VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis

MI Cornwell, M Vangala, L Taing, Z Herbert, J Köster… - BMC …, 2018 - Springer
Background RNA sequencing has become a ubiquitous technology used throughout life
sciences as an effective method of measuring RNA abundance quantitatively in tissues and …

[HTML][HTML] The START App: a web-based RNAseq analysis and visualization resource

JW Nelson, J Sklenar, AP Barnes, J Minnier - Bioinformatics, 2017 - academic.oup.com
Transcriptional profiling using RNA sequencing (RNAseq) has emerged as a powerful
methodology to quantify global gene expression patterns in various contexts from single …

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 …

dittoSeq: universal user-friendly single-cell and bulk RNA sequencing visualization toolkit

DG Bunis, J Andrews, GK Fragiadakis, TD Burt… - …, 2020 - academic.oup.com
A visualization suite for major forms of bulk and single-cell RNAseq data in R. dittoSeq is
color blindness-friendly by default, robustly documented to power ease-of-use and allows …

RaNA-Seq: Interactive RNA-Seq analysis from FASTQ files to functional analysis

C Prieto, D Barrios - 2020 - academic.oup.com
RaNA-Seq is a cloud platform for the rapid analysis and visualization of RNA-Seq data. It
performs a full analysis in minutes by quantifying FASTQ files, calculating quality control …

Current RNA-seq methodology reporting limits reproducibility

J Simoneau, S Dumontier, R Gosselin… - Briefings in …, 2021 - academic.oup.com
Ribonucleic acid sequencing (RNA-seq) identifies and quantifies RNA molecules from a
biological sample. Transformation from raw sequencing data to meaningful gene or isoform …

Nextpresso: next generation sequencing expression analysis pipeline

O Graña, M Rubio-Camarillo… - Current …, 2018 - ingentaconnect.com
Background: Many bioinformatics pipelines are available nowadays to analyze
transcriptomics data produced by high-throughput RNA sequencing. They implement …

ARMOR: An A utomated R eproducible MO dular Workflow for Preprocessing and Differential Analysis of R NA-seq Data

S Orjuela, R Huang, KM Hembach… - G3: Genes …, 2019 - academic.oup.com
The extensive generation of RNA sequencing (RNA-seq) data in the last decade has
resulted in a myriad of specialized software for its analysis. Each software module typically …

RNA‐seq: Basic bioinformatics analysis

F Ji, RI Sadreyev - Current protocols in molecular biology, 2018 - Wiley Online Library
Quantitative analysis of gene expression is crucial for understanding the molecular
mechanisms underlying genome regulation. RNA‐seq is a powerful platform for …

BP4RNAseq: a babysitter package for retrospective and newly generated RNA-seq data analyses using both alignment-based and alignment-free quantification …

S Sun, L Xu, Q Zou, G Wang - Bioinformatics, 2021 - academic.oup.com
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 …