mirTools statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Bioinformatics workflows ncRNA identification chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

Protocols

To access compelling stats and trends, optimize your time and resources and pinpoint new correlations, you will need to subscribe to our premium service.

Subscribe

mirTools specifications

Information


Unique identifier OMICS_00365
Name mirTools
Interface Web user interface
Restrictions to use None
Output data The typical output consists of six parts: Basic statistics, annotation, miRNA, miRNA targets, ncRNA and differential expression.
Output format HTML
Computer skills Basic
Version 2.0
Stability No
Maintained No

Maintainers


This tool is not available anymore.

Publications for mirTools

mirTools in pipelines

 (3)
2018
PMCID: 5761873
PMID: 29320577
DOI: 10.1371/journal.pone.0190485

[…] (hg19) used for this purpose were downloaded from the ucsc genome browser., the uniquely mapped reads showing length distribution within the range of 16–40 nts were analyzed using imir [] and mirtools2.0 [] to predict known and novel pirnas as well as mirnas and their differential expression with respect to normal ovarian tissue as a control. the annotations of genomic regions […]

2018
PMCID: 5892942
PMID: 29570727
DOI: 10.1371/journal.ppat.1006942

[…] and eluted from the gel, concentrated and the libraries validated, quantified and finally pooled and sequenced on a hiseq 2000 and hiseq 4000., raw mirnaseq reads are quality checked by fastqc []. mirtools2.0 [] pipeline is used for trimming (“adaptor_trim.pl” script) and downstream analysis of known mirnas. sequencing reads are aligned to the bostau7 genome using soap []. annotations […]

2012
PMCID: 3708110
PMID: 22298343
DOI: 10.1002/jcb.24084

[…] including predicted micrornas, were downloaded using biomart (http://www.biomart.org/). rna secondary structure was assessed using the vienna rnafold webserver (http://rna.tbi.univie.ac.at/). the mirtools web server [zhu et al., ] was used to identify putative novel mirnas. the co-ordinates of bovine trna genes were obtained from the genomic trna database (gtrnadb: […]


To access a full list of citations, you will need to upgrade to our premium service.

mirTools in publications

 (19)
PMCID: 5808213
PMID: 29467792
DOI: 10.3389/fgene.2018.00022

[…] tools for mirna-seq data analysis and some have been evaluated for different purposes in previous studies. compared eight tools: mirdeep (), miranalyzer (), mirexpress (), mirtrap (), dsap (), mirtools (), mirena (), mirnakey (), and mireap (). they selected three data sets (caenorhabditis elegans, gallus gallus, and human embryonic stem cells) to evaluate the sensitivity, accuracy […]

PMCID: 5761873
PMID: 29320577
DOI: 10.1371/journal.pone.0190485

[…] (hg19) used for this purpose were downloaded from the ucsc genome browser., the uniquely mapped reads showing length distribution within the range of 16–40 nts were analyzed using imir [] and mirtools2.0 [] to predict known and novel pirnas as well as mirnas and their differential expression with respect to normal ovarian tissue as a control. the annotations of genomic regions […]

PMCID: 5615367
PMID: 28925938
DOI: 10.3390/genes8090234

[…] prediction tools for novel micrornas or isoforms of mirnas (isomirs) quantification. however, they do not generally offer functional downstream analysis or data visualization. some exceptions are mirtools 2.0 [], which includes a target prediction and a functional analysis module, uea srna workbench which includes a visualization tool and srnabench for multi-species analysis []. srnatoolbox […]

PMCID: 5529372
PMID: 28747726
DOI: 10.1038/s41598-017-07013-1

[…] the combination of mir-100, mir-9c-5p and mir-283 was chosen with a coefficient of variation less than 0.05., analysis of small rna sequencing data was performed using the pipeline of mirpro and mirtools v2.0 with adaptation. in brief, the low-quality reads were filtered out using the fastx-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html), and the 3′ adapter was trimmed […]

PMCID: 5432660
PMID: 28540181
DOI: 10.1016/j.gdata.2017.05.006

[…] were gel-purified and ligated to the 3′ adaptor and 5′ adaptor oligonucleotides. samples were allowed for deep sequencing on the illumina gaii platform., in order to make statistics of mirna reads, mirtools was used. reads were mapped to the university of california at santa cruz (ucsc) mm10 assembly of the murine genome by using megablast. mirnas profiling was according to mirna (mirbase […]


To access a full list of publications, you will need to upgrade to our premium service.

mirTools institution(s)
Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, Hefei, China; University of Science and Technology of China, Hefei, China; Institute of Genomic Medicine; Wenzhou Medical College, Wenzhou, China; Department of Laboratory Medicine, Third People’s Hospital of Wenzhou, Wenzhou, China; Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
mirTools funding source(s)
Supported by the National Natural Science Foundation of China (grant no. 31171236), the National High Technology Research and Development Program of China (2012AA02A201), the Key Science and Technology Innovation Team of Zhejiang Province (2012R10048-05), and the International S&T Cooperation Program of China (2011DFA30670).

mirTools reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review mirTools