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Protocols

RandA specifications

Information


Unique identifier OMICS_15763
Name RandA
Alternative name ncRNA Read-and-Analyze
Software type Framework/Library
Interface Command line interface, Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages Java, Perl
License Academic Free License version 3.0
Computer skills Advanced
Version 1.1.4
Stability Stable
Requirements
BWA, fastq-mcf, R, DESeq
Maintained Yes

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Maintainer


  • person_outline Noam Shomron

Publication for ncRNA Read-and-Analyze

RandA citations

 (2)
call_split

MicroRNA mediated regulation of p21 and TASK1 cellular restriction factors enhances HIV 1 infection

2015
PMCID: 4406127
PMID: 25717002
DOI: 10.1242/jcs.167817
call_split See protocol

[…] a sequences were screened for the sequence of the small-RNA adaptor, and the adaptor sequences were trimmed using standard settings in Illumina's GAPipeline1.0. Processed Illumina data was managed by RandA software (). The reads were aligned to the human subset miRNAs in the miRbase database using BWA-aligner software. The number of reads was standardized by mapping each transcript according to it […]

library_books

Bioinformatics of Cancer ncRNA in High Throughput Sequencing: Present State and Challenges

2012
Front Genet
PMCID: 3523245
PMID: 23251139
DOI: 10.3389/fgene.2012.00287

[…] entify novel transcripts, calculate differential expression, and provide fast annotation of genomic coordinates and single nucleotide variations (revised by Li et al., ; Table ). One exception is the RandA pipeline (Isakov et al., ), that uses the whole Rfam database, and can be applied to different ncRNAs. Segtor (Renaud et al., ) is another tool that works to assist in one important step in the […]


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RandA institution(s)
Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
RandA funding source(s)
Supported by Chief Scientist Office, Ministry of Health, Israel; Israel Cancer Association and the Wolfson family Charitable Fund; I-CORE Program of the Planning and Budgeting Committee; The Israel Science Foundation (grant number 41/11); Fellowship from the Edmond J. Safra Bioinformatics program at Tel-Aviv University.

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