BP4RNAseq: a babysitter package for retrospective and newly generated RNA-seq data analyses using both alignment-based and alignment-free quantification …
Processing raw reads of RNA-sequencing (RNA-seq) data, no matter public or newly
sequenced data, involves a lot of specialized tools and technical configurations that are …
sequenced data, involves a lot of specialized tools and technical configurations that are …
[HTML][HTML] RASflow: an RNA-Seq analysis workflow with Snakemake
X Zhang, I Jonassen - BMC bioinformatics, 2020 - Springer
Background With the cost of DNA sequencing decreasing, increasing amounts of RNA-Seq
data are being generated giving novel insight into gene expression and regulation. Prior to …
data are being generated giving novel insight into gene expression and regulation. Prior to …
RNAontheBENCH: computational and empirical resources for benchmarking RNAseq quantification and differential expression methods
RNA sequencing (RNAseq) has become the method of choice for transcriptome analysis, yet
no consensus exists as to the most appropriate pipeline for its analysis, with current …
no consensus exists as to the most appropriate pipeline for its analysis, with current …
[PDF][PDF] RNAsik: A Pipeline for complete and reproducible RNA-seq analysis that runs anywhere with speed and ease
K Tsyganov, A James Perry, S Kenneth Archer… - Journal of Open Source …, 2018 - theoj.org
RNA sequencing (RNA-seq) is one of many applications of high throughput sequencing, in
which millions of short sequence reads, typically around 100 bases long, are produced from …
which millions of short sequence reads, typically around 100 bases long, are produced from …
[HTML][HTML] OneStopRNAseq: a web application for comprehensive and efficient analyses of RNA-Seq data
Over the past decade, a large amount of RNA sequencing (RNA-seq) data were deposited
in public repositories, and more are being produced at an unprecedented rate. However …
in public repositories, and more are being produced at an unprecedented rate. However …
RNA-Skim: a rapid method for RNA-Seq quantification at transcript level
Motivation: RNA-Seq technique has been demonstrated as a revolutionary means for
exploring transcriptome because it provides deep coverage and base pair-level resolution …
exploring transcriptome because it provides deep coverage and base pair-level resolution …
[HTML][HTML] RNA-Seq workflow: gene-level exploratory analysis and differential expression
Here we walk through an end-to-end gene-level RNA-Seq differential expression workflow
using Bioconductor packages. We will start from the FASTQ files, show how these were …
using Bioconductor packages. We will start from the FASTQ files, show how these were …
[HTML][HTML] Limitations of alignment-free tools in total RNA-seq quantification
Background Alignment-free RNA quantification tools have significantly increased the speed
of RNA-seq analysis. However, it is unclear whether these state-of-the-art RNA-seq analysis …
of RNA-seq analysis. However, it is unclear whether these state-of-the-art RNA-seq analysis …
RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics
Recent rapid advances in next generation RNA sequencing (RNA-Seq)-based provide
researchers with unprecedentedly large data sets and open new perspectives in …
researchers with unprecedentedly large data sets and open new perspectives in …
The hitchhikers' guide to RNA sequencing and functional analysis
DNA and RNA sequencing technologies have revolutionized biology and biomedical
sciences, sequencing full genomes and transcriptomes at very high speeds and reasonably …
sciences, sequencing full genomes and transcriptomes at very high speeds and reasonably …