wapRNA statistics

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Citations per year

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

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

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Popular tool citations

chevron_left Read quality control Read alignment Gene Ontology annotation Gene fusion detection Bioinformatics workflows Reference-based transcriptome assembly Bioinformatics workflows miRNA target site detection chevron_right
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Protocols

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

Versioning


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Maintainers


This tool is not available anymore.

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 citations

 (4)
library_books

EXPath tool—a system for comprehensively analyzing regulatory pathways and coexpression networks from high throughput transcriptome data

2017
PMCID: 5737374
PMID: 28338930
DOI: 10.1093/dnares/dsx009

[…] ot 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 of re […]

library_books

Transcriptomic analysis of human breast cancer cells reveals differentially expressed genes and related cellular functions and pathways in response to gold nanorods

2015
Biophysics Rep
PMCID: 4762141
PMID: 26942225
DOI: 10.1007/s41048-015-0005-0

[…] 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 reads […]

library_books

Male and Female Biased Gene Expression of Olfactory Related Genes in the Antennae of Asian Corn Borer, Ostrinia furnacalis (Guenée) (Lepidoptera: Crambidae)

2015
PLoS One
PMCID: 4463852
PMID: 26062030
DOI: 10.1371/journal.pone.0128550

[…] were conducted with the BLASTx algorithm, followed by collection of gene ontology (GO) terms from the GO database and retrieval of KEGG Pathway designations. The BLASTx output was then processed with wapRNA []. Contigs receiving putative annotation as OR gene family members were investigated in greater detail. Assembly of contigs from iterative ABySS assemblies were achieved using CAP3 (default pa […]

call_split

Mechanism Analysis of Acid Tolerance Response of Bifidobacterium longum subsp. longum BBMN 68 by Gene Expression Profile Using RNA Sequencing

2012
PLoS One
PMCID: 3517610
PMID: 23236393
DOI: 10.1371/journal.pone.0050777
call_split See protocol

[…] were 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 tha […]


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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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