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INSTALL.md

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Installing HemaScopeR:

Quick Installation

1. Install R, python and optionally RStudio

HemaScopeR is a package written in R and Python. It can also be utilized within the interactive environment of RStudio.

R can be obtained and installed from https://cran.rstudio.com.

Python can be obtained and installed from https://www.python.org.

Please install R version 4.2 and python version 3.11.4 or higher.

Following installation of R, Rstudio can be obtained and installed from https://www.rstudio.com/products/rstudio/download/. The free version of RStudio Desktop is sufficient.

2. Install required R-packages, Python-packages and HemaScopeR

A. Install required R-packages and HemaScopeR automatically

We wrote a script that will attempt to install all required R-packages for HemaScopeR and then HemaScopeR itself. Start RStudio and then run the installation script from the console:

source("https://github.com/ZhenyiWangTHU/HemaScopeR/blob/master/HemaScopeR-install.R")

If something went wrong previously, you may need to try manually installing some of HemaScopeR's dependent R-packages, as well as HemaScopeR itself, following steps B, C and E:

B. Install and attach the devtools package

devtools is required to compile and install HemaScopeR, since it's distributed through GitHub.

install.packages("devtools")

C. Install required R-packages

Installation of these R-packages is necessary prior to HemaScopeR installation.

shiny 1.7.5
textshaping 0.3.6
shinyjs 2.1.0
Seurat 4.3.0.1
phateR 1.0.7
DoubletFinder 2.0.3
monocle 2.28.0
slingshot 2.8.0
GSVA 1.48.3
limma 3.56.2
plyr 1.8.8
dplyr 1.1.2
org.Mm.eg.db 3.17.0
org.Hs.eg.db 3.17.0
CellChat 1.6.1
velocyto.R 0.6
SeuratWrappers 0.3.1
stringr 1.5.0
scran 1.28.2
ggpubr 0.6.0
viridis 0.6.4
pheatmap 1.0.12
parallel 4.3.1
reticulate 1.31
SCENIC 1.1.2.1
feather 0.3.5
AUCell 1.22.0
RcisTarget 1.20.0
Matrix 1.6.1
foreach 1.5.2
doParallel 1.0.17
clusterProfiler 4.8.3
OpenXGR 1.0.0
RColorBrewer 1.1.3
Rfast2 0.1.5.1
SeuratDisk 0.0.0.9020
abcCellmap 0.1.0
biomaRt 2.56.1
copykat 1.1.0
gelnet 1.2.1
ggplot2 3.4.4
parallelDist 0.2.6
patchwork 1.1.3
markdown 1.10

D. Install required Python-packages

These Python-packages must be installed for Python-based steps in HemaScopeR.

numpy 1.23.5
pandas 1.3.5
scvelo 0.2.5
arboreto 0.1.6
pot 0.9.1
anndata 0.9.2
scanpy 1.9.4
scipy 1.11.2
seaborn 0.12.2
commot 0.0.3
matplotlib 3.7.2
cell2location 0.1.3
scvi-tools 1.0.3
phate 1.0.11

E. Install HemaScopeR

HemaScopeR can be installed directly from the GitHub repository

library(devtools)
install_github(repo="ZhenyiWangTHU/HemaScopeR")

If you do not want to update the installed dependencies, you could run this command

install_github(repo="ZhenyiWangTHU/HemaScopeR", dep = FALSE)

Or download HemaScopeR_1.0.0.tar.gz and install in R

install.packages('HemaScopeR_1.0.0.tar.gz')

F. Download databases

In addition to the R-packages and Python-packages, you will also need to download the databases for HemaScopeR. The databases are available in our Cloud Drive via this link https://cloud.tsinghua.edu.cn/d/759fd04333274d3f9946/.

G. Configure HemaScopeR

Please note the installation path of Python and the storage path of databases. When running HemaScopeR, assign these two paths respectively to 'pythonPath' and 'databasePath' parameters.

3. Pull Docker image 'hemascoper' from Docker Hub

HemaScopeR can be accessed via Docker Hub at https://hub.docker.com/r/l1hj/hemascoper or through Docker pull command

docker pull l1hj/hemascoper