Xtail protocols

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Xtail specifications

Information


Unique identifier OMICS_20317
Name Xtail
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.1.5
Stability Stable
Requirements
DESeq, parallel
Source code URL https://codeload.github.com/xryanglab/xtail/tar.gz/v1.1.5
Maintained Yes

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Maintainer


  • person_outline Xuerui Yang <>

Publication for Xtail

Xtail in pipeline

2017
PMCID: 5668566
PMID: 29069603
DOI: 10.1016/j.celrep.2017.10.010

[…] million mapped fragments). differentially expressed genes and transcripts in rna-seq and pol-seq samples were detected with cuffdiff (p < 0.05). translation efficiency analysis was performed with xtail (), and genes showing differential translation efficiency values were selected using a threshold on xtail p value (< 0.05). functional annotation of gene lists and enrichment analysis […]


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Xtail in publications

 (7)
PMCID: 5742586
PMID: 29311811
DOI: 10.3389/fnmol.2017.00419

[…] and huber, ). translational efficiency was estimated, for each gene and genotype, as the ratio between heavy polysomal fractions associated mrna counts and cytosolic steady-state mrna counts. the xtail 1.1.5 (xiao et al., ) r package was used to identify genes showing differential translation efficiency values between genotypes. data were normalized using the bioconductor (gentleman et al., ) […]

PMCID: 5668566
PMID: 29069603
DOI: 10.1016/j.celrep.2017.10.010

[…] million mapped fragments). differentially expressed genes and transcripts in rna-seq and pol-seq samples were detected with cuffdiff (p < 0.05). translation efficiency analysis was performed with xtail (), and genes showing differential translation efficiency values were selected using a threshold on xtail p value (< 0.05). functional annotation of gene lists and enrichment analysis […]

PMCID: 5673677
PMID: 29031842
DOI: 10.1016/j.gpb.2017.04.005

[…] 45 °c, respectively., to explore how e. coli deals with heat stress, we examined the relative variations at both transcription and translation levels between normal and heat-treated conditions. the xtail package was used to normalize the read counts for mapped genes and to identify differential translation events. the distribution of genes in terms of read counts is shown in . we focused […]

PMCID: 5448784
PMID: 28558012
DOI: 10.1371/journal.pone.0178461

[…] model at the moment of water entry. images were sampled every 50 frames (δt = 0.05s)from the 1000 frames per second taken by the high-speed camera to obtain the coordinates (xhead, yhead) and (xtail,ytail) of the head and tail of the experimental model relative to the exit of the launch tube. the coordinate values of the center of gravity (xc, yc) and the pitch angle θ of the experimental […]

PMCID: 5314775
PMID: 27923997
DOI: 10.1093/nar/gkw1190

[…] () is a collection of translation initiation sites predicted from riboseq data. several stand alone tools were developed for differential gene expression analysis (anota (), babel (), ribodiff (), xtail ()), and for the prediction of translated orfs (ribotaper (), orf-rator () and ribohmm ()). ribomap () estimates footprint origins in the presence of multiple splice isoforms and repetitive […]


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Xtail institution(s)
MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China; School of Life Sciences, Tsinghua University, Beijing, China; Joint Graduate Program of Peking–Tsinghua–National Institute of Biological Science, Tsinghua University, Beijing, China
Xtail funding source(s)
Supported by the National Natural Science Foundation of China (81472855 and 91540109), the Tsinghua University Initiative Scientific Research Program (20131089278, 2014z21046), the Tsinghua–Peking Joint Center for Life Sciences and the 1000 Talent Program (Youth Category).

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