EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering

Abstract

EMSAR is a method for quantifying transcripts from RNA-seq data with high accuracy and low computational cost. EMSAR is available at https://github.com/parklab/emsar.

Keywords

DNA microarrayComputational biologyAbundance estimationAbundance (ecology)BiologyGeneticsRNAGeneGene expressionEcology

Affiliated Institutions

Related Publications

GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis

Zefang Tang , Boxi Kang , Chenwei Li +2 more

Abstract Introduced in 2017, the GEPIA (Gene Expression Profiling Interactive Analysis) web server has been a valuable and highly cited resource for gene expression analysis bas...

2019 Nucleic Acids Research 4967 citations

Minimap2: pairwise alignment for nucleotide sequences

Heng Li

Abstract Motivation Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic cont...

2018 Bioinformatics 14625 citations

HTSeq—a Python framework to work with high-throughput sequencing data

Simon Anders , Paul Theodor Pyl , Wolfgang Huber

Abstract Motivation: A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from stand...

2014 Bioinformatics 21465 citations

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

Pierre-Alain Chaumeil , Aaron J. Mussig , Philip Hugenholtz +1 more

Abstract Summary The Genome Taxonomy Database Toolkit (GTDB-Tk) provides objective taxonomic assignments for bacterial and archaeal genomes based on the GTDB. GTDB-Tk is computa...

2019 Bioinformatics 4811 citations

Fast, sensitive and accurate integration of single-cell data with Harmony

Ilya Korsunsky , Nghia Millard , Jean Fan +7 more

The emerging diversity of single-cell RNA-seq datasets allows for the full transcriptional characterization of cell types across a wide variety of biological and clinical condit...

2019 Nature Methods 8827 citations

Publication Info

Year: 2015
Type: article
Volume: 16
Issue: 1
Pages: 278-278
Citations: 19
Access: Closed

External Links

View on DOI.org

Social Impact

Altmetric

EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering

PlumX Metrics

Social media, news, blog, policy document mentions

Citation Metrics

OpenAlex

Cite This

APA Style

                            
                                
                                    Soohyun Lee, 
                                
                                    Chae Hwa Seo, 
                                
                                    B. Alver
                                
                                et al.
                            
                            (2015). 
                            EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering. 
                            BMC Bioinformatics
                            , 16
                            (1)
                            , 278-278.
                            https://doi.org/10.1186/s12859-015-0704-z
                        

Identifiers

DOI: 10.1186/s12859-015-0704-z