RNA CoMPASS statistics

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Citations per year

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

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Popular tool citations

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RNA CoMPASS specifications

Information


Unique identifier OMICS_01410
Name RNA CoMPASS
Alternative name RNA Comprehensive Multi-Processor Analysis System for Sequencing
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use None
Input format FASTQ
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 2.0
Computer skills Medium
Version 1.1
Stability Stable
Requirements
Novoalign, SAMMate, BALST, MEGAN
Maintained Yes

Versioning


No version available

Documentation


Maintainers


  • person_outline Christophe Taylor
  • person_outline Guorong Xu

Publication for RNA Comprehensive Multi-Processor Analysis System for Sequencing

RNA CoMPASS citations

 (4)
library_books

A comprehensive next generation sequencing based virome assessment in brain tissue suggests no major virus tumor association

2016
PMCID: 4940872
PMID: 27402152
DOI: 10.1186/s40478-016-0338-z

[…] samples with the remaining 15 samples showing low abundance HAdV-C read levels Additional file : File S3 and Additional file : Figures S109-S132. HAdV-C was also detected in the same 9 samples using RNA CoMPASS (Additional file : Figures S112-S132). Despite detecting HAdV-C in these samples, viral read coverage was primarily limited to the same three small regions of the genome in the majority of […]

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Transcriptomic Crosstalk between Fungal Invasive Pathogens and Their Host Cells: Opportunities and Challenges for Next Generation Sequencing Methods

2016
PMCID: 5753088
PMID: 29376924
DOI: 10.3390/jof2010007

[…] a holistic fashion to infer inter-species regulatory networks []. Several computer applications have been designed with the objective of analyzing dual RNA-seq data in different contexts. Among them, RNA CoMPASS is a user-friendly RNA-seq pipeline for the analysis of transcriptomes from diverse biological specimens that can be adapted to dual RNA-seq data []. Other applications, such as NetGenerat […]

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Microbial Contamination in Next Generation Sequencing: Implications for Sequence Based Analysis of Clinical Samples

2014
PLoS Pathog
PMCID: 4239086
PMID: 25412476
DOI: 10.1371/journal.ppat.1004437

[…] removal (ROUT) method in GraphPad Prism [version 6 Mac, www.graphpad.com]) and excluded from the analysis.Metatranscriptome analysis was performed using our computational pathogen detection pipeline, RNA CoMPASS . Briefly, reads ranging from 42–101 nucleotides long were aligned to the human reference genome, hg19 (UCSC), plus a splice junction database (which was generated using the make transcrip […]

library_books

Differences in Gastric Carcinoma Microenvironment Stratify According to EBV Infection Intensity: Implications for Possible Immune Adjuvant Therapy

2013
PLoS Pathog
PMCID: 3649992
PMID: 23671415
DOI: 10.1371/journal.ppat.1003341

[…] RNA CoMPASS (Xu et al., unpublished) a graphical user interface (GUI) based parallel computation pipeline, RNA comprehensive multi-processor analysis system for sequencing (RNA CoMPASS) for the analysis of both exogenous and human sequences from RNA-seq data (). Briefly, for the analysis of both exogenous […]


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RNA CoMPASS institution(s)
Department of Computer Science, University of New Orleans Lakefront, New Orleans, LA, USA; Department of Pathology, Tulane University, New Orleans, LA, USA; Department of Mathematics, Tulane University, New Orleans, LA, USA; Department of Mathematics, Tulane University, New Orleans, LA, USA; Department of Pathology, Tulane University, New Orleans, LA, USA; Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, USA; Research Institute for Children, Children's Hospital of New Orleans, New Orleans, LA, USA

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