CSD3 – Cambridge Service for Data Driven Discovery
This repository details use of many software for generic purpose and genetic analysis; over time they largely become entries of the ceuadmin modules which are ready to use.
graph LR;
jekyll-rtd-theme --> csd3
csd3 --> system["THE SYSTEM"]
csd3 --> Python["Python packages"]
csd3 --> R["R packages"]
csd3 --> applications["APPLICATIONS"]
csd3 --> cardio["CARDIO (legacy materials)"]
system --> System
system --> sysdot["..."]
system --> Acknowledgement
applications --> ABCtoolbox
applications --> appdot["..."]
applications --> vsc["Visual Studio Code"]
Python --> gwas2vcf
Python --> Pythondot["..."]
Python --> Synase
R --> brms
R --> Rdot["..."]
R --> xlsx
- The system
- Python packages
- R packages
- Applications
- ABCtoolbox
- AEGIS
- akt
- ANNOVAR
- aria2
- bcftools
- bedops
- bgenix
- CaVEMaN
- CAVIAR/eCAVIAR
- circos
- citeproc
- CookHLA
- Cytoscape
- DNAnexus
- DosageConverter
- finemap
- GATK
- GCTA
- geany
- Genotype-Harmonizer
- gsutil
- hail
- HESS
- KentUtils
- lapack
- LEMMA
- LocusZoom
- METAL
- MetaXcan
- pandoc
- PCA projection
- peer
- pgsc_calc
- PLINK
- polyphen-2
- poppler
- PRSice
- PRSoS
- pspp
- AlphaPept and PyOpenMS
- qpdf
- qtltools
- quarto
- regenie
- R
- RStudio
- Rust
- shapeit
- SMR
- snipar
- SNPTEST
- sra-tools
- SurvivalGWAS_SV
- tabix
- VEP
- Visual Studio code
- Appendix B. Notes on emsembl-vep
- /applications/files/
- cardio