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Hi @jluebeck
I'm trying your classification script and one of my amplicons showed up as "complex non cyclic"
![image](https://user-images.githubusercontent.com/53702866/95832656-7d800580-0d32-1…
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After running AC, I can get a gene list file and some classfication bed file. But when I compare that with AA produced cycle file, they are a litter different. for example, this is one bed file that a…
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https://mp.weixin.qq.com/s/98o-tpTViuhyQP8NjYNk8A
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I want to know that in the new version of AmpliconClassified, which method do you use for classifing the AA segment? Is it the same as the paper "Extrachromosomal DNA is associated with oncogene ampli…
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目前核心的分析是基因水平的建模,这样可以得到ecDNA genes,然后基于ecDNA gene的计数评估作为一个指标建立样本ecDNA状态的判定。
另外可以增加直接基于样本水平的建模和预测,直接判定样本ecDNA状态。这样多一种分析策略,并可以与上一种策略的第二步比较。
与第一种策略将CNV记录映射到基因水平不同的是,样本水平的建模需要将区间水平的CNV提炼聚合为样本水平表征。目前考…
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First, thank ou very much for expanding AA to the use of mouse data!
I downloaded the reference data from https://drive.google.com/drive/folders/18T83A12CfipB0pnGsTs3s-Qqji6sSvCu but the directory …
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Fit FISH data but first implement the other statistics since "_the copy number is a bit higher and we will need larger population sizes for the simulation_". Understand if the cluster can be used with…
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Maybe the iter API of rayon is such that it waits until all tasks have been performed instead of dropping them along the way? Required for the cluster #6. Right now, we have for 20 cores more than 640…
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Understand the trade-off between number of CPUs and memory: how many parallel tasks can we run before running out of memory? It will depend on the nb of cells. If we cannot find satisfactory trades-of…
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对TCGA所有SNP的allele specific拷贝数数据进行分析,发现正常组织的ec样本和肿瘤的差不多。尝试增加阈值至少减少总数,正常和肿瘤的ecDNA+例数还是差不多。这违背了已知背景。
约1000例样本,其中~5000肿瘤。
```
> table(type = data_snp$sample_type, class = data_snp$class)
c…