• Voom

• Referenced in 17 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 23 articles [sw17157]
• popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper, we describe TopHat2...

• STAR

• Referenced in 12 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 11 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 6 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...

• ZIFA

• Referenced in 8 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...

• recount

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

• HTSeq

• Referenced in 8 articles [sw16898]
• tool developed with HTSeq that preprocesses RNA-Seq data for differential expression analysis by counting...

• 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...

• CIDR

• Referenced in 5 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...

• QuasiSeq

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

• SC3

• Referenced in 4 articles [sw23914]
• consensus clustering of single-cell RNA-seq data. Single-cell RNA-seq enables the quantitative...

• 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 a data-based ... simulation algorithm for RNA-seq data. The vector of read counts simulated for a given ... matches the distribution of a source RNA-seq dataset provided by the user. Users control...

• 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...

• Oases

• Referenced in 3 articles [sw17027]
• Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Motivation ... difficult, it is possible to use RNA-seq to sequence mRNA. In the absence ... named Oases designed to heuristically assemble RNA-seq reads in the absence of a reference ... tested on human and mouse RNA-seq data and is shown to improve significantly...

• 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...