https://github.com/campbio/camplab

Camplab wiki

https://github.com/campbio/camplab

Repository

Camplab wiki

https://github.com/campbio/camplab/blob/master/

# Camplab Wiki
## Meeting schedule
All following meetings take place at the big conference room (E605).

| Recurring meetings | Time | Description |
| --- | --- | --- |
| Camplab lab meeting | Every Friday 10:00 am - 11:00 am | Lab meeting |
| CBM seminar | Usually every other Tuesday 3:00 pm - 4:30 pm | Each time two students/post-docs/staffs will talk about their research. Check your email for exact date and time. |
| Computational meeting (Spira-Lenburg Lab) | Every Wednesday 1:00 pm - 3:00 pm | Useful for getting an idea about what other students are doing and practising your presentation skills. Talk to Marc if you want to go to this meeting. |
| Single-cell working group meeting | Once a month | Campus-wide seminar. Check email for exact date and time. |

## Lab meeting
See link for lab meeting schedule (BU email required):
https://docs.google.com/spreadsheets/d/1qzpoEEwaj6YNmaUcqKC1CC1_cj0wcP8X6cnwUogQKWQ/edit#gid=0

## Email lists
Send an email to Josh be added to these lists
- Camplab: camplab-list@bu.edu
- Single cell working group: cbmsc-list@bu.edu
## Slack workspaces
- Camplab: https://camp-lab.slack.com
- Compbiomed: https://compbiomed.slack.com/
- Single Cell Core: https://bucores.slack.com

## SCC4 directories
- `/restricted/projectnb/camplab`. Camplab root directory.
- `/restricted/projectnb/camplab/home`. Lab members' own workspaces. Create a folder with the same name as your BU username and put your stuff in it.
- `/restricted/projectnb/camplab/projects/celda/Datasets/10X`. Publicly available 10X datasets.

## Running interactive sessions on SCC
- Computational Biomedicine has its own node where interactive jobs can be run. Put the following line in your `~/.bashrc` file on SCC: ```alias cb1="ssh scc-cb1.scc.bu.edu"```. Then you will be able to type the command `cb1` to start an interactive session.
- Alternatively, you can request an interactive session on SCC using ```qrsh```

## R Package development tips
- [R Packages (Hadley Wickham)](http://r-pkgs.had.co.nz/)
- [Coding Style Guide](https://github.com/campbio/celda/wiki/Celda-Development-Coding-Style-Guide)
- [Robust and Efficient Code](https://github.com/campbio/celda/wiki/Celda-Development-Robust-and-Efficient-Code)
- [Rstudio configuration](https://github.com/campbio/celda/wiki/Celda-Development-Rstudio-configuration)
- [FAQ on package development](https://github.com/campbio/celda/wiki/FAQ-on-package-development)
- Vim
  - [Interactive Vim tutorial](https://openvim.com/)
  - [Vim cheetsheet (by Allison McKnight)](https://www.cs.cmu.edu/~15131/f17/topics/vim/vim-cheatsheet.pdf)
- Git
  - [Git cheetsheet](https://about.gitlab.com/images/press/git-cheat-sheet.pdf)
  - [Git mergetool tutorial](https://gist.github.com/karenyyng/f19ff75c60f18b4b8149)
- GitHub
  - [Hello World](https://guides.github.com/activities/hello-world/)
- [Object documentation](http://r-pkgs.had.co.nz/man.html)

## Useful links:
### CBM Bootcamp Videos and Slides
Bootcamp1: Nuts and Bolts of Sequencing

https://echo360.org/media/b5c27b50-965c-4b78-bb1c-7ceb46e16351/public
https://www.dropbox.com/s/67tnpire1hcqqpy/20161130_Sequencing_Bootcamp_Session1.pptx?dl=0

Bootcamp2: RNA-seq analysis

https://echo360.org/media/ff432a03-11a5-4501-adc3-947370c8f17e/public
https://www.dropbox.com/s/2jfci3wwtim1k6v/20161207_Sequencing_Bootcamp_Session2.pptx?dl=0

Bootcamp3: DNA-seq / cancer genome analysis

https://echo360.org/media/37f30058-7631-4985-8d0a-1ba9301c78b0/public
https://www.dropbox.com/s/n8qse44negjttq4/20161214_Sequencing_Bootcamp_Session3.pptx?dl=0

### Single Cell Data Analysis Tutorials:
- Analysis of single cell RNA-seq data: https://scrnaseq-course.cog.sanger.ac.uk/website/index.html
- Orchestrating Single-Cell Analysis with Bioconductor: https://osca.bioconductor.org/
- Introduction to single cell RNA-seq analysis: https://hbctraining.github.io/scRNA-seq/lessons/pseudobulk_DESeq2_scrnaseq.html
### Reviews:
#### Single Cell:
- [Papalexi E, Satija R. Single-cell RNA sequencing to explore immune cell heterogeneity. Nat Rev Immunol. 2018;18(1):35-45.](https://www.nature.com/articles/nri.2017.76)
- [Potter SS. Single-cell RNA sequencing for the study of development, physiology and disease. Nat Rev Nephrol. 2018;14(8):479-92.](https://www.nature.com/articles/s41581-018-0021-7)
- [Svensson V, Vento-Tormo R, Teichmann SA. Exponential scaling of single-cell RNA-seq in the past decade. Nat Protoc. 2018;13(4):599-604.](https://www.nature.com/articles/nprot.2017.149)
- [Tanay A, Regev A. Scaling single-cell genomics from phenomenology to mechanism. Nature. 2017;541(7637):331-8.](https://www.nature.com/articles/nature21350)
- [Luecken MD, Theis FJ. Current best practices in single-cell RNA-seq analysis: a tutorial. Mol Syst Biol. 2019;15(6):e8746. Published 2019 Jun 19.](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582955/)

### Research Computing Services Tutorials
The Research Computing Services (RCS) group, part of Boston University Information Services & Technology, offers a series of tutorials on **programming**, **high performance computing**, and **scientific visualization**. These tutorials are free and open to all members of the Boston University community.
- [Tutorials Schedule](https://www.bu.edu/tech/about/training/classroom/rcs-tutorials/)
- [Tutorial Slide Sets](http://www.bu.edu/tech/support/research/training-consulting/live-tutorials/)

### Marker gene list
Google sheet containing information about marker genes and their corresponding cell types:
https://docs.google.com/spreadsheets/d/1XZ1oAI74ZhCj7gEGgvZUB_ybHF9iFkJGXam6dPTh1gs

## Set up network printer
Instructions: https://www.bumc.bu.edu/it/support/printers/install/

The BU tag number for the printer (Ricoh Aficio MP C4502A) is: **920622**.

## Get an account on the SCC
Ask Josh to add you to the `camplab` project.

More information: http://www.bu.edu/tech/support/research/system-usage/scc-quickstart/#ACCOUNT

## BU ID card access:
Go to [710 Albany St.](https://goo.gl/maps/1e6iaxfQnMz) for card access to the floor.
- https://www.bumc.bu.edu/publicsafety/services/id/
- https://www.bu.edu/terriercard/

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