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Dependencies
Paul Hoffman edited this page Aug 9, 2016
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12 revisions
Below is a list of all dependencies for ANGSD-wrapper
| Dependency | Version | Use | Installed Automatically? |
|---|---|---|---|
| ANGSD | 0.911-44-g1c0ebb6 | Performs most analyses and serves as the backbone for ANGSD-wrapper |
Yes, upon running ./angsd-wrapper setup dependencies
|
| ngsF | v1.0.0 | Estimate inbreeding coefficients |
Yes, upon running ./angsd-wrapper setup dependencies
|
| ngsPopGen | Commit bbd73d5
|
Performs principal component analyses and estimates FST values |
Yes, upon running ./angsd-wrapper setup dependencies
|
| ngsAdmix | 32 | Performs admixture analyses |
Yes, upon running ./angsd-wrapper setup dependencies
|
| SAMTools | 1.3 | Works with ANGSD for analyses |
Yes, upon running ./angsd-wrapper setup dependencies
|
| HTSLib | 1.3.1-30-gbb03b02 | Lets ANGSD work with BAM and CRAM files |
Yes, upon running ./angsd-wrapper setup dependencies
|
| R | 3.2.4 | Performs some data analyses and provides basis for visualization package | No, please install on your own |
ape |
3.3 | R library used in visualization package |
Yes, upon running angsd-wrapper shiny graphing
|
BiocGenerics |
0.14.0 | Bioconductor library used in visualization package |
Yes, upon running angsd-wrapper shiny graphing
|
data.table |
1.9.6 | R library used in visualization package |
Yes, upon running angsd-wrapper shiny graphing
|
datasets |
3.2.4 | R library used in visualization package |
Yes, upon running angsd-wrapper shiny graphing
|
DT |
0.1 | R library used in visualization package |
Yes, upon running angsd-wrapper shiny graphing
|
Formula |
1.2-1 | R library used in visualization package |
Yes, upon running angsd-wrapper shiny graphing
|
genomeIntervals |
1.24.1 | Bioconductor library used in visualization package |
Yes, upon running angsd-wrapper shiny graphing
|
ggplot2 |
1.0.1 | R library used in visualization package |
Yes, upon running angsd-wrapper shiny graphing
|
graphics |
3.2.4 | R library used in visualization package |
Yes, upon running angsd-wrapper shiny graphing
|
grDevices |
3.2.4 | R library used in visualization package |
Yes, upon running angsd-wrapper shiny graphing
|
grid |
3.2.4 | R library used in visualization package |
Yes, upon running angsd-wrapper shiny graphing
|
Hmisc |
3.17-0 | R library used in visualization package |
Yes, upon running angsd-wrapper shiny graphing
|
intervals |
0.15.1 | R library used in visualization package |
Yes, upon running angsd-wrapper shiny graphing
|
lattice |
0.20-33 | R library used in visualization package |
Yes, upon running angsd-wrapper shiny graphing
|
methods |
3.2.4 | R library used in visualization package |
Yes, upon running angsd-wrapper shiny graphing
|
parallel |
3.2.4 | R library used in visualization package |
Yes, upon running angsd-wrapper shiny graphing
|
shiny |
0.12.2 | R library used in visualization package |
Yes, upon running angsd-wrapper shiny graphing
|
shinythemes |
1.0.1 | R library used in visualization package |
Yes, upon running angsd-wrapper shiny graphing
|
stats |
3.2.4 | R library used in visualization package |
Yes, upon running angsd-wrapper shiny graphing
|
survival |
2.38-3 | R library used in visualization package |
Yes, upon running angsd-wrapper shiny graphing
|
utils |
3.2.4 | R library used in visualization package |
Yes, upon running angsd-wrapper shiny graphing
|