QuasR is a package for the integrated analysis of high-throughput sequencing data in R, covering all steps from read preprocessing, alignment and quality control to quantification. QuasR supports different experiment types (including RNA-seq, ChIP-seq and Bis-seq) and analysis variants (e.g. ...
Read More »A defining decade in DNA (and RNA) sequencing
from Nature Methods The past decade has seen a transformation, fueled by the availability of NGS platforms, in applications based on generating DNA and RNA sequence. There are more than 50 multiletter-acronym or ‘MLA-seq’ applications for interrogating a wide variety ...
Read More »BADGE – A novel Bayesian model for accurate abundance quantification and differential analysis of RNA-Seq data
Recent advances in RNA sequencing (RNA-Seq) technology have offered unprecedented scope and resolution for transcriptome analysis. However, precise quantification of mRNA abundance and identification of differentially expressed genes are complicated due to biological and technical variations in RNA-Seq data. Researchers ...
Read More »Application of RNA-seq to the comprehensive analysis of plant mitochondrial transcriptomes
Researchers at the Academy of Sciences of the Czech Republic propose ways to improve read mapping accuracy and sensitivity such as modifying a reference genome at RNA editing sites, using splicing- and ambiguity-competent aligners, and masking chloroplast- or nucleus-derived sequences. ...
Read More »MIRPIPE – quantification of microRNAs in niche model organisms
MicroRNAs represent an important class of small non-coding RNAs regulating gene expression in eukaryotes. Present algorithms typically rely on genomic data to identify miRNAs and require extensive installation procedures. Niche model organisms lacking genomic sequences cannot be analyzed by such ...
Read More »MaLTA – a method for simultaneous transcriptome assembly and quantification from Ion Torrent RNA-Seq data
High throughput RNA sequencing (RNA-Seq) can generate whole transcriptome information at the single transcript level providing a powerful tool with multiple interrelated applications including transcriptome reconstruction and quantification. The sequences of novel transcripts can be reconstructed from deep RNA-Seq data, ...
Read More »FlipFlop – Efficient RNA Isoform Identification and Quantification from RNA-Seq Data with Network Flows
Several state-of-the-art methods for isoform identification and quantification are based on l1-regularized regression, such as the Lasso. However, explicitly listing the-possibly exponentially-large set of candidate transcripts is intractable for genes with many exons. For this reason, existing approaches using the ...
Read More »