TBtools protocols

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TBtools specifications

Information


Unique identifier OMICS_28210
Name TBtools
Alternative name Toolbox for Biologists
Software type Toolkit/Suite
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 0.58
Stability Stable
Requirements
JRE
Maintained Yes

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Maintainers


  • person_outline Yehua He <>
  • person_outline Rui Xia <>
  • person_outline Chengjie Chen <>

Publication for Toolbox for Biologists

TBtools in pipelines

 (3)
2018
PMCID: 5924554
PMID: 29659525
DOI: 10.3390/genes9040212

[…] in the multi-group comparison, it was considered to be a significantly different expression level. the degs were further annotated with go functional and kegg pathway analyses using the software tbtools []. p-values generated from the enrichment analyses were subjected to multiple hypotheses testing by perlscript [], and a p-value of <0.05 considering statistically significant. […]

2016
PMCID: 5033252
PMID: 27656892
DOI: 10.1371/journal.pone.0163315

[…] cors were similar to the ones obtained from the rnaseq results (), indicating that the method used to determine differentially expressed genes in this study was valid., the home made application ‘tbtools’ (http://cj-chen.github.io/tbtools/) was used to identify go terms that were remarkably enriched in cors. enriched go terms in up-regulated and down-regulated cors were identified separately […]


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TBtools in publications

 (16)
PMCID: 5943715
PMID: 29774047
DOI: 10.3389/fpls.2018.00604

[…] predicted using the multiple expectation maximization for motif elicitation (meme)/motif alignment and search tool (mast) system (http://meme-suite.org/) (bailey et al., ) and visualized using the tbtools (version 0.4999) (https://github.com/cj-chen/tbtools)., non-coding rnas were predicted by aligned a. ipaensis genome assembly to against the rfam databese (version 12.1) (nawrocki et al., ). […]

PMCID: 5932188
PMID: 29755419
DOI: 10.3389/fmicb.2018.00654

[…] ). identification of differentially expressed genes (degs) from rna-seq data was conducted by using cufflinks (trapnell et al., ). detection of genes differentially enriched was analyzed with tbtools (https://github.com/cj-chen/tbtools). primary metabolism-associated genes were download from the fungal and oomycete genomics resource database (http://fungidb.org/) with go term “0044238, […]

PMCID: 5893799
PMID: 29670641
DOI: 10.3389/fgene.2018.00103

[…] of brrmtp genes was analyzed by using the online gene structure display server (). the chromosomal location of the brrmtp genes was mapped according to the gene position information using the tbtools., the pfam tool and the meme program were used to search for conserved domains and motifs in the brrmtp protein sequences, respectively (; ); subsequently, the domain and motif diagrams […]

PMCID: 5786745
PMID: 29403523
DOI: 10.3389/fpls.2018.00018

[…] number of non-overlapping occurrences of each motif, number of different motifs as 20, range of motif width as 6 to 100. all of the functions of those motifs were analyzed by interpro and drawn by tbtools software, and the position of the annotated motifs were displayed by the r package “ggplot2”. the structures of tacngc genes were exhibited using the gene structure display server (gsds). […]

PMCID: 5857177
PMID: 29576971
DOI: 10.7717/peerj.4502

[…] aliphatic index, and grand average of hydropathicity, were predicted by protparam ()., protein sequence motifs were identified by the meme method (), and then the motif logos were obtained using the tbtools (https://github.com/cj-chen/tbtools). annotations of motifs were obtained from pfam database and interproscan (, ; )., we also downloaded the gene sequences from phytozome (; ). structures […]


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TBtools institution(s)
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Ministry of Agriculture, Guangzhou, China; Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, Guangzhou, China; College of Horticulture, South China Agricultural University, Guangzhou, China; Oilseed Crops Institute, Hunan Agricultural University, Changsha, China

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