wapRNA protocols

View wapRNA computational protocol

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wapRNA specifications

Information


Unique identifier OMICS_00370
Name wapRNA
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Life Technologies
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained No

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Information


Unique identifier OMICS_00370
Name wapRNA
Interface Web user interface
Restrictions to use None
Biological technology Illumina, Life Technologies
Computer skills Basic
Stability Stable
Maintained No

Maintainers


This tool is not available anymore.

Publication for wapRNA

wapRNA in pipelines

 (3)
2015
PMCID: 4689453
PMID: 26698122
DOI: 10.1371/journal.pone.0145702

[…] expression folds were expressed as mean ± s.e.m.., functional annotation was implemented by gene ontology (go) and kyoto encyclopedia of genes and genomes (kegg) pathway analyses using online waprna []. downstream functional classification was achieved through integrated localization of go [] and kegg pathway databases []. p-values were computed using the hyper-geometric test, […]

2014
PMCID: 5155352
PMID: 25483034
DOI: 10.4161/rna.36281

[…] m6a modification peak identification., gene expression levels were measured as numbers of reads per kilo bases of exon model in a gene per million uniquely mapped reads (rpkm) and quantified using waprna. genes with rpkm ≥ 1 were used for further analysis. differentially expressed genes (degs) between callus and leaf were identified with an r package named ‘degseq’. genes with p ≤ 0.001 […]

2013
PMCID: 3634072
PMID: 23626677
DOI: 10.1371/journal.pone.0061378

[…] ligation and detection (solid) , . data analysis strategy is shown in . atlantic halibut solid sequence reads were mapped to zebrafish genome sequences (zv9.62) and hairpins were extracted using waprna tools in default setting . mirbase 18 hairpin sequences were mapped to the 454 sequences to identify conserved pre-mirnas. novel pre-mirnas were identified by extracting hairpins from 454 […]


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wapRNA in publications

 (5)
PMCID: 5737374
PMID: 28338930
DOI: 10.1093/dnares/dsx009

[…] only displays the normalized expression level of each condition, but also combines the expression level and kegg pathway map. unfortunately, degust is only supplied for rna-seq data. additionally, waprna is a good tool to analyze go terms and kegg pathways of the degs. however, the significance of go and pathways could not be easily identified in the output results, neither can the number […]

PMCID: 4689453
PMID: 26698122
DOI: 10.1371/journal.pone.0145702

[…] expression folds were expressed as mean ± s.e.m.., functional annotation was implemented by gene ontology (go) and kyoto encyclopedia of genes and genomes (kegg) pathway analyses using online waprna []. downstream functional classification was achieved through integrated localization of go [] and kegg pathway databases []. p-values were computed using the hyper-geometric test, […]

PMCID: 4762141
PMID: 26942225
DOI: 10.1007/s41048-015-0005-0

[…] 2000 sequencing system (illumina) according to the manufacturer’s instructions., after illumina hiseq™ 2000 sequencing with a read length of 100 bp, raw data from the sequencer were uploaded to the waprna (zhao et al. ), which is a free web-based application for the processing of high-throughput rna-seq data from ngs platforms, such as genome analyzer of illumina inc. (solexa). low-quality […]

PMCID: 5155352
PMID: 25483034
DOI: 10.4161/rna.36281

[…] m6a modification peak identification., gene expression levels were measured as numbers of reads per kilo bases of exon model in a gene per million uniquely mapped reads (rpkm) and quantified using waprna. genes with rpkm ≥ 1 were used for further analysis. differentially expressed genes (degs) between callus and leaf were identified with an r package named ‘degseq’. genes with p ≤ 0.001 […]

PMCID: 3517610
PMID: 23236393
DOI: 10.1371/journal.pone.0050777

[…] represented in peng cui's study . all sequenced reads were aligned to the bifidobacterium longum subsp. longum bbmn68 (nc_014656.1) using ab's solid corona_lite_v4.2 software available at http://waprna.big.ac.cn. we used a recursive strategy to improve the usable sequenced reads information, that is 50 mers reads were first mapped to the genome with a tolerance of ≤5 mismatches. the reads […]


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wapRNA institution(s)
Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; Graduate University of Chinese Academy of Sciences, Beijing, China
wapRNA funding source(s)
Supported by Natural Science Foundation of China (30900831); Ministry of Science and Technology of the People’s Republic of China (BSDN2009-15); Knowledge Innovation Program of the Chinese Academy of Sciences (KSCX2-EW-R-01-04).

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