• RSEM

  • Referenced in 11 articles [sw17160]
  • RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. Background ... challenge in transcript quantification from RNA-Seq data is the handling of reads that ... from single-end or paired-end RNA-Seq data. RSEM outputs abundance estimates, 95% credibility ... visualization files and can also simulate RNA-Seq data. In contrast to other existing tools...
  • DEGseq

  • Referenced in 11 articles [sw07998]
  • genes from RNA-seq data. High-throughput RNA sequencing (RNA-seq) is rapidly emerging ... differentially expressed genes or isoforms for RNA-seq data from different samples. In this package...
  • STAR

  • Referenced in 12 articles [sw02515]
  • Motivation: Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved ... sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping...
  • ZIFA

  • Referenced in 7 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...
  • MapSplice

  • Referenced in 6 articles [sw31868]
  • 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...
  • HTSeq

  • Referenced in 7 articles [sw16898]
  • gene model information, variant calls, and provides data structures that allow for querying via genomic ... tool developed with HTSeq that preprocesses RNA-Seq data for differential expression analysis by counting...
  • Voom

  • Referenced in 17 articles [sw14009]
  • better than count-based RNA-seq methods even when the data are generated according...
  • 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...
  • CIDR

  • Referenced in 4 articles [sw32140]
  • clustering through imputation for single-cell RNA-seq data. Most existing dimensionality reduction ... clustering packages for single-cell RNA-seq (scRNA-seq) data deal with dropouts by heavy...
  • 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...
  • SimSeq

  • Referenced in 3 articles [sw34306]
  • package SimSeq: Nonparametric Simulation of RNA-Seq Data. RNA sequencing analysis methods are often derived ... view of the performance of an RNA-seq analysis method. We develop ... data-based simulation algorithm for RNA-seq data. The vector of read counts simulated ... matches the distribution of a source RNA-seq dataset provided by the user. Users control...
  • GSVA

  • Referenced in 3 articles [sw17293]
  • variation analysis for microarray and RNA-seq data. Background: Gene set enrichment (GSE) analysis ... model pathway activity within highly heterogeneous data sets. Results: To address this challenge, we introduce ... GSVA works analogously with data from both microarray and RNA-seq experiments. Conclusions: GSVA provides ... current need of GSE methods for RNA-seq data. GSVA is an open source software...
  • GPSeq

  • Referenced in 3 articles [sw34565]
  • software tool to analyze RNA-seq data to estimate gene and exon expression, identify differentially ... model to improve the analysis of RNA-seq data. Nucleic Acids Research...
  • SpliceTrap

  • Referenced in 3 articles [sw29591]
  • exon inclusion levels using paired-end RNA-seq data. Unlike other tools, which focus ... tested SpliceTrap both by simulation and real data analysis, and compared it to state ... local exon-inclusion ratios from RNA-seq data. Availability and Implementation: SpliceTrap can be implemented...
  • QuasiSeq

  • Referenced in 7 articles [sw11359]
  • Identify differentially expressed genes in RNA-seq count data using quasi-Poisson or quasi-negative...
  • SC3

  • Referenced in 3 articles [sw23914]
  • consensus clustering of single-cell RNA-seq data. Single-cell RNA-seq enables the quantitative...
  • EDAseq

  • Referenced in 5 articles [sw10345]
  • EDASeq: Exploratory Data Analysis and Normalization for RNA-Seq ... Numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust...
  • RSeQC

  • Referenced in 2 articles [sw17144]
  • 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...
  • zinbwave

  • Referenced in 2 articles [sw36151]
  • Zero-Inflated Negative Binomial Model for RNA-Seq Data. Implements a general and flexible zero ... dimensional representations of single-cell RNA-seq data. The model accounts for zero inflation (dropouts...
  • 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...