Python 3.10 Python 3.11 Python 3.12 Python 3.13 License: GPL v3 Code style: ruff codecov Python package PyPI - Version Documentation Status

tidesurf

This repository provides a Tool for IDentification and Enumeration of Spliced and Unspliced Read Fragments using Python.

Installation

From PyPI

Set up a virtual environment using Conda with Python version >=3.10 and activate it (here: using Python 3.12):

conda create -n <envName> python=3.12
conda activate <envName>

Install the package from PyPI:

pip install tidesurf

Latest version from GitHub

Clone the repository:

git clone git@github.com:janschleicher/tidesurf.git

Change into the directory and install with pip:

cd tidesurf
pip install -e .

Usage

usage: tidesurf [-h] [-v] [--orientation {sense,antisense}] [-o OUTPUT]
                [--no_filter_cells] [--bam_path BAM_PATH [BAM_PATH ...]]
                [--whitelist WHITELIST [WHITELIST ...] | --num_umis NUM_UMIS]
                [--min_intron_overlap MIN_INTRON_OVERLAP]
                [--multi_mapped_reads] [--export_umi_tables]
                SAMPLE_DIR GTF_FILE

Program: tidesurf (Tool for IDentification and Enumeration of Spliced and Unspliced Read Fragments)
Version: 0.4.0

positional arguments:
  SAMPLE_DIR            Sample directory containing Cell Ranger output.
  GTF_FILE              GTF file with transcript information.

options:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit
  --orientation {sense,antisense}
                        Orientation of reads with respect to transcripts. For
                        10x Genomics, use 'sense' for three prime and
                        'antisense' for five prime.
  -o OUTPUT, --output OUTPUT
                        Output directory.
  --no_filter_cells     Do not filter cells.
  --bam_path BAM_PATH [BAM_PATH ...]
                        Explicit path to one or more BAM files. The sample
                        directory will be ignored if this is given. If this
                        argument is used, the positional arguments must be
                        separated from it by another argument, by ' -- ', or
                        they must precede it.
  --whitelist WHITELIST [WHITELIST ...]
                        Whitelist for cell filtering. Set to 'cellranger' to
                        use barcodes in the sample directory. Alternatively,
                        provide a path to a whitelist. If multiple BAM files
                        are passed to 'bam_path', one whitelist can be passed
                        per BAM file. If this argument is used, the positional
                        arguments must be separated from it by another
                        argument, by ' -- ', or they must precede it.
  --num_umis NUM_UMIS   Minimum number of UMIs for filtering a cell.
  --min_intron_overlap MIN_INTRON_OVERLAP
                        Minimum number of bases that a read must overlap with
                        an intron to be considered intronic.
  --multi_mapped_reads  Take reads mapping to multiple genes into account
                        (default: reads mapping to more than one gene are
                        discarded).
  --export_umi_tables   Export tables with splice type for UMIs.

Contributing

For contributing, you should install tidesurf in development mode:

pip install -e ".[dev]"

This will install the additional dependencies ruff and pytest, which are used for formatting and code style, and testing, respectively. Please run these before commiting new code.

Citation

If you use tidesurf in your research, please cite the following publication:

Schleicher, J.T., Klingler, D., and Claassen, M. (2026). Accurate quantification of spliced and unspliced transcripts for single-cell RNA sequencing with tidesurf. PLoS One 21(8): e0355867; DOI: 10.1371/journal.pone.0355867.

@article{10.1371/journal.pone.0355867,
    doi = {10.1371/journal.pone.0355867},
    author = {Schleicher, Jan T. AND Klingler, Doreen AND Claassen, Manfred},
    journal = {PLOS ONE},
    publisher = {Public Library of Science},
    title = {Accurate quantification of spliced and unspliced transcripts for single-cell RNA sequencing with tidesurf},
    year = {2026},
    month = {08},
    volume = {21},
    url = {https://doi.org/10.1371/journal.pone.0355867},
    pages = {1-23},
    number = {8},
}

Project links

Data verified by PyPI on Aug 24, 2026
Data provided by the project maintainers, verified at the time the release was uploaded to PyPI.

Key dates

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  • Released:
Latest release

1 maintainer

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Avatar for janschleicher from gravatar.com janschleicher

Credits

Author: Jan T. Schleicher

GitHub Statistics

Data verified by PyPI on Aug 24, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License expression

GPL-3.0-only
View SPDX License List

Requires

Python >=3.10

Provides Extra

dev doc

Tags

scRNA-seq quantification splicing velocity

Classifiers

Report project as malware

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This release

0.4.0 This release

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0.3.1

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0.3.0

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0.2.1

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0.2.0

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0.1.0

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