kataegis: an R package for identification and visualization of the genomic localized hypermutation regions using high-throughput sequencing.
kataegis: an R package for identification and visualization of the genomic localized hypermutation regions using high-throughput sequencing.
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kataegis：一个 R 包，用于使用高通量测序识别和可视化基因组局部超突变区域
DOI：
10.1186/s12864-021-07696-x
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发表时间：
2021-06-12
期刊：
影响因子：
4.4
通讯作者：
Li J
中科院分区：
文献类型：
--
作者：
Lin X;Hua Y;Gu S;Lv L;Li X;Chen P;Dai P;Hu Y;Liu A;Li J
基因组局部高突变区域在癌症中被发现，据报道其与癌症的预后有关。这种基因组局部高突变在发生频率和基因组密度上与通常的体细胞突变有很大不同。它就像一个突变的“猛烈的风暴”，这正是希腊语“kataegis”的意思。结果需要一种轻量级和简单易用的工具来识别和可视化基因组中的局部高突变区域。因此，我们开发了R包“kataegis”来满足这些需求。该软件包仅使用三步来识别基因组超突变区域，即：i)以标准格式读取变异文件；Ii)计算突变间距离；Iii)用适当的参数确定高突变区域，最后一步可视化中心和侧翼区域的核苷酸含量和光谱，以及这些区域的基因组景观。kataegis软件包可在Bionconductor/Github （https://github.com/flosalbizziae/kataegis）上获得，它提供了一个轻量级且易于使用的工具包，用于快速识别和可视化基因组超突变区域。
BackgroundGenomic localized hypermutation regions were found in cancers, which were reported to be related to the prognosis of cancers. This genomic localized hypermutation is quite different from the usual somatic mutations in the frequency of occurrence and genomic density. It is like a mutations “violent storm”, which is just what the Greek word “kataegis” means.ResultsThere are needs for a light-weighted and simple-to-use toolkit to identify and visualize the localized hypermutation regions in genome. Thus we developed the R package “kataegis” to meet these needs. The package used only three steps to identify the genomic hypermutation regions, i.e., i) read in the variation files in standard formats; ii) calculate the inter-mutational distances; iii) identify the hypermutation regions with appropriate parameters, and finally one step to visualize the nucleotide contents and spectra of both the foci and flanking regions, and the genomic landscape of these regions.ConclusionsThe kataegis package is available on Bionconductor/Github (https://github.com/flosalbizziae/kataegis), which provides a light-weighted and simple-to-use toolkit for quickly identifying and visualizing the genomic hypermuation regions.
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影响因子：
30.8
作者：
Ho, Allen S.;Kannan, Kasthuri;Roy, David M.;Morris, Luc G. T.;Ganly, Ian;Katabi, Nora;Ramaswami, Deepa;Walsh, Logan A.;Eng, Stephanie;Huse, Jason T.;Zhang, Jianan;Dolgalev, Igor;Huberman, Kety;Heguy, Adriana;Viale, Agnes;Drobnjak, Marija;Leversha, Margaret A.;Rice, Christine E.;Singh, Bhuvanesh;Iyer, N. Gopalakrishna;Leemans, C. Rene;Bloemena, Elisabeth;Ferris, Robert L.;Seethala, Raja R.;Gross, Benjamin E.;Liang, Yupu;Sinha, Rileen;Peng, Luke;Raphael, Benjamin J.;Turcan, Sevin;Gong, Yongxing;Schultz, Nikolaus;Kim, Seungwon;Chiosea, Simion;Shah, Jatin P.;Sander, Chris;Lee, William;Chan, Timothy A.
通讯作者：
Chan, Timothy A.
影响因子：
64.5
作者：
Nik-Zainal S;Van Loo P;Wedge DC;Alexandrov LB;Greenman CD;Lau KW;Raine K;Jones D;Marshall J;Ramakrishna M;Shlien A;Cooke SL;Hinton J;Menzies A;Stebbings LA;Leroy C;Jia M;Rance R;Mudie LJ;Gamble SJ;Stephens PJ;McLaren S;Tarpey PS;Papaemmanuil E;Davies HR;Varela I;McBride DJ;Bignell GR;Leung K;Butler AP;Teague JW;Martin S;Jönsson G;Mariani O;Boyault S;Miron P;Fatima A;Langerød A;Aparicio SA;Tutt A;Sieuwerts AM;Borg Å;Thomas G;Salomon AV;Richardson AL;Børresen-Dale AL;Futreal PA;Stratton MR;Campbell PJ;Breast Cancer Working Group of the International Cancer Genome Consortium
通讯作者：
Breast Cancer Working Group of the International Cancer Genome Consortium
影响因子：
30.8
作者：
Chan K;Roberts SA;Klimczak LJ;Sterling JF;Saini N;Malc EP;Kim J;Kwiatkowski DJ;Fargo DC;Mieczkowski PA;Getz G;Gordenin DA
通讯作者：
Gordenin DA
影响因子：
4.7
作者：
Mace, K;Aguilar, F;Pfeifer, AMA
通讯作者：
Pfeifer, AMA
影响因子：
16
作者：
Roberts, Steven A.;Sterling, Joan;Thompson, Cole;Harris, Shawn;Mav, Deepak;Shah, Ruchir;Klimczak, Leszek J.;Kryukov, Gregory V.;Malc, Ewa;Mieczkowski, Piotr A.;Resnick, Michael A.;Gordenin, Dmitry A.
通讯作者：
Gordenin, Dmitry A.