Software & Database & Tools
Our software, tools, etc. are open-source, and free for anyone around the world to use and modify. We strive to make resources that are high quality in every aspect: cleanly written, robustly constructed and tested, well-documented, easy-to-use, accessible, customizable, and as effective as possible in real-world use.
Software
PyComplexHeatmapPyComplexHeatmap, A Python package to visualize multimodal genomics dataPyComplexHeatmap was designed to visualize matrix data and associated metadata through sophisticated, richly annotated heatmap layouts. We have integrated the R grammar-of-graphics semantics with the Python-native matplotlib/Pandas-based data science ecosystem, allowing users to utilize built-in matplotlib colormaps and project Pandas DataFrame directly as horizontal or vertical color bars. PyComplexHeatmap supports high-level data abstraction and can display up to five data dimensions within a single heatmap visualization.
ChunkZIPChunkZIP, Efficient Compression and Analysis for Single-Cell DNA Methylation DataAn innovative compression algorithm that significantly reduces storage requirements while streamlining downstream analysis of single-cell biological data, especially for DNA methylation data
pyballcBAllCools is a comprehensive tool designed to handle binary AllC files (BAllC). The tool aims to solve the challenges posed by the large number of single-cell data. The conventional AllC files store methylation data as text, which becomes significantly bulky when dealing with single-cell data. BAllCools provides an efficient way to store and retrieve data by converting these text files into binary files, thereby saving substantial storage space. The BAllC format save >55% storage compared to AllC the format, and BAllCools accelorates BAllC operation like data merging (ballcools merge) ~30x.
SeSAMeTools For analyzing Illumina Infinium DNA methylation arrays. SeSAMe provides utilities to support analyses of multiple generations of Infinium DNA methylation BeadChips, including preprocessing, quality control, visualization and inference. SeSAMe features accurate detection calling, intelligent inference of ethnicity, sex and advanced quality control routines.
Database
DNMIVDDNA Methylation Interactive Visualization DatabaseDNMIVD is a comprehensive annotation and interactive visualization database for DNA methylation profile of diverse human cancer constructed with high throughput microarray data from TCGA and GEO databases, and it also integrates some data from Pancan-meQTL and HACER databases. Overall, DNMIVD mainly contains lots of important resources.