edgeR is an R/Bioconductor software package for statistical analysis of replicated count data. Methods are designed for assessing differential expression in comparative RNA-Seq experiments, but are generally applicable to count data from other genome-scale platforms (ChIP-Seq, MeDIP-Seq...
标签：RNA-Seq, RNA-Seq Quantitation,ChIP-Seq, Gene Expression Analysis, DNA methylation
Cufflinks assembles transcripts and estimates their abundances in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support ...
标签：RNA-Seq Alignment, RNA-Seq Quantitation, Alternative Splicing, Transcriptome, RNA-Seq
We present a generative statistical model and associated inference methods that handle read mapping uncertainty in a principled manner. Through simulations parameterized by real RNASeq data, we show that our method is more accurate than previous methods. Our improved accuracy is the res...
SpliceTrap is a statistic tool for quantifying exon inclusion ratios in paired-end RNA-seq data. Instead of full transcript quantification, SpliceTrap approaches to exon inclusion level estimation as a Bayesian inference problem. For every exon it quantifies the extent to which it is in...
Mapsembler is a targeted assembly software. It takes as input a set of NGS raw reads and a set of input sequences (starters). It first determines if each starter is read-coherent, e.g. whether reads confirm the presence of each starter in the original sequence. Then for each read-cohere...