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"read_only": false, + "read_only_alternatives": [] +} \ No newline at end of file diff --git a/.Rproj.user/11F4C4A8/sources/session-632a36d8/6F98DDE3-contents b/.Rproj.user/11F4C4A8/sources/session-632a36d8/6F98DDE3-contents new file mode 100644 index 0000000..921e17e --- /dev/null +++ b/.Rproj.user/11F4C4A8/sources/session-632a36d8/6F98DDE3-contents @@ -0,0 +1,854 @@ +# Installation + +## Create a new conda environment and activate it + +``` +conda create --name HemaScope_env +conda activate HemaScope_env +``` + +## Set the channels in conda + +``` +# Add the default channel +conda config --add channels defaults + +# Add default channel URLs +conda config --add default_channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main +conda config --add default_channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/r +conda config --add default_channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/msys2 + +# Add custom channels +conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge +conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/msys2 +conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda +conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/menpo +conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch +conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch-lts +conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/simpleitk +conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/deepmodeling + +# Set to show channel URLs +conda config --set show_channel_urls true +``` + +## Install R and python + +- R 4.3.3 and python 3.11.4 + +``` +conda install R-base=4.3.3 +conda install python=3.11.4 +``` + +## Install required R-packages + +- From conda + +``` +conda install -c conda-forge r-devtools=2.4.5 +conda install -c conda-forge r-Seurat=4.3.0.1 +conda install -c conda-forge r-Rfast2=0.1.5.1 +conda install -c conda-forge r-hdf5r=1.3.10 +conda install -c conda-forge r-ggpubr=0.6.0 +conda install pwwang::r-seuratwrappers +conda install -c bioconda bioconductor-monocle=2.28.0 +conda install -c bioconda bioconductor-slingshot=2.8.0 +conda install -c bioconda bioconductor-GSVA=1.48.2 +conda install -c bioconda bioconductor-org.Mm.eg.db=3.17.0 +conda install -c bioconda bioconductor-org.Hs.eg.db=3.17.0 +conda install -c bioconda bioconductor-scran=1.28.1 +conda install -c bioconda bioconductor-AUCell=1.22.0 +conda install -c bioconda bioconductor-RcisTarget=1.20.0 +conda install -c bioconda bioconductor-GENIE3=1.24.0 +conda install -c bioconda bioconductor-biomaRt=2.56.1 +conda install -c bioconda r-velocyto.r=0.6 +#conda install -c bioconda bioconductor-limma=3.56.2 +``` +- Enter the R language environment + +We suggest users do not manually update any already installed R packages during the installation of the following R packages. +``` +R +``` +- From BiocManager + +``` +# BiocManager(version = "1.30.23") should already be installed as a dependency of r-seuratwrappers. +# If it is not installed, please run the following code to install it. +# install.packages("BiocManager",version="1.30.23") +BiocManager::install("ComplexHeatmap") +BiocManager::install("scmap") +BiocManager::install("clusterProfiler") +``` + +- From CRAN + +``` +remotes::install_version("shinyjs", version = "2.1.0") +remotes::install_version("phateR", version = "1.0.7") +remotes::install_version("gelnet", version = "1.2.1") +remotes::install_version("parallelDist", version = "0.2.6") +remotes::install_version("kableExtra", version = "1.3.4") +remotes::install_version("transport", version = "0.14-6") +remotes::install_version("feather", version = "0.3.5") +remotes::install_version("markdown", version = "1.10") +``` + +- From GitHub + +tips: + +Sometimes network connection issues may occur, resulting in an error message indicating that GitHub cannot be connected. Please try installing again when the network conditions improve. + +Usage limitations: Sometimes an API rate limit error occurs, and a GitHub token is needed to provide the GitHub API rate limit. The steps to resolve this are as follows: Register for an account or log in to an existing account on the GitHub website. Then click on your profile picture in the top right corner, go to the dropdown menu and select "Settings." Next, find "Developer settings" and click on it, then find "Personal access tokens (classic)." Click on it, then click "Create new token (classic)." Create a new token by first naming it anything you like. Then choose the expiration time for the token. Finally, check the "repo" box; the token will be used to download code repositories from GitHub. Click "Generate token." Copy the generated token password. + +After that, set the token in the environment variable in R. Since we are using conda, enter R by typing R in the terminal. Then, enter the command: usethis::edit_r_environ(). This will open a file. Press the i key to edit. Paste the token you copied into the code area as follows: GITHUB_TOKEN="your_token". + +Then press Esc, type :wq! (force save). After that, you need to exit Linux and re-enter R. Close and reopen the terminal to apply the environment variable. Reopen Linux, activate the conda environment, and enter R again. + +``` +devtools::install_github("sqjin/CellChat@9e1e605") +devtools::install_github("aertslab/SCENIC@fde9774") +devtools::install_github("pzhulab/abcCellmap@f44c14b") +devtools::install_github("navinlabcode/copykat@d7d6569") +devtools::install_github('chris-mcginnis-ucsf/DoubletFinder@8c7f76e') +devtools::install_github("mojaveazure/seurat-disk@877d4e1") +``` + +- Install HemaScopeR from github + +``` +devtools::install_github(repo="ZhenyiWangTHU/HemaScopeR", dep = FALSE) +``` + +- Exist the R language environment +``` +quit() +``` + +## Install required Python-packages + +- Upgrade pip and set mirrors + +``` +python -m pip install -i https://pypi.tuna.tsinghua.edu.cn/simple --upgrade pip +pip config set global.index-url https://pypi.tuna.tsinghua.edu.cn/simple +pip config set global.extra-index-url http://mirrors.aliyun.com/pypi/simple/ +``` + +- Install required packages + +``` +pip install matplotlib==3.7.2 +pip install pot==0.9.1 +pip install anndata==0.9.2 +pip install scanpy==1.9.4 +pip install scipy==1.11.2 +pip install seaborn==0.12.2 +pip install commot==0.0.3 +pip install scvi-tools==1.0.3 +pip install cell2location==0.1.3 +pip install phate==1.0.11 +pip install scvelo==0.2.5 +pip install arboreto==0.1.6 +pip install numpy==1.23.5 +pip install pandas==1.3.5 +``` + +## The installed packages with versions +- R packages with versions +``` +Package Version +------- ------- +abcCellmap 0.1.0 +abind 1.4-5 +annotate 1.78.0 +AnnotationDbi 1.64.1 +ape 5.8 +aplot 0.2.3 +arrow 17.0.0 +askpass 1.2.0 +assertthat 0.2.1 +AUCell 1.22.0 +backports 1.5.0 +base 4.3.3 +base64enc 0.1-3 +beachmat 2.16.0 +BH 1.84.0-0 +Biobase 2.60.0 +BiocFileCache 2.8.0 +BiocGenerics 0.46.0 +BiocManager 1.30.23 +BiocNeighbors 1.18.0 +BiocParallel 1.34.2 +BiocSingular 1.16.0 +BiocVersion 3.18.1 +biocViews 1.68.1 +biomaRt 2.56.1 +Biostrings 2.68.1 +bit 4.0.5 +bit64 4.0.5 +bitops 1.0-7 +blob 1.2.4 +bluster 1.10.0 +boot 1.3-30 +brew 1.0-10 +brio 1.1.5 +broom 1.0.6 +bslib 0.7.0 +cachem 1.1.0 +callr 3.7.6 +car 3.1-2 +carData 3.0-5 +caret 6.0-94 +caTools 1.18.2 +CellChat 1.5.0 +cellranger 1.1.0 +circlize 0.4.16 +class 7.3-22 +cli 3.6.3 +clipr 0.8.0 +clock 0.7.0 +clue 0.3-65 +cluster 2.1.6 +clusterProfiler 4.10.1 +coda 0.19-4.1 +codetools 0.2-20 +colorspace 2.1-0 +combinat 0.0-8 +commonmark 1.9.1 +compiler 4.3.3 +ComplexHeatmap 2.18.0 +conquer 1.3.3 +copykat 1.1.0 +corrplot 0.92 +cowplot 1.1.3 +cpp11 0.4.7 +crayon 1.5.3 +credentials 2.0.1 +crosstalk 1.2.1 +curl 5.2.1 +data.table 1.15.4 +datasets 4.3.3 +DBI 1.2.3 +dbplyr 2.5.0 +DDRTree 0.1.5 +DelayedArray 0.26.6 +DelayedMatrixStats 1.22.1 +deldir 2.0-4 +Deriv 4.1.3 +desc 1.4.3 +devtools 2.4.5 +diagram 1.6.5 +diffobj 0.3.5 +digest 0.6.36 +dlm 1.1-6 +doBy 4.6.22 +docopt 0.7.1 +doParallel 1.0.17 +DOSE 3.28.2 +dotCall64 1.1-1 +DoubletFinder 2.0.3 +downlit 0.4.4 +downloader 0.4 +dplyr 1.1.4 +dqrng 0.3.2 +dynamicTreeCut 1.63-1 +e1071 1.7-14 +edgeR 3.42.4 +ellipsis 0.3.2 +enrichplot 1.22.0 +evaluate 0.24.0 +expm 0.999-9 +fansi 1.0.6 +farver 2.1.2 +fastDummies 1.7.3 +fastICA 1.2-4 +fastmap 1.2.0 +fastmatch 1.1-4 +feather 0.3.5 +fgsea 1.28.0 +fields 16.2 +filelock 1.0.3 +fitdistrplus 1.1-11 +FNN 1.1.4 +fontawesome 0.5.2 +forcats 1.0.0 +foreach 1.5.2 +foreign 0.8-87 +formatR 1.14 +fs 1.6.4 +futile.logger 1.4.3 +futile.options 1.0.1 +future 1.33.2 +future.apply 1.11.2 +gelnet 1.2.1 +generics 0.1.3 +GENIE3 1.24.0 +GenomeInfoDb 1.36.1 +GenomeInfoDbData 1.2.11 +GenomicRanges 1.52.0 +gert 2.0.1 +GetoptLong 1.0.5 +ggalluvial 0.12.5 +ggforce 0.4.2 +ggfun 0.1.5 +ggnetwork 0.5.13 +ggnewscale 0.4.10 +ggplot2 3.5.1 +ggplotify 0.1.2 +ggpubr 0.6.0 +ggraph 2.2.1 +ggrepel 0.9.5 +ggridges 0.5.6 +ggsci 3.2.0 +ggsignif 0.6.4 +ggtree 3.10.1 +gh 1.4.1 +gitcreds 0.1.2 +GlobalOptions 0.1.2 +globals 0.16.3 +glue 1.7.0 +GO.db 3.18.0 +goftest 1.2-3 +googleVis 0.7.3 +GOSemSim 2.28.1 +gower 1.0.1 +gplots 3.1.3.1 +graph 1.78.0 +graphics 4.3.3 +graphlayouts 1.1.1 +grDevices 4.3.3 +grid 4.3.3 +gridBase 0.4-7 +gridExtra 2.3 +gridGraphics 0.5-1 +GSEABase 1.62.0 +gson 0.1.0 +GSVA 1.48.2 +gtable 0.3.5 +gtools 3.9.5 +hardhat 1.4.0 +haven 2.5.4 +HDF5Array 1.28.1 +hdf5r 1.3.10 +HDO.db 0.99.1 +HemaScopeR 1.0.0 +here 1.0.1 +hexbin 1.28.3 +highr 0.11 +hms 1.1.3 +HSMMSingleCell 1.20.0 +htmltools 0.5.8.1 +htmlwidgets 1.6.4 +httpuv 1.6.15 +httr 1.4.7 +httr2 1.0.2 +ica 1.0-3 +igraph 2.0.3 +ini 0.3.1 +ipred 0.9-14 +IRanges 2.34.1 +irlba 2.3.5.1 +isoband 0.2.7 +iterators 1.0.14 +jquerylib 0.1.4 +jsonlite 1.8.8 +kableExtra 1.3.4 +KEGGREST 1.40.0 +kernlab 0.9-32 +KernSmooth 2.23-24 +knitr 1.48 +labeling 0.4.3 +lambda.r 1.2.4 +later 1.3.2 +lattice 0.22-6 +lava 1.7.3 +lazyeval 0.2.2 +leiden 0.4.3.1 +leidenbase 0.1.27 +lifecycle 1.0.4 +limma 3.56.2 +listenv 0.9.1 +lme4 1.1-35.5 +lmtest 0.9-40 +locfit 1.5-9.9 +lsei 1.3-0 +lubridate 1.9.3 +magrittr 2.0.3 +maps 3.4.2 +maptools 1.1-8 +markdown 1.1 +MASS 7.3-60.0.1 +Matrix 1.6-5 +MatrixGenerics 1.12.2 +MatrixModels 0.5-3 +matrixStats 1.3.0 +mcmc 0.9-8 +MCMCpack 1.7-0 +memoise 2.0.1 +metapod 1.8.0 +methods 4.3.3 +mgcv 1.9-1 +microbenchmark 1.4.10 +mime 0.12 +miniUI 0.1.1.1 +minqa 1.2.7 +mixtools 2.0.0 +ModelMetrics 1.2.2.2 +modelr 0.1.11 +monocle 2.28.0 +munsell 0.5.1 +network 1.18.2 +nlme 3.1-165 +nloptr 2.0.3 +NMF 0.27 +nnet 7.3-19 +npsurv 0.5-0 +numDeriv 2016.8-1.1 +openssl 2.2.0 +org.Hs.eg.db 3.17.0 +org.Mm.eg.db 3.17.0 +parallel 4.3.3 +parallelDist 0.2.6 +parallelly 1.37.1 +patchwork 1.2.0 +pbapply 1.7-2 +pbkrtest 0.5.2 +pcaMethods 1.92.0 +phateR 1.0.7 +pheatmap 1.0.12 +pillar 1.9.0 +pkgbuild 1.4.4 +pkgconfig 2.0.3 +pkgdown 2.1.0 +pkgload 1.3.4 +plogr 0.2.0 +plotly 4.10.4 +plyr 1.8.9 +png 0.1-8 +polyclip 1.10-6 +polynom 1.4-1 +praise 1.0.0 +prettyunits 1.2.0 +princurve 2.1.6 +pROC 1.18.5 +processx 3.8.4 +prodlim 2024.06.25 +profvis 0.3.8 +progress 1.2.3 +progressr 0.14.0 +promises 1.3.0 +proxy 0.4-27 +ps 1.7.7 +purrr 1.0.2 +qlcMatrix 0.9.8 +quantreg 5.98 +qvalue 2.34.0 +R.methodsS3 1.8.2 +R.oo 1.26.0 +R.utils 2.12.3 +R6 2.5.1 +ragg 1.3.2 +randomForest 4.7-1.1 +RANN 2.6.1 +rappdirs 0.3.3 +RBGL 1.76.0 +RcisTarget 1.20.0 +rcmdcheck 1.4.0 +RColorBrewer 1.1-3 +Rcpp 1.0.13 +RcppAnnoy 0.0.22 +RcppArmadillo 14.0.0-1 +RcppEigen 0.3.4.0.0 +RcppGSL 0.3.13 +RcppHNSW 0.6.0 +RcppParallel 5.1.6 +RcppProgress 0.4.2 +RcppTOML 0.2.2 +RcppZiggurat 0.1.6 +RCurl 1.98-1.16 +readr 2.1.5 +readxl 1.4.3 +recipes 1.1.0 +registry 0.5-1 +rematch 2.0.0 +rematch2 2.1.2 +remotes 2.5.0 +reshape2 1.4.4 +reticulate 1.38.0 +Rfast 2.1.0 +Rfast2 0.1.5.1 +rhdf5 2.44.0 +rhdf5filters 1.12.1 +Rhdf5lib 1.22.0 +rio 1.1.1 +rjson 0.2.21 +rlang 1.1.4 +rmarkdown 2.27 +rngtools 1.5.2 +ROCR 1.0-11 +roxygen2 7.3.2 +rpart 4.1.23 +rprojroot 2.0.4 +RSpectra 0.16-2 +RSQLite 2.3.7 +rstatix 0.7.2 +rstudioapi 0.16.0 +rsvd 1.0.5 +Rtsne 0.17 +RUnit 0.4.33 +rversions 2.1.2 +rvest 1.0.4 +S4Arrays 1.0.4 +S4Vectors 0.38.1 +sass 0.4.9 +ScaledMatrix 1.8.1 +scales 1.3.0 +scattermore 1.2 +scatterpie 0.2.3 +SCENIC 1.3.0 +scmap 1.24.0 +scran 1.28.1 +sctransform 0.4.1 +scuttle 1.10.1 +segmented 2.1-0 +selectr 0.4-2 +sessioninfo 1.2.2 +Seurat 4.3.0.1 +SeuratDisk 0.0.0.9021 +SeuratObject 5.0.2 +SeuratWrappers 0.3.1 +shadowtext 0.1.4 +shape 1.4.6.1 +shiny 1.8.1.1 +shinyjs 2.1.0 +SingleCellExperiment 1.22.0 +sitmo 2.0.2 +slam 0.1-51 +slingshot 2.8.0 +sna 2.7-2 +snow 0.4-4 +sourcetools 0.1.7-1 +sp 2.1-4 +spam 2.10-0 +SparseM 1.84 +sparseMatrixStats 1.12.2 +sparsesvd 0.2-2 +spatstat.data 3.1-2 +spatstat.explore 3.2-6 +spatstat.geom 3.2-9 +spatstat.random 3.2-3 +spatstat.sparse 3.1-0 +spatstat.univar 3.0-0 +spatstat.utils 3.0-5 +splines 4.3.3 +SQUAREM 2021.1 +statmod 1.5.0 +statnet.common 4.9.0 +stats 4.3.3 +stats4 4.3.3 +stringi 1.8.4 +stringr 1.5.1 +SummarizedExperiment 1.30.2 +survival 3.7-0 +svglite 2.1.3 +sys 3.4.2 +systemfonts 1.1.0 +tcltk 4.3.3 +tensor 1.5 +testthat 3.2.1.1 +textshaping 0.3.7 +tibble 3.2.1 +tidygraph 1.3.1 +tidyr 1.3.1 +tidyselect 1.2.1 +tidytree 0.4.6 +timechange 0.3.0 +timeDate 4032.109 +tinytex 0.51 +tools 4.3.3 +TrajectoryUtils 1.8.0 +transport 0.14-6 +treeio 1.26.0 +tweenr 2.0.3 +tzdb 0.4.0 +urlchecker 1.0.1 +usethis 2.2.3 +utf8 1.2.4 +utils 4.3.3 +uwot 0.1.16 +vctrs 0.6.5 +velocyto.R 0.6 +VGAM 1.1-11 +viridis 0.6.5 +viridisLite 0.4.2 +vroom 1.6.5 +waldo 0.5.2 +webshot 0.5.5 +whisker 0.4.1 +withr 3.0.0 +writexl 1.5.0 +xfun 0.46 +XML 3.99-0.17 +xml2 1.3.6 +xopen 1.0.1 +xtable 1.8-4 +XVector 0.40.0 +yaml 2.3.9 +yulab.utils 0.1.4 +zip 2.3.1 +zlibbioc 1.46.0 +zoo 1.8-12 +``` +- Python packages with versions +``` +Package Version +------------------------ -------------- +absl-py 2.1.0 +access 1.1.9 +affine 2.4.0 +aiohttp 3.9.5 +aiosignal 1.3.1 +anndata 0.10.8 +annotated-types 0.7.0 +anyio 4.4.0 +arboreto 0.1.6 +argcomplete 3.4.0 +array_api_compat 1.7.1 +arrow 1.3.0 +attrs 23.2.0 +backoff 2.2.1 +beautifulsoup4 4.12.3 +blessed 1.20.0 +bokeh 3.5.0 +boto3 1.34.145 +botocore 1.34.145 +cell2location 0.1.3 +certifi 2024.7.4 +charset-normalizer 3.3.2 +chex 0.1.7 +click 8.1.7 +click-plugins 1.1.1 +cligj 0.7.2 +cloudpickle 3.0.0 +commot 0.0.3 +contextlib2 21.6.0 +contourpy 1.2.1 +croniter 1.4.1 +cycler 0.12.1 +dask 2024.7.0 +dask-expr 1.1.8 +dateutils 0.6.12 +decorator 4.4.2 +deepdiff 7.0.1 +Deprecated 1.2.14 +deprecation 2.1.0 +distributed 2024.7.0 +dm-tree 0.1.8 +dnspython 2.6.1 +docrep 0.3.2 +editor 1.6.6 +email_validator 2.2.0 +esda 2.4.3 +etils 1.9.2 +fastapi 0.111.1 +fastapi-cli 0.0.4 +filelock 3.15.4 +fiona 1.9.6 +flax 0.8.5 +fonttools 4.53.1 +frozenlist 1.4.1 +fsspec 2024.6.1 +future 1.0.0 +gensim 4.3.3 +geopandas 0.13.2 +giddy 2.3.5 +graphtools 1.5.3 +h11 0.14.0 +h5py 3.11.0 +httpcore 1.0.5 +httptools 0.6.1 +httpx 0.27.0 +idna 3.7 +igraph 0.11.6 +importlib_metadata 8.0.0 +importlib_resources 6.4.0 +inequality 1.0.0 +inquirer 3.3.0 +itsdangerous 2.2.0 +jax 0.4.30 +jaxlib 0.4.30 +Jinja2 3.1.4 +jmespath 1.0.1 +joblib 1.4.2 +karateclub 1.3.3 +kiwisolver 1.4.5 +legacy-api-wrap 1.4 +leidenalg 0.10.2 +Levenshtein 0.25.1 +libpysal 4.7.0 +lightning 2.0.9.post0 +lightning-cloud 0.5.70 +lightning-utilities 0.11.5 +llvmlite 0.43.0 +locket 1.0.0 +loompy 3.0.7 +lz4 4.3.3 +mapclassify 2.6.0 +markdown-it-py 3.0.0 +MarkupSafe 2.1.5 +matplotlib 3.7.2 +mdurl 0.1.2 +mgwr 2.2.1 +ml_collections 0.1.1 +ml-dtypes 0.4.0 +momepy 0.6.0 +mpmath 1.3.0 +msgpack 1.0.8 +mudata 0.2.4 +multidict 6.0.5 +multipledispatch 1.0.0 +natsort 8.4.0 +nest-asyncio 1.6.0 +networkx 2.6.3 +numba 0.60.0 +numpy 1.23.5 +numpy-groupies 0.11.1 +numpyro 0.15.1 +nvidia-cublas-cu12 12.1.3.1 +nvidia-cuda-cupti-cu12 12.1.105 +nvidia-cuda-nvrtc-cu12 12.1.105 +nvidia-cuda-runtime-cu12 12.1.105 +nvidia-cudnn-cu12 8.9.2.26 +nvidia-cufft-cu12 11.0.2.54 +nvidia-curand-cu12 10.3.2.106 +nvidia-cusolver-cu12 11.4.5.107 +nvidia-cusparse-cu12 12.1.0.106 +nvidia-nccl-cu12 2.20.5 +nvidia-nvjitlink-cu12 12.5.82 +nvidia-nvtx-cu12 12.1.105 +opencv-python 4.10.0.84 +opt-einsum 3.3.0 +optax 0.2.1 +orbax-checkpoint 0.5.21 +ordered-set 4.1.0 +packaging 24.1 +pandas 1.3.5 +partd 1.4.2 +patsy 0.5.6 +phate 1.0.11 +pillow 10.4.0 +pip 24.1.2 +platformdirs 4.2.2 +plotly 5.22.0 +pointpats 2.4.0 +POT 0.9.1 +protobuf 5.27.2 +psutil 6.0.0 +PuLP 2.9.0 +pyarrow 17.0.0 +pyarrow-hotfix 0.6 +pydantic 2.1.1 +pydantic_core 2.4.0 +Pygments 2.18.0 +PyGSP 0.5.1 +PyJWT 2.8.0 +pynndescent 0.5.13 +pyparsing 3.0.9 +pyproj 3.6.1 +pyro-api 0.1.2 +pyro-ppl 1.9.1 +pysal 24.1 +python-dateutil 2.9.0.post0 +python-dotenv 1.0.1 +python-igraph 0.11.6 +python-Levenshtein 0.25.1 +python-louvain 0.16 +python-multipart 0.0.9 +pytorch-lightning 2.3.3 +pytz 2024.1 +PyYAML 6.0.1 +quantecon 0.7.2 +rapidfuzz 3.9.4 +rasterio 1.3.10 +rasterstats 0.19.0 +readchar 4.1.0 +requests 2.32.3 +rich 13.7.1 +Rtree 1.3.0 +runs 1.2.2 +s_gd2 1.8.1 +s3transfer 0.10.2 +scanpy 1.9.4 +scikit-learn 1.5.1 +scipy 1.11.2 +scprep 1.2.3 +scvelo 0.2.5 +scvi-tools 1.0.3 +seaborn 0.12.2 +segregation 2.5 +session_info 1.0.0 +setuptools 71.0.1 +shapely 2.0.5 +shellingham 1.5.4 +simplejson 3.19.2 +six 1.16.0 +smart-open 7.0.4 +sniffio 1.3.1 +snuggs 1.4.7 +sortedcontainers 2.4.0 +soupsieve 2.5 +spaghetti 1.7.4 +sparse 0.15.4 +spglm 1.0.8 +spint 1.0.7 +splot 1.1.5.post1 +spopt 0.5.0 +spreg 1.4 +spvcm 0.3.0 +starlette 0.37.2 +starsessions 1.3.0 +statsmodels 0.14.1 +stdlib-list 0.10.0 +sympy 1.13.1 +tasklogger 1.2.0 +tblib 3.0.0 +tenacity 8.5.0 +tensorstore 0.1.63 +texttable 1.7.0 +threadpoolctl 3.5.0 +tobler 0.11.2 +toml 0.10.2 +tomlkit 0.13.0 +toolz 0.12.1 +torch 2.3.1 +torchmetrics 1.4.0.post0 +tornado 6.4.1 +tqdm 4.66.4 +traitlets 5.14.3 +triton 2.3.1 +typer 0.12.3 +types-python-dateutil 2.9.0.20240316 +typing_extensions 4.12.2 +tzdata 2024.1 +umap-learn 0.5.6 +urllib3 2.2.2 +uvicorn 0.30.1 +uvloop 0.19.0 +watchfiles 0.22.0 +wcwidth 0.2.13 +websocket-client 1.8.0 +websockets 12.0 +wheel 0.43.0 +wrapt 1.16.0 +xarray 2024.6.0 +xmltodict 0.13.0 +xmod 1.8.1 +xyzservices 2024.6.0 +yarl 1.9.4 +yq 3.4.3 +zict 3.0.0 +zipp 3.19.2 +``` diff --git a/.Rproj.user/11F4C4A8/sources/session-e1bc8c0f/9B03DA3B 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b/.Rproj.user/shared/notebooks/77C62CB4-HemaScope_installation_tutorial/1/s/chunks.json new file mode 100644 index 0000000..7fcea13 --- /dev/null +++ b/.Rproj.user/shared/notebooks/77C62CB4-HemaScope_installation_tutorial/1/s/chunks.json @@ -0,0 +1 @@ +{"chunk_definitions":[],"doc_write_time":1721438416} \ No newline at end of file diff --git a/.Rproj.user/shared/notebooks/paths b/.Rproj.user/shared/notebooks/paths index 7236ec0..498cdcc 100644 --- a/.Rproj.user/shared/notebooks/paths +++ b/.Rproj.user/shared/notebooks/paths @@ -1,2 +1,3 @@ C:/Users/zywan/Documents/GitHub/HemaScope_Tutorial/HemaScope_Tutorial.Rmd="F3266CC1" +C:/Users/zywan/Documents/GitHub/HemaScope_Tutorial/HemaScope_installation_tutorial.Rmd="77C62CB4" C:/Users/zywan/Documents/GitHub/HemaScope_Tutorial/index.Rmd="5A59C67F" diff --git a/HemaScope_installation_tutorial.Rmd b/HemaScope_installation_tutorial.Rmd index 01fa541..921e17e 100644 --- a/HemaScope_installation_tutorial.Rmd +++ b/HemaScope_installation_tutorial.Rmd @@ -66,6 +66,7 @@ conda install -c bioconda r-velocyto.r=0.6 #conda install -c bioconda bioconductor-limma=3.56.2 ``` - Enter the R language environment + We suggest users do not manually update any already installed R packages during the installation of the following R packages. ``` R @@ -128,7 +129,7 @@ quit() ## Install required Python-packages -- upgrade pip and set mirrors +- Upgrade pip and set mirrors ``` python -m pip install -i https://pypi.tuna.tsinghua.edu.cn/simple --upgrade pip @@ -136,14 +137,10 @@ pip config set global.index-url https://pypi.tuna.tsinghua.edu.cn/simple pip config set global.extra-index-url http://mirrors.aliyun.com/pypi/simple/ ``` -- install required packages +- Install required packages ``` -pip install numpy==1.23.5 -pip install pandas==1.3.5 -pip install matplotlib==3.5.2 -pip install scvelo==0.2.5 -pip install arboreto==0.1.6 +pip install matplotlib==3.7.2 pip install pot==0.9.1 pip install anndata==0.9.2 pip install scanpy==1.9.4 @@ -153,8 +150,10 @@ pip install commot==0.0.3 pip install scvi-tools==1.0.3 pip install cell2location==0.1.3 pip install phate==1.0.11 -pip install jax==0.4.20 -pip install jaxlib==0.4.20 +pip install scvelo==0.2.5 +pip install arboreto==0.1.6 +pip install numpy==1.23.5 +pip install pandas==1.3.5 ``` ## The installed packages with versions @@ -679,8 +678,8 @@ importlib_resources 6.4.0 inequality 1.0.0 inquirer 3.3.0 itsdangerous 2.2.0 -jax 0.4.20 -jaxlib 0.4.20 +jax 0.4.30 +jaxlib 0.4.30 Jinja2 3.1.4 jmespath 1.0.1 joblib 1.4.2 @@ -700,7 +699,7 @@ lz4 4.3.3 mapclassify 2.6.0 markdown-it-py 3.0.0 MarkupSafe 2.1.5 -matplotlib 3.8.4 +matplotlib 3.7.2 mdurl 0.1.2 mgwr 2.2.1 ml_collections 0.1.1 @@ -757,7 +756,7 @@ Pygments 2.18.0 PyGSP 0.5.1 PyJWT 2.8.0 pynndescent 0.5.13 -pyparsing 3.1.2 +pyparsing 3.0.9 pyproj 3.6.1 pyro-api 0.1.2 pyro-ppl 1.9.1 diff --git a/_book/installation.html b/_book/installation.html index 342b9a1..fbc43e7 100644 --- a/_book/installation.html +++ b/_book/installation.html @@ -323,9 +323,9 @@

2.4 Install required R-packages +

We suggest users do not manually update any already installed R packages during the installation of the following R packages.

R