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- 安装补充包 conda activate seurat conda install -c conda-forge r-nmf -y conda install -c conda-forge r-fastica -y 获取非负表达矩阵 使用《使用metacell进行分群聚类》中的数据 1234567891011121314151617sce <- readRDS('SRX8890
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- 【迁移】使用metacell进行分群聚类
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- 预处理 12345678910111213141516171819202122232425262728293031f_QC_plot <- function(sce){ options(repr.plot.width = 12, repr.plot.height = 6) print(Seurat::VlnPlot(sce, features = c("nFe
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- 2022-10-01
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- 处理参考样本 12345678910111213ref_sce <- readRDS('~/upload/zl_liu/data/pca.rds')ref_sce <- subset(ref_sce, group == 'CRPC')table(ref_sce@meta.data$cell_type_fig3)g2m_genes <- Se
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- 2022-09-29
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- 安装包 conda create -n seurat -c conda-forge r-seurat=4.1.1 -y conda activate seurat conda install -c conda-forge r-tidyverse -y conda install -c conda-forge r-irkernel -y Rscript -e “IRkernel::installs
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- 2022-09-29
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- <a href="/tags/sctransform/">#SCTransform</a>
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- 【迁移】使用Bootstrap法计算自举置信区间
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- 计算药物LD50用Bliss法最严谨,而改良寇氏法计算的结果误差也不大,因此做了一次改良寇氏法计算LD50的实验。最后需要计算一下结果的可信区间,于是来试试万能的Bootstrap法 安装包(这个例子用不上) conda activate MICE conda install -c conda-forge r-boot=1.3_28 -y 构造样本 组别 剂量 mg/kg 动物数 死亡数
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- 2022-09-27
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- <a href="/tags/bootstrap/">#Bootstrap</a>
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- <a class="index-excerpt " href="/cellranger-ding-liang--One-Library--Multiple-Flowcells" target="_self">
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- 重命名R1、R2 原始数据质控 重命名前 ├── SRR12391722 │ ├── SRR12391722_1.fastq.gz │ └── SRR12391722_2.fastq.gz ├── SRR12391723 │ ├── SRR12391723_1.fastq.gz │ └── SRR12391723_2.fastq.gz ├── SRR12391724 │ ├── SRR1239
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- 从 ENI 数据库下载 进入ENA Browser,搜索对应的GSE号,进入study项目,选择TSV格式的Download report。 从TSV表格中提取下载链接,一行一个写入url.txt,前面加上ftp://,接着使用wget -c -i url.txt下载 批量重命名脚本: 1234ls *.fastq.gz | cut -d '_' -f 1 | while r
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- 安装包 conda activate clusterprofiler conda install -c conda-forge r-sysfonts -y conda install -c conda-forge r-showtext -y 绘图 1234567sysfonts::font_add("Arial Narrow", "~/font/Arial Nar
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