BrainArch is intended for studying and sharing knowledge about neuroscience, bioinformatics, and related fields. It is not intended for commercial use.
Documentation is available in the Blogs menu, and tools can be found under the Tools menu or in the home page.
Have an idea? I’d love to hear it — share it with me!
Julia packages
YRUtils.jl: https://gitee.com/yruf/yrutils.jl/.
GFFUtils.jl: https://gitee.com/yruf/gffutils.jl/.
UniApp.jl: https://gitee.com/yruf/uniapp.jl/.
R packages
R-YRUtils: https://gitee.com/yruf/r-yrutils/.
R Shiny App for Data Visualization: https://gitee.com/yruf/r-shiny-web-app-neuroborder/.
Misc
Galaxy Tools: https://gitee.com/yruf/galaxy-tools/.
Deploy Galaxy with Ansible: https://gitee.com/yruf/deploy-galaxy/.
Useful Ansible Roles: https://gitee.com/yruf/ansible-roles/.
BrainArch Web Page Source: https://gitee.com/yruf/neuroborder-web-page-source/.
Below is a list of links for various purposes:
Metascape: https://metascape.org/gp/index.html#/main/step1/. You can perform various annotation analyses over a gene set like GO enrichment analysis. It can cluster significantly similar GO terms together when you perform GO enrichment analysis. This is quite useful for picking interesting GO terms from an extensive list of GO terms.
g:Profiler: https://biit.cs.ut.ee/gprofiler/gost/. Used for ORA (Over-Representation Analysis) or GSEA (Gene Set Enrichment Analysis) (Recommended).
Enrichr: https://maayanlab.cloud/Enrichr/. The same as g:Profiler.
DAVID: https://davidbioinformatics.nih.gov/. The same as g:Profiler.
GSEA official: https://www.gsea-msigdb.org/gsea/index.jsp/.
Comparative Mammalian Brain Collections: https://brains.anatomy.msu.edu/museum/brain/.
WashU Epigenome Browser: https://epigenomegateway.wustl.edu/.
UCSC Genome Browser: https://genome.ucsc.edu/.
Timetree of Life: https://timetree.org/home/.
NIH’s Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative - Cell Census Network (BICCN): https://www.biccn.org/.
Easy use for Windows 10/11: https://www.bilibili.com/opus/904672369138729017/. It provides one of the most convenient ways to disable Windows update for decades.