SPAR: small RNA-seq portal for analysis of sequencing experiments.
SPAR: small RNA-seq portal for analysis of sequencing experiments.
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SPAR：用于测序实验分析的小型RNA-seq门户。
DOI：
10.1093/nar/gky330
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发表时间：
2018-07-02
影响因子：
14.9
通讯作者：
Leung YY
中科院分区：
文献类型：
--
作者：
Kuksa PP;Amlie-Wolf A;Katanic Ž;Valladares O;Wang LS;Leung YY
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) and mouse (mm10) sequencing data. SPAR is freely available at https://www.lisanwanglab.org/SPAR.
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影响因子：
14.9
作者：
Sloan CA;Chan ET;Davidson JM;Malladi VS;Strattan JS;Hitz BC;Gabdank I;Narayanan AK;Ho M;Lee BT;Rowe LD;Dreszer TR;Roe G;Podduturi NR;Tanaka F;Hong EL;Cherry JM
通讯作者：
Cherry JM
影响因子：
14.9
作者：
Leung YY;Ryvkin P;Ungar LH;Gregory BD;Wang LS
通讯作者：
Wang LS
DOI：
10.1093/bioinformatics/btr598
发表时间：
2012-01-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Langenberger D;Pundhir S;Ekstrøm CT;Stadler PF;Hoffmann S;Gorodkin J
通讯作者：
Gorodkin J
影响因子：
14.9
作者：
Tyner C;Barber GP;Casper J;Clawson H;Diekhans M;Eisenhart C;Fischer CM;Gibson D;Gonzalez JN;Guruvadoo L;Haeussler M;Heitner S;Hinrichs AS;Karolchik D;Lee BT;Lee CM;Nejad P;Raney BJ;Rosenbloom KR;Speir ML;Villarreal C;Vivian J;Zweig AS;Haussler D;Kuhn RM;Kent WJ
通讯作者：
Kent WJ
影响因子：
7
作者：
Siepel, A;Bejerano, G;Haussler, D
通讯作者：
Haussler, D