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Voom
- Referenced in 19 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...
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STAR
- Referenced in 15 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...
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DESeq2
- Referenced in 27 articles
[sw41938]
- fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology...
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RSEM
- Referenced in 12 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...
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TopHat
- Referenced in 23 articles
[sw17157]
- popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper, we describe TopHat2...
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ZIFA
- Referenced in 13 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...
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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...
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EBSeq
- Referenced in 8 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...
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SC3
- Referenced in 8 articles
[sw23914]
- consensus clustering of single-cell RNA-seq data. Single-cell RNA-seq enables the quantitative...
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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...
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CIDR
- Referenced in 7 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...
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recount
- Referenced in 10 articles
[sw17315]
- multi-experiment resource of analysis-ready RNA-seq gene count datasets. Explore and download data...
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Segmentor3IsBack
- Referenced in 9 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...
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SimSeq
- Referenced in 4 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...
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HTSeq
- Referenced in 8 articles
[sw16898]
- tool developed with HTSeq that preprocesses RNA-Seq data for differential expression analysis by counting...
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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...
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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...
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zinbwave
- Referenced in 5 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...
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HISAT
- Referenced in 5 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...
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QuasiSeq
- Referenced in 7 articles
[sw11359]
- likelihood. Identify differentially expressed genes in RNA-seq count data using quasi-Poisson or quasi...