algebra_ver822

How to start

Initial settings

1. clone this repository with git clone git@github.com:yo-aka-gene/algebra_ver822.git
2. install Docker to your local env
3. swich your working dir to /algebra_ver822
4. run make init

Run Python codes

You can run python codes in jupyterlab virtual environment. Run make start-py or make start to start the docker container for jupyterlab; otherwise follow the instructions below. Note that *.ipynb files are indexed with numbers. Please follow the numbering.
Notes: some codes require that R scripts already done. Please check the description.

1. run docker start algebra_ver822-jupyterlab-1
2. access localhost:8080 via your local browser (edit docker-compose.yml to use different port)
3. run codes interactively with *.ipynb files in jupyter notebook environment
4. run make lib-py or make lib to install packages in dependencies (preinstalled with make init command)
5. you can stop the virtual computer by running make stop-py code in your local env (run make stop to stop all docker containers regarding this project).

Run R codes

You can run r codes in rstudio virtual environment. Run make start-r or make start to start the docker container for rstudio; otherwise follow the instructions below. Note that *.Rmd files are indexed with numbers. Please follow the numbering.
Notes: some packages are only installed rstuio environment. Please use algebra_ver822-rstudio-1 container.

1. run docker start algebra_ver822-rstudio-1
2. access localhost:8787 via your local browser (edit docker-compose.yml to use different port)
3. run codes interactively with *.Rmd files in rstudio environment (or you can check the overview of the analysis as *.md files)
4. run make lib-r or make lib to install packages in dependencies (preinstalled with make init command)
5. you can stop the virtual computer by running make stop-r code in your local env (run make stop to stop all docker containers regarding this project).

Troubleshooting

• when you want to remove the docker containers, run make terminate in your local environment.
• when you renew (remove and rebuild) the docker containers, run make reboot in your local environment.

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Preference of Docker in local environment

• Resource
  • CPUs: 8
  • Memory: 24.00 GB
  • Swap: 2 GB
• Note: the author used MacBook Pro(15inch, 2019)

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Copyright of the dataset

1. Allen Institute for Brain Science
   • human primary mortor cortex: https://portal.brain-map.org/atlases-and-data/rnaseq/human-m1-10x
   • run make m1_10x or make all-data or make init to install this data.
   • For the sake of the data size, we seplit the original files (make command includes this process as well)
2. HuaQiao University (GSE165388)
   • Interneuron origin and molecular diversity in the human fetal brain: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE165388
   • Contributors: Yu Y, Sun T
   • Citation: Yu Y, Zeng Z, Xie D, Chen R et al. Interneuron origin and molecular diversity in the human fetal brain. Nat Neurosci 2021 Dec;24(12):1745-1756. PMID: 34737447
   • Contact name: Yuan Yu
   • E-mail: yuyuan@stu.hqu.edu.cn
   • run make gse or make all-data or make init to install this data.
   • data contain four subgroups GW9, GW10, GW11, and GW12.
   • the cmd will make dirs for each subgroups and rename files to adjust CreateSeuratObject function of Seurat.

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For developers

• please use pip instead of conda for installing Python packages