cytozip: index-free, chunk-compressed storage for scalable single-cell DNA methylation analysis
A scalable, cloud-native ecosystem for single-cell and population DNA methylation analysis
Installation
conda
https://anaconda.org/bioconda/cytozip
mamba install -c wubinding -c bioconda cytozip
# or
conda install -c wubinding -c bioconda cytozip
pip
# Prerequisites (one of):
conda install -c bioconda htslib libdeflate samtools # recommended
# apt-get install libhts-dev libdeflate-dev samtools # Debian/Ubuntu
# brew install htslib libdeflate samtools # macOS
pip install cytozip
# or reinstall
pip uninstall -y cytozip && pip install git+http://github.com/DingWB/cytozip
Implementation
| allcools | ballcools | cytozip | |
|---|---|---|---|
| Format | .tsv.gz | .ballc | .cz |
| Compression algorithm | bgzip | bgzip | cytozip |
| Support Random Access ? | Yes | Yes | Yes |
| Need extra index file for query? | Yes | yes | No |
| Quickly Merge? | No | No | Yes |
Usage
Example dataset
https://figshare.com/articles/dataset/cytozip_example_data/32095567
1 maintainer
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
cytozip-0.3.8.tar.gz
(282.2 kB
view details)
File details
Details for the file cytozip-0.3.8.tar.gz.
File metadata
- Download URL: cytozip-0.3.8.tar.gz
- Upload date:
- Size: 282.2 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via:
twine/6.1.0 CPython/3.13.14
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
f4d5f0d3c2d786fcb294c09af3f7d6edd493cbcb86fe6152507893a41698a55a
|
|
| MD5 |
cb7f0cca9deef140fcb06d17bd72db49
|
|
| BLAKE2b-256 |
3ed8ba4c66f13179c077089d4237e1547a92bf676b348af39fe179a95aa6b350
|
