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},
}
1 maintainer
Metadata
1 maintainer
Release files for tidesurf 0.4.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| tidesurf-0.4.0.tar.gz | 20.5 MB | With provenance | Details for tidesurf-0.4.0.tar.gz |
Built distributions (wheels)
Total release size: 47.0 MB
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