empirical Bayes Shrinkage ... Parameter. Differential exon usage test for RNA-Seq data via an empirical Bayes shrinkage method...