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R语言实现突变信号（Mutational Signatures）分析

突变信号（Mutational Signatures）首次2013年在《nature》进行报道。...实例： nmf_res_s signatures(mut_mat_s_rep,rank = 2) nmf_res signatures(mut_mat,rank...计算后获得NMF 的权重值（contribution），特征矩阵（signatures）以及重构后的矩阵（reconstructed）。...signatures.ref 主要是你要参看的数据集，在deconstructSigs中提供的数据集是signatures.nature2013。...2. plot_192_profile 实例： plot_192_profile(nmf_res_s$signatures) ?

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「R」sigminer 和 sigflow 介绍

The patterns are named mutational signatures....and the other is to represent the contribution of signatures....This slide shows three mutational signatures, they are visualized as bar plots that x represents 96 types...To help study mutational signatures in cancer, in the last two years, I am developing an R package sigminer...This package provides many features to import data, extract mutational signatures and visualize results

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SBS、DBS、INDEL（简写为 ID），见文章 The repertoire of mutational signatures in human cancer[1]。...另外还有人研究拷贝数变异，2018 年 Macintyre 等人基于浅 WGS 测序对 ovarian cancer 进行了研究，见 Copy number signatures and mutational...分析 Signatures 的工具很多，但这应该是第一个实现如此丰富类型的 R 包。...参考资料 [1] The repertoire of mutational signatures in human cancer: https://www.nature.com/articles/s41586...-020-1943-3 [2] Copy number signatures and mutational processes in ovarian carcinoma: https://www.nature.com

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TS - Index Signatures

TS - Index Signatures 你有 2 个描述，软件开发人员薪水的对象： const salary1 = { baseSalary: 100_000,

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嫌弃cosmic数据库的30个肿瘤突变signatures?

如下图；https://en.wikipedia.org/wiki/Mutational_signatures ?...不同的特征有不同的生物学含义，https://en.wikipedia.org/wiki/Mutational_signatures 比如文章 https://www.nature.com/articles...https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753213/ 对我们而言，主要是R包deconstructSigs用法： Decomposition of mutational...signatures was performed using deconstructSigs based on the set of 30 mutational signatures (‘signature.cosmic...可以和https://cancer.sanger.ac.uk/signatures_v2/Signature_patterns.png的30个signature的96碱基排列组合比例进行对比。

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deconstructSigs|探寻cosmic的独特“气质”-mutation signature ！

Mutational Signatures 出现在2013年的nature文章Signatures of mutational processes in human cancer中（https://www.nature.com...sample1 sample_1 = whichSignatures(tumor.ref = sigs.input, signatures.ref...：已知的signatures参考文件，可选signatures.nature2013和signatures.cosmic sample.id：对应tumor.ref文件中的样本名 contexts.needed...of the input signatures matrix tumor -- matrix of the trinucleotide contexts for the tumor sample used...= signatures.cosmic, sample.id = 1, associated

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Validating ECDSA Signatures in Golang

cryptography (ECC) seems to be used quite extensively in blockchain applications, and so naturally digital signatures...Validating ECDSA signatures in Golang seems trivial at first, but then one quickly gets lost down a rabbit...I thought I would document how I personally went about doing this when transmitting ECDSA signatures...major questions/problems I ran into while trying to implement this were: How do I represent ECDSA signatures...OpenSSL and Python, where there are some really cool libraries available for Python to handle ECDSA signatures

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下载TCGA所有癌症的maf文件做signature分析

然后根据MAF文件制作signature 我是根据这篇文章Mutational Profile of Metastatic Breast Cancers: A Retrospective Analysis...里面的方法来做的，他们的方法描述如下： De novo mutational signature analysis was done using the Matlab Welcome Trust Sanger...each sample mutational profile with more than 50 somatic mutations....We considered the 13 signatures (Signatures 1, 2, 3, 5, 6, 8, 10, 13, 17, 18, 20, 26, and 30) operative...A signature was defined as operative or predominant if its contribution to the mutational pattern was

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mutagene:肿瘤突变频谱数据库

Mutational profiles 根据以下4种条件，分别计算突变频谱 Cancer types Primary tumor sites Benign samples Cancer Census Genes...Mutational signatures 采用NMF非负矩阵分解算法，从突变频谱中提取突变特征，提供了以下几种特变特征 MUTAGENE-5 signatures MUTAGENE-10 signaltures...COSMIC-30 signatures 结果如下所示 ?

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COSMIC数据库简介

Mutational Signatures 在癌症中，突变位点是非常多。...研究人员提出了Mutational Signatures这个概念，突变的特征集合，共划分了96种突变类型，首先根据碱基突变的类型，有C>A, C>G, C>T, T>A, T>C, T>G共6种基本类型...Cosmic基于10952给外显子和1048个全基因组数据，总结出了30种Mutational Signatures。其中Signature1示例如下 ? 在网站上，还提供了一系列的工具。 1.

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生信代码：mutation signature

ref = "ref", alt = "alt") # Determine the signatures...to the example sample1 sample_1 = whichSignatures(tumor.ref = sigs.input, signatures.ref...= signatures.cosmic, sample.id = 1, contexts.needed...参考资料： A mutational signature associated with alcohol consumption and prognostically significantly mutated

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几乎不提供任何有用信息的肿瘤外显子你还做吗

nasopharyngeal carcinoma》，就是有一个肿瘤外显子队列，样品数量很少： To determine the genomic landscape, identify active mutational...signatures, and explore the utility of tumor mutation burden (TMB) as a biomarker of response, whole-exome...因为早期已经是有了七八个鼻咽癌的肿瘤外显子队列文章，这样的话，他们的这个数据分析得到的结论基本上没有什么新颖之处： mutational landscape of these tumors was generally...The most frequently mutated genes included TP53, FAM135B, COL3A1 and EP300 突变全景图 The most common mutational...signatures were Cosmic signatures SBS5 and SBS40 突变特征也就是说，仅仅是看了看somatic突变信息里面的SNV，这些分析我们五年前就都系统性梳理过

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比较不同的肿瘤somatic突变的signature

【1】https://software.broadinstitute.org/cancer/cga/msp 【2】https://en.wikipedia.org/wiki/Mutational_signatures...不同signature对比 signatures的本质就是96突变形式的比例，所以可以直接在R里面进行相关性计算。...11个自定义的signature的96突变频谱然后查看cosmic的30个signature的96突变频谱需要读取网络文件，signatures_probabilities.txt，代码如下： #...https://cancer.sanger.ac.uk/cancergenome/assets/signatures_probabilities.txt cosmic=read.table('https...://cancer.sanger.ac.uk/cancergenome/assets/signatures_probabilities.txt', header =

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barplot3d|圣诞节送你一个mutation signature搭建的“乐高”

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使用R包deconstructSigs根据已知的signature进行比例推断

【1】https://software.broadinstitute.org/cancer/cga/msp 【2】https://en.wikipedia.org/wiki/Mutational_signatures...和 signatures.nature2013，这两个内置的signature，比如signatures.cosmic，其实在网络文件，signatures_probabilities.txt 可以查看...和 signatures.nature2013，代码如下： signatures.cosmic rowSums(signatures.cosmic) colnames(signatures.cosmic...和 signatures.nature2013。...这个时候，就会根据自己的11个signature进行分解，而不是原来的R包内置的signatures.cosmic 和 signatures.nature2013两种分解模式。

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TCGA体细胞突变系列教程--胃癌

of mutational processes in human cancer[https://www.nature.com/articles/nature12477]。...文章中提到Different mutational processes often generate different combinations of mutation types, termed ‘...signatures’....核心的函数就是whichSignatures() w=lapply(unique(a2$Sample), function(i){ ## signatures.cosmic signatures.nature2013...sample_1 = whichSignatures(tumor.ref = sigs.input, signatures.ref =

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余弦相似度及其生物信息学应用

再次尝试搜索cosine similarity（余弦相似度），发现在 The repertoire of mutational signatures in human cancer 文章里面也提到了：...比如，同样的是对cosmic内置的30个signature互相计算相关性，如下： # https://cancer.sanger.ac.uk/cancergenome/assets/signatures_probabilities.txt...cosmic=read.table('https://cancer.sanger.ac.uk/cancergenome/assets/signatures_probabilities.txt',

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惊！量化肿瘤样品的基因组不稳定性靠的是突变数量？

2020发表在《Briefings in Bioinformatics》期刊的文章：《Computational identification of mutator-derived lncRNA signatures...其实这个somatic的SNV的数量，毕竟是TMB的概念了吗，使用这个指标分组，应该是 Mutational Burden-Associated LncRNA Signature 而不是mutator-derived...lncRNA signatures of genome instability。...参考；https://en.wikipedia.org/wiki/Mutational_signatures，他们的生物学函数，这里有一个中文翻译：https://mp.weixin.qq.com/s

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热点基因集：中性粒细胞相关genes signatures分享

最近我们整了很多热点相关的基因集，收藏在专辑《热点基因集专辑》，已经有下面这么多了，后续还会不断地更新，欢迎关注： Nature杂志用的Mouse 和 Human gene signatures分享 Nature...杂志用的23个与癌症特征密切相关的基因集signature分享单细胞转录组分析中一些常见QC相关基因集合细胞程序性死亡相关基因都一两千个了啊 CNS大刊超爱用的CD8+ T cells亚群的gene signatures...套娃似的找了四个文献才找到的巨噬细胞 M1 和 M2 signatures，不来看一下吗？...上一次整理基因集一列一列截图搞得，今天想了一下可以这样：用DeepSeek提取，指令如下按列提取出来图片中的基因，生成一个Rlist对象，第一行作为名称，然后要自己检查一下生成的结果对不对： # 创建Rlist对象 gene_signatures..."NOD2", "PI3", "PLAU", "PPIF", "TGM3", "TOM1", "UBR5-AS1", "ZNF267") ) # 检查结果 str(gene_signatures

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全基因组癌症分析(PCAWG)文献精读

of somatic structural variation in human cancer genomes. 5 FEB 2020, Nature ---- 3.The repertoire of mutational...signatures in human cancer. 5 FEB 2020, Nature ---- 4.The evolutionary history of 2,658 cancers. 5 FEB...Inferring structural variant cancer cell fraction. 5 FEB 2020, Nature Communications ---- 21.Divergent mutational

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R语言实现突变信号（Mutational Signatures）分析

「R」sigminer 和 sigflow 介绍

「r

TS - Index Signatures

嫌弃cosmic数据库的30个肿瘤突变signatures?

deconstructSigs|探寻cosmic的独特“气质”-mutation signature ！

Validating ECDSA Signatures in Golang

下载TCGA所有癌症的maf文件做signature分析

mutagene:肿瘤突变频谱数据库

COSMIC数据库简介

生信代码：mutation signature

几乎不提供任何有用信息的肿瘤外显子你还做吗

比较不同的肿瘤somatic突变的signature

barplot3d|圣诞节送你一个mutation signature搭建的“乐高”

使用R包deconstructSigs根据已知的signature进行比例推断

TCGA体细胞突变系列教程--胃癌

余弦相似度及其生物信息学应用

惊！量化肿瘤样品的基因组不稳定性靠的是突变数量？

热点基因集：中性粒细胞相关genes signatures分享

全基因组癌症分析(PCAWG)文献精读

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