...
| Software | Description |
|---|---|
| scons | Software build tool |
| swig | Software development tool |
| sqlite3 | SQL Lite databases |
| git | Version control utilities |
Additional Python Tools (cqb-devel_tools/manifests/python.pp) find version with pip (pip3 freeze | grep xopen)
| Software | Description | in devel_tools |
|---|---|---|
| all-dev | y | |
| blaze | An interface to query data on different storage systems | y |
| cutadapt | Finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads | y |
| dendropy | phylogenetic computing | y |
| freetype-dev (libfreetype6-dev) | y | |
| leukgen-disambiguate | y | |
| MACS2 | Model Based Analysis for ChIP-Seq data | y |
| maplot | y | |
| matplotlib | python 2D plotting library | y |
| networkx | Creation, manipulation, and study of the structure, dynamics, and functions of complex networks. | y |
| nimfa | Nonnegative matrix factorization | y |
| numpy | scientific computing with Python | y |
| pandas | Python Data Analysis Library | y |
| patsy | y | |
| pip | Python installation program (to install python modules) | y |
| plotly | y | |
| pysam | y | |
| pyvttbl | y | |
| reportlab (->biopython?) | y | |
| rpy2 | Python interface to R | y |
| seaborn | y | |
| scipy | Collection of Python software for mathematics, science, and engineering. | y |
| sklearn | Machine Learning in Python | y |
| skimage | Image processing in Python | y |
| statsmodels | Estimation of statistical models | y |
...