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deepTools
By Martin Jones 4137 days agoUser-friendly tools for the normalization and visualization of deep-sequencing dataStringTie Transcript assembly and quantification for RNA-Seq
By Jit 2097 days agoccb.jhu.edu - StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length...Understanding RNA-Seq Normalization Methods: TPM vs. FPKM vs. CPM
By Neel 451 days agoChoosing the right normalization method depends on the specific objectives of your RNA-Seq analysis. TPM’s proportionality and robustness make it the preferred choice for most applications, while CPM serves well for differential expression...dupRadar package
By Jit 2953 days agobioconductor.org - The dupRadar package gives an insight into the duplication problem by graphically relating the gene expression level and the duplication rate present on it. Thus, failed experiments can be easily identified at a glanceIntegrated mRNA and microRNA transcriptome analysis in Strand NGS
By Strand 3868 days agoIntegrated mRNA and microRNA transcriptome analysis in Strand NGSWebinar on Fast and Accurate DNA Variant Calling on 26 Apr 2017
By Yeshodari 3242 days agoContinuing our DNA-Seq webinar series, we'll present Strand NGS v3.0 best-practices: a workflow that identifies highly accurate variants from raw reads. Our best practices workflow is twice as fast as its GATK counterpart, and results in...Webinar on 'An integrated RNA and DNA approach to unravel genetic regulation in cancer'
By Yeshodari 4042 days agoWebinar, next generation sequencing data analysisRNA-seq Analysis Workshop Course Materials
By Jit 2804 days agochagall.med.cornell.edu - RNAseq can be roughly divided into two "types": Reference genome-based - an assembled genome exists for a species for which an RNAseq experiment is performed. It allows reads to be aligned against the reference genome and significantly improves...Modular, efficient and constant-memory single-cell RNA-seq preprocessing
By Jit 1797 days ago Comments (1)pachterlab.github.io - With kallisto | bustools you can Generate a cell x gene or cell x transcript equivalence class count matrix Perform RNA velocity and single-nuclei RNA-seq analsis Quantify data from numerous technologies such as...New RNA Seq tool
By Rahul Agarwal 4334 days ago Comments (4)www.genengnews.com - "By removing the time-consuming step of read mapping, the authors reported, Sailfish able to provide quantification estimates 20–30 times faster than current methods without loss of accuracy." Tool...
