QuickRNASeq statistics

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Citations per year

Number of citations per year for the bioinformatics software tool QuickRNASeq
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Tool usage distribution map

This map represents all the scientific publications referring to QuickRNASeq per scientific context
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Associated diseases

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Popular tool citations

chevron_left Read quality control Read alignment SNP detection Alignment evaluation Normalization Known transcript quantification File format conversion Differential expression Bioinformatics workflows Spliced read alignment Gene expression visualization chevron_right
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Protocols

QuickRNASeq specifications

Information


Unique identifier OMICS_10985
Name QuickRNASeq
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data In addition to raw sequence reads in FASTQ format, the only other required inputs are a reference genome file in FASTA format and a corresponding gene annotation file in GTF (gene transfer format).
Input format FASTQ, GTF
Output data The dynamic visualization features enable end users to explore and digest RNA-seq data analyses results intuitively and interactively, and to gain deep insights into RNA-seq datasets.
Operating system Unix/Linux
Programming languages Javascript, Perl, R, Shell (Bash)
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.2
Stability Stable
Requirements
edgeR, reshape, ggplot
Maintained Yes

Download


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Versioning


No version available

Documentation


Maintainer


Additional information


http://baohongz.github.io/QuickRNASeq/

Publications for QuickRNASeq

QuickRNASeq citations

 (2)
call_split

Evaluation of two main RNA seq approaches for gene quantification in clinical RNA sequencing: polyA+ selection versus rRNA depletion

2018
Sci Rep
PMCID: 5859127
PMID: 29556074
DOI: 10.1038/s41598-018-23226-4
call_split See protocol

[…] o Gold for colon RNA and Globin-Zero for blood (both abbreviated as RiboZ). After sequencing, 50 M reads were randomly sampled from each replicate library, and then processed by an in-house developed QuickRNASeq. pipeline.Figure 1The annotations for the blood and colon samples and replicates, the number of reads uniquely mapped to the human reference genome GRCh38, and the number of reads falling […]

library_books

B Cell Intrinsic Role for IRF5 in TLR9/BCR Induced Human B Cell Activation, Proliferation, and Plasmablast Differentiation

2018
Front Immunol
PMCID: 5768180
PMID: 29367853
DOI: 10.3389/fimmu.2017.01938

[…] Tom Motif Comparison suite (MEME Suite 4.8) (). Peaks were visualized using IGV genome browser (). RNA-Seq data QC, read mapping by STAR (), read counting by featureCounts () were handled through the QuickRNASeq pipeline developed at Pfizer (). Subsequently, EdgeR was used to determine differentially expressed genes; a p-value ≤ 0.05 and a false discovery rate (FDR) <0.05 after Benjamin-Hochberg c […]


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QuickRNASeq institution(s)
Early Clinical Development, Pfizer Worldwide R&D, Cambridge, MA, USA; Inflammation & Immunology Research Unit, Pfizer WRD, Cambridge, MA, USA

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