https://github.com/timoast/sinto

Tools for single-cell data processing
https://github.com/timoast/sinto

bioinformatics single-cell

Last synced: 8 months ago
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Tools for single-cell data processing

• Host: GitHub
• URL: https://github.com/timoast/sinto
• Owner: timoast
• License: mit
• Created: 2019-03-28T16:44:41.000Z (about 7 years ago)
• Default Branch: master
• Last Pushed: 2024-05-27T13:31:40.000Z (about 2 years ago)
• Last Synced: 2025-09-02T03:59:37.917Z (9 months ago)
• Topics: bioinformatics, single-cell
• Language: Python
• Homepage: https://timoast.github.io/sinto/
• Size: 6.15 MB
• Stars: 126
• Watchers: 1
• Forks: 26
• Open Issues: 6
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE

Awesome Lists containing this project

• awesome-single-cell - Sinto - [python] - A toolkit for working with aligned single-cell reads. Includes functions to split BAM files by cell barcode, add cell barcodes as read tags, move cell barcode information to read groups, and create a scATAC-seq fragment file from a BAM file. (Software packages / Other applications)

README

          
Sinto: single-cell analysis tools

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.. image:: https://github.com/timoast/sinto/workflows/pytest/badge.svg

   :target: https://github.com/timoast/sinto/actions

.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat

   :target: http://bioconda.github.io/recipes/sinto/README.html

.. image:: https://badge.fury.io/py/sinto.svg

    :target: https://badge.fury.io/py/sinto

.. image:: https://pepy.tech/badge/sinto

    :target: https://pepy.tech/project/sinto

Sinto is a toolkit for processing aligned single-cell data. Sinto includes functions to:

- Subset reads from a BAM file by cell barcode

- Create a scATAC-seq fragments file from a BAM file

- Add read tags to a BAM file according to cell barcode information

- Add read groups based on read tags

- Copy or move read tags to another read tag

- Copy cell barcodes to/from read names or read tags

- Add cell barcodes to FASTQ read names

Read the documentation at https://timoast.github.io/sinto