"Calling cards data analysis in Python."
Project description
Pycallingcards
Pycallingcards is a package for calling cards data analysis developed and maintained by Mitra Lab at Washington University in St. Louis.
Calling cards is a sequencing technology to assay TF binding which could be done in vitro and in vivo at both bulk and single-cell level. To know more about calling cards technology, please check Moudgil et al and Wang et al.
Pycallingcards is composed of five different part: datasets, reading (rd), preprocessing (pp), tools (tl) and plotting (pl). For single-cell calling cards anaysis, Pycallingcards interacts with Scanpy and the main structure of Pycallingcards also follows the Scanpy.
- Datasets contains four main published datasets for callingcards data.
- Reading (rd) includes several functions to read and save qbed and peak data.
- Preprocessing (pp) helps to preprocess data from qbed data to call peaks, make annotation, make Anndata object and filter peaks.
- Tools (tl) calls motif of the peaks, completes differential peaks and pair differential peaks with gene expression,
- Plotting (pl) proveides an allround plottting system. It could plot genome areas, link with WashU Epigenome Browser, show signal comparison with Chip-seq(BigWig file), display differential peaks, demonstrate potenial binding-gene expression relationships.
Documentation.
Please check here for detailed documentation.
Installation
pip install pycallingcards
Development
Use pre-commit to format code at git commit
.
pip install pre-commit
pre-commit install
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