https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02132-x
SAVER-X
https://github.com/jingshuw/SAVERX
- conda create -n imputation -c conda-forge r-base=4.1.3 -y
- conda activate imputation
- conda install -c conda-forge r-seurat=4.1.0 -y
- conda install -c conda-forge r-tidyverse=1.3.1 -y
- conda install -c conda-forge r-biocmanager=1.30.16 -y
- conda install -c conda-forge r-devtools=2.4.3 -y
- conda install -c conda-forge r-reticulate=1.24 -y
- conda install -c conda-forge r-irkernel=1.3 -y
- wget https://github.com/jingshuw/SAVERX/archive/refs/heads/master.zip -O SAVERX-master.zip
- devtools::install_local("SAVERX-master.zip")
- IRkernel::installspec(name='imputation', displayname='r-imputation')
- # IO错误 请修改xui2.json内的DNS服务器ip
- ~/dev/xray/xray -c ~/etc/xui2.json &
- wget -e "https_proxy=http://127.0.0.1:20809" https://www.dropbox.com/sh/4u22cfuswcfcwvu/AAC4hl-f7P5lD8EZU1CFVt6-a/human_Immune.hdf5?dl=0 -O human_Immune.hdf5
- wget -e "https_proxy=http://127.0.0.1:20809" https://www.dropbox.com/sh/4u22cfuswcfcwvu/AABv0YxcNAChwEPS-D9hnDM6a/human_Tcells.hdf5?dl=0 -O human_Tcells.hdf5
- fg
- 垃圾程序让人高血压!!!
- conda deactivate
- conda create -n imputation_saver_x -c conda-forge python=3.7 -y
- conda activate imputation_saver_x
- pip install scanpy==1.4.4
- pip install tensorflow==2.1.0
- pip install Keras==2.3.1
- https://github.com/tensorflow/tensorflow/issues/38589
- nano -K /opt/conda/envs/imputation_saver_x/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py
- 按说明重定义 is_tensor 函数
- pip install sctransfer
- 修改 /opt/conda/envs/imputation_saver_x/lib/python3.7/site-packages/keras/engine/saving.py
- 删除全部的 .decode('utf8')和.encode('utf8')
conda deactivateconda create -n imputation_saver_x -c conda-forge python=3.7 -yconda activate imputation_saver_xpip install scanpy==1.4.4pip install tensorflow==1.15.0pip install Keras==2.3.1pip install sctransfer
Sys.setenv(RETICULATE_PYTHON = "/opt/conda/envs/imputation_saver_x/bin/python3.7")
library('reticulate')
use_condaenv("imputation_saver_x")
py_config()
library(SAVERX)
MAGIC
- conda deactivate
- conda activate imputation
- conda install -c conda-forge r-viridis=0.6.2 -y
- conda install -c conda-forge r-ggplot2=3.3.5 -y
- conda install -c conda-forge r-readr=2.1.2 -y
- conda install -c conda-forge r-phater=1.0.7 -y
- conda deactivate
- conda create -n imputation_magic -c conda-forge numpy=1.22.3 -y
- conda activate imputation_magic
- pip install phate
- pip install magic-impute
Sys.setenv(RETICULATE_PYTHON = "/opt/conda/envs/imputation_magic/bin/python3.8")
library('reticulate')
use_condaenv("imputation_magic")
py_config()
library(Rmagic)
harmony
- conda install -c bioconda r-harmony -y
require(tidyverse)
f_ScaleData_RunPCA <- function(scRNA){
scRNA <- FindVariableFeatures(scRNA, selection.method = "vst", nfeatures = 2000)
lc_all.genes <- rownames(scRNA)
scRNA <- ScaleData(scRNA, features = lc_all.genes)
scRNA <- RunPCA(scRNA, features = VariableFeatures(object = scRNA))
print(ElbowPlot(scRNA, ndims = 40))
scRNA
}
require(harmony)
f_RunHarmony <- function(scRNA, dims=1:30, batchN="batch"){
scRNA = scRNA %>% RunHarmony(batchN, plot_convergence = TRUE, max.iter.harmony = 30)
scRNA <- scRNA %>% RunUMAP(reduction = "harmony", dims = dims)
scRNA
}
f_FindNeighbors <- function(scRNA, resolution = 0.5){
scRNA <- scRNA %>% FindNeighbors(reduction = "harmony") %>% FindClusters(resolution = resolution)
scRNA[[paste0('h_resolution_', resolution)]] <- Idents(scRNA)
scRNA
}
Comments 2 条评论
IO错误 请修改xui2.json内的DNS服务器ip
~/dev/xray/xray -c ~/etc/xui2.json &
wget -e "https_proxy=https://127.0.0.1:20809" https://www.dropbox.com/sh/4u22cfuswcfcwvu/AAC4hl-f7P5lD8EZU1CFVt6-a/human_Immune.hdf5?dl=0 -O human_Immune.hdf5
wget -e "https_proxy=https://127.0.0.1:20809" https://www.dropbox.com/sh/4u22cfuswcfcwvu/AABv0YxcNAChwEPS-D9hnDM6a/human_Tcells.hdf5?dl=0 -O human_Tcells.hdf5
fg
教训:python程序一定要单独设立环境,尤其是涉及到机器学习的程序!!!!!@