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@@ -20,7 +20,7 @@ HiCBricks is a **R/Bioconductor** package for handling high-resolution Hi-C data | |
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## Features | ||
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- Import Hi-C data in multiple data formats. Currently, NxN dimensional matrices and _mcool_ files are supported, with more to come. | ||
- Import Hi-C data in multiple data formats. Currently, NxN dimensional matrices, _mcool_ files and sparse matrices are supported, with more to come. | ||
- Fetch different subset of the Hi-C data by their features with easy to use functions. Feature examples: by distance, matrix squares, rows or columns. | ||
- Keep user-defined annotations associated to the HDF files. | ||
- Use HiCBricks accessors to build more complex analysis such as TAD calling and visualizations. | ||
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@@ -31,7 +31,7 @@ To install the most stable development version from Bioconductor, run this from | |
``` | ||
if (!requireNamespace("BiocManager", quietly = TRUE)) | ||
install.packages("BiocManager") | ||
BiocManager::install("HiCBricks", version = "3.10") | ||
BiocManager::install("HiCBricks", version = "3.11") | ||
``` | ||
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@@ -40,7 +40,7 @@ To install the stable release version from Bioconductor, run this from a R conso | |
``` | ||
if (!requireNamespace("BiocManager", quietly = TRUE)) | ||
install.packages("BiocManager") | ||
BiocManager::install("HiCBricks", version = "3.10") | ||
BiocManager::install("HiCBricks", version = "3.11") | ||
``` | ||
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To install the most cutting-edge stable version of HiCBricks, do this from a R console to download it directly from GitHub. | ||
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@@ -56,21 +56,22 @@ To start working with **HiCBricks**, please checkout the vignette (tutorial) [he | |
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- Loading data from text 2D files. | ||
- Loading data from mcool files. | ||
- Loading data from sparse matrices. | ||
- Making TAD calls and spohisticated heatmaps with example functions built using HiCBricks accessor functions. | ||
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## Development Notes | ||
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- **HiCBricks** API is now stable. While we may move to sparse or feather representations later, this API will not change. | ||
- With Bioconductor release 3.10, a formal S4 class has been implemented for a better user experience. | ||
- With Bioconductor release 3.11, sparse matrix support has been implemented. | ||
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## Future Roadmap | ||
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There are many new developments which are planned for future releases of HiCBricks. Broadly speaking, | ||
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- In v1, I will try to implement `read and export functions` for as many new Hi-C data formats as possible. On top priority is the `sparse matrix`, HiCExplorer and diffHiC, in that exact order. Support for `.hic` is planned and requires some time. | ||
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- I will try to implement `read and export functions` for as many new Hi-C data formats as possible. On top priority is HiCExplorer and .hic. | ||
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## Contributing | ||
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If you would like to help out, let me know via email. | ||
If you would like to help out, let me know via email at [email protected]. | ||
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