• Voom

  • Referenced in 15 articles [sw14009]
  • unlock linear model analysis tools for RNA-seq read counts. New normal linear modeling strategies ... presented for analyzing read counts from RNA-seq experiments. The voom method estimates the mean ... analysis pipeline. This opens access for RNA-seq analysts to a large body of methodology ... well or better than count-based RNA-seq methods even when the data are generated...
  • TopHat

  • Referenced in 21 articles [sw17157]
  • popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper, we describe TopHat2...
  • STAR

  • Referenced in 11 articles [sw02515]
  • STAR: ultrafast universal RNA-seq aligner. Motivation: Accurate alignment of high-throughput RNA-seq data ... sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping ... large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment ... software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable...
  • RSEM

  • Referenced in 9 articles [sw17160]
  • RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. Background ... RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript ... quantification from RNA-Seq data is the handling of reads that map to multiple genes ... significant issue is the design of RNA-Seq experiments, in terms of the number...
  • DEGseq

  • Referenced in 11 articles [sw07998]
  • identifying differentially expressed genes from RNA-seq data. High-throughput RNA sequencing ... RNA-seq) is rapidly emerging as a major quantitative transcriptome profiling platform. Here, we present ... differentially expressed genes or isoforms for RNA-seq data from different samples. In this package...
  • EBSeq

  • Referenced in 7 articles [sw17161]
  • Bayes hierarchical model for inference in RNA-seq experiments. Motivation: Messenger RNA expression is important ... well as in manifestation of disease. RNA-seq experiments allow for the identification of differentially ... identifying DE isoforms in an RNA-seq experiment comparing two or more biological conditions. Results...
  • MapSplice

  • Referenced in 5 articles [sw31868]
  • MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery. The accurate mapping ... analytic techniques that work with RNA-seq data. We introduce a second generation splice detection ... SpliceMap on a set of simulated RNA-seq data. Experimental studies also support the accuracy ... junctions derived from eight breast cancer RNA-seq datasets recapitulated the extensiveness of alternative splicing...
  • recount

  • Referenced in 9 articles [sw17315]
  • multi-experiment resource of analysis-ready RNA-seq gene count datasets. Explore and download data...
  • ZIFA

  • Referenced in 6 articles [sw32141]
  • cell gene expression analysis. Single-cell RNA-seq data allows insight into normal cellular function ... visualization and analysis, but single-cell RNA-seq data are challenging for classical dimensionality-reduction...
  • EDAseq

  • Referenced in 5 articles [sw10345]
  • Exploratory Data Analysis and Normalization for RNA-Seq. Numerical and graphical summaries ... RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect...
  • RUVseq

  • Referenced in 5 articles [sw10348]
  • RUVSeq: Remove Unwanted Variation from RNA-Seq Data. This package implements the remove unwanted variation ... normalization of RNA-Seq read counts between samples...
  • QuasiSeq

  • Referenced in 7 articles [sw11359]
  • likelihood. Identify differentially expressed genes in RNA-seq count data using quasi-Poisson or quasi...
  • HTSeq

  • Referenced in 7 articles [sw16898]
  • tool developed with HTSeq that preprocesses RNA-Seq data for differential expression analysis by counting...
  • HISAT

  • Referenced in 4 articles [sw28860]
  • sensitive spliced alignment program for mapping RNA-seq reads. In addition to one global ... alignment strategies enable effective alignment of RNA-seq reads, in particular, reads spanning multiple exons...
  • GSVA

  • Referenced in 3 articles [sw17293]
  • variation analysis for microarray and RNA-seq data. Background: Gene set enrichment (GSE) analysis ... with data from both microarray and RNA-seq experiments. Conclusions: GSVA provides increased power ... current need of GSE methods for RNA-seq data. GSVA is an open source software...
  • Segmentor3IsBack

  • Referenced in 5 articles [sw21077]
  • fast and exact segmentation of Seq-data. Genome annotation is an important issue in biology ... domain: the segmentation of RNA-Seq data to determine gene boundaries. Because of its almost...
  • casper

  • Referenced in 5 articles [sw09370]
  • summarization and analysis of alternative splicing RNA-seq studies. We provide a software implementation...
  • RSeQC

  • Referenced in 2 articles [sw17144]
  • RSeQC: quality control of RNA-seq experiments. Motivation: RNA-seq has been extensively used ... critical to ensure that RNA-seq data are of high quality and suitable for subsequent ... massive size and versatile nature of RNA-seq data. Therefore, a convenient and comprehensive ... tool to assess RNA-seq quality is sorely needed. Results: We developed the RSeQC package...
  • CIDR

  • Referenced in 3 articles [sw32140]
  • clustering through imputation for single-cell RNA-seq data. Most existing dimensionality reduction and clustering ... packages for single-cell RNA-seq (scRNA-seq) data deal with dropouts by heavy modeling...
  • SpliceTrap

  • Referenced in 3 articles [sw29591]
  • exon inclusion levels using paired-end RNA-seq data. Unlike other tools, which focus ... local exon-inclusion ratios from RNA-seq data. Availability and Implementation: SpliceTrap can be implemented...