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CanDI - A global cancer data integrator

PyPI Downloads Documentation Status DOI Dataverse

Installation

CanDI is now available on PyPI and can be installed with pip. Then, a command from CanDI will automatically download stable datasets from Dataverse.

# Package Installation
pip install PyCanDI

# Prepare Datasets
candi-install

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

Note:

: Currently, DepMap API is not available for public use. Therefore, we are providing the preprocessed datasets for the users based on DepMap 21Q4 release. DepMap API will be available in the future to download the latest datasets.

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.

Demos

Name Description
Getting Started Link to notebook
BRCA Heatmap Link to notebook
KRAS and EGFR Scatter plot Link to notebook
CanDI and DESeq2 Link to notebook

Citation

If you use CanDI in your research, please cite the following paper:

Yogodzinski C, Arab A, Pritchard JR, Goodarzi H, Gilbert LA. 
A global cancer data integrator reveals principles of synthetic lethality, sex disparity and immunotherapy. 
Genome Med. 2021;13(1):167. Published 2021 Oct 18. doi:10.1186/s13073-021-00987-8