Paper Info
Title
SPAR: small RNA-seq portal for analysis of sequencing experiments.
Abstract
The introduction of new high-throughput small RNA sequencing protocols that generate large-scale genomics datasets along with increasing evidence of the significant regulatory roles of small non-coding RNAs (sncRNAs) have highlighted the urgent need for tools to analyze and interpret large amounts of small RNA sequencing data. However, it remains challenging to systematically and comprehensively discover and characterize sncRNA genes and specifically-processed sncRNA products from these datasets. To fill this gap, we present Small RNA-seq Portal for Analysis of sequencing expeRiments (SPAR), a user-friendly web server for interactive processing, analysis, annotation and visualization of small RNA sequencing data. SPAR supports sequencing data generated from various experimental protocols, including smRNA-seq, short total RNA sequencing, microRNA-seq, and single-cell small RNA-seq. Additionally, SPAR includes publicly available reference sncRNA datasets from our DASHR database and from ENCODE across 185 human tissues and cell types to produce highly informative small RNA annotations across all major small RNA types and other features such as co-localization with various genomic features, precursor transcript cleavage patterns, and conservation. SPAR allows the user to compare the input experiment against reference ENCODE/DASHR datasets. SPAR currently supports analyses of human (hg19, hg38) andmouse (mm10) sequencing data. SPAR is freely available at https://www.lisanwanglab.org/SPAR.
Year
DOI
Venue
2018
10.1093/nar/gky330
NUCLEIC ACIDS RESEARCH
Field
DocType
Volume
Genome,Spar,Small RNA,Biology,Genomics,Genetics
Journal
46
Issue
ISSN
Citations 
W1
0305-1048
1
PageRank 
References 
Authors
0.36
10
6
Name
Order
Citations
PageRank
Pavel Kuksa139924.10
Alexandre Amlie-Wolf271.19
Živadin Katanic310.70
Otto Valladares4112.82
Li-San Wang5486.23
Yuk Yee Leung692.70