A cancer data integration package
Project description
Package Installation
CanDI is now available on PyPI and can be installed with pip:
pip install CanDI
___ For the latest version (development version) install from GitHub:
pip install git+https://github.com/GilbertLabUCSF/CanDI.git
Prepare Datasets
The python command from CanDI will automatically download and modify datasets.
python CanDI/CanDI/setup/install.py
Downloaded and formatted datasets would organize this way:
.
├── config.ini # modified after Installation
├── depmap
│ ├── CCLE_expression.csv
│ ├── CCLE_fusions.csv
│ ├── CCLE_gene_cn.csv
│ ├── CCLE_mutations.csv
│ ├── CCLE_RNAseq_reads.csv
│ ├── CRISPR_gene_dependency.csv
│ ├── CRISPR_gene_effect.csv
│ └── sample_info.csv
├── genes
│ └── gene_info.csv
└── locations
└── merged_locations.csv
Package Usage
Import CanDI into python
from CanDI import candi
CanDI Objects
data : Container for all candi datasets. All access to datasets go through data object.
Gene : Provides cross dataset indexing from the gene perspective.
CellLine : Provides cross dataset indexing from the cell line perspective.
Cancer : Provides cross dataset indexing by a group of cell lines that are all the same tissue.
Organelle: Provides cross dataset indexing for a group of genes whose proteins localize to the same organelle.
CellLineCluster : Provides cross dataset indexing for a group of user defined cell lines.
GeneCluster : Provides cross dataset indexing for a group of user defined genes.
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