From 9b9b4be4b8e98cbf6eff0f0b60091ecb90cb1f70 Mon Sep 17 00:00:00 2001 From: Malte Benedikt Kuehl Date: Mon, 14 Oct 2024 12:20:09 +0200 Subject: [PATCH 1/2] Remove esbonio recommendation --- .vscode/extensions.json | 1 - 1 file changed, 1 deletion(-) diff --git a/.vscode/extensions.json b/.vscode/extensions.json index 93ed23d..de7cbc9 100644 --- a/.vscode/extensions.json +++ b/.vscode/extensions.json @@ -10,7 +10,6 @@ "ms-python.black-formatter", "ms-python.flake8", "shardulm94.trailing-spaces", - "swyddfa.esbonio", "ms-vscode.makefile-tools", ] } From b0e74410344debf1e7ba387950064452f80546e7 Mon Sep 17 00:00:00 2001 From: Malte Benedikt Kuehl Date: Wed, 20 Nov 2024 17:51:04 +0100 Subject: [PATCH 2/2] Add citation for manuscript --- CITATION.cff | 74 +++++++++++++++++++++++++++++++++++++++----- README.md | 11 ++++--- docs/source/start.md | 11 ++++--- 3 files changed, 78 insertions(+), 18 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index b864eb0..a81f115 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,11 +1,69 @@ cff-version: 1.2.0 -message: "If you use pytximport, please cite it as below. Please also cite the original tximport package." +title: >- + Gene count estimation with pytximport enables reproducible + analysis of bulk RNA sequencing data in Python +message: >- + If you use this software, please cite it using the + metadata from this file. +type: software authors: - - family-names: "Kuehl" - given-names: "Malte" - - family-names: "Puelles" - given-names: "Victor" -title: "pytximport: Gene count estimation from transcript quantification files in Python" + - given-names: Malte + family-names: Kuehl + affiliation: Aarhus University + orcid: 'https://orcid.org/0000-0003-4167-2498' + - given-names: Milagros N. + family-names: Wong + affiliation: Aarhus University + - given-names: Nicola + family-names: Wanner + affiliation: University Medical Center Hamburg-Eppendorf + - given-names: Stefan + family-names: Bonn + affiliation: University Medical Center Hamburg-Eppendorf + - given-names: Victor G. + family-names: Puelles + orcid: 'https://orcid.org/0000-0002-7735-5462' + affiliation: Aarhus University +identifiers: + - type: doi + value: 10.1093/bioinformatics/btae700 + description: Bioinformatics manuscript +repository-code: 'https://github.com/complextissue/pytximport' +url: 'https://pytximport.readthedocs.io' +abstract: >- + Transcript quantification tools efficiently map bulk RNA + sequencing reads to reference transcriptomes. However, + their output consists of transcript count estimates that + are subject to multiple biases and cannot be readily used + with existing differential gene expression analysis tools + in Python. + + + Here we present pytximport, a Python implementation of the + tximport R package that supports a variety of input + formats, different modes of bias correction, inferential + replicates, gene-level summarization of transcript counts, + transcript-level exports, transcript-to-gene mapping + generation and optional filtering of transcripts by + biotype. pytximport is part of the scverse ecosystem of + open-source Python software packages for omics analyses + and includes both a Python as well as a command-line + interface. + + + With pytximport, we propose a bulk RNA sequencing analysis + workflow based on Bioconda and scverse ecosystem packages, + ensuring reproducible analyses through Snakemake rules. We + apply this pipeline to a publicly available RNA-sequencing + dataset, demonstrating how pytximport enables the creation + of Python-centric workflows capable of providing insights + into transcriptomic alterations. +keywords: + - RNA-Seq + - tximport + - Python + - scverse +license: GPL-3.0-or-later +commit: d9533f5 version: 0.10.0 -date-released: 2024-07-11 -url: "https://github.com/complextissue/pytximport" +date-released: '2024-11-20' diff --git a/README.md b/README.md index 006014c..063bca9 100755 --- a/README.md +++ b/README.md @@ -15,6 +15,11 @@ `pytximport` is a Python package for efficient (gene-)count estimation from transcript quantification files produced by pseudoalignment/quasi-mapping tools such as `salmon`, `kallisto`, `rsem` and others. `pytximport` is a port of the popular [tximport Bioconductor R package](https://bioconductor.org/packages/release/bioc/html/tximport.html). +## Manuscript & Documentation + +The pytximport manuscript can be accessed at: [https://doi.org/10.1093/bioinformatics/btae700](https://doi.org/10.1093/bioinformatics/btae700). +Detailled documentation is made available at: [https://pytximport.readthedocs.io](https://pytximport.readthedocs.io/en/latest/start.html). + ## Installation The recommended way to install `pytximport` is through Bioconda: @@ -78,10 +83,6 @@ Common options are: - `-tx`: Provide this flag to return transcript-level instead of gene-summarized data. Incompatible with gene-level input and `counts_from_abundance=length_scaled_tpm`. - `--help`: Display all configuration options. -## Documentation - -Detailled documentation is made available at: [https://pytximport.readthedocs.io](https://pytximport.readthedocs.io/en/latest/start.html). - ## Development status `pytximport` is still in development and has not yet reached version 1.0.0 in the [SemVer](https://semver.org/) versioning scheme. While it should work for almost all use cases and we regularly compare outputs against the R implementation, breaking changes between minor versions may occur. If you encounter any problems, please open a GitHub issue. If you are a Python developer, we welcome pull requests implementing missing features, adding more extensive unit tests and bug fixes. @@ -95,7 +96,7 @@ The `tximport` package has become a main stay in the bulk RNA sequencing communi Please cite both the original publication as well as this Python implementation: -- Kuehl, M., & Puelles, V. (2024). pytximport: Gene count estimation from transcript quantification files in Python (Version 0.10.0) [Computer software]. https://github.com/complextissue/pytximport +- Kuehl, M., Wong, M. N., Wanner, N., Bonn, S., & Puelles, V. G. (2024). Gene count estimation with pytximport enables reproducible analysis of bulk RNA sequencing data in Python. Bioinformatics, btae700. https://doi.org/10.1093/bioinformatics/btae700 - Charlotte Soneson, Michael I. Love, Mark D. Robinson. Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences, F1000Research, 4:1521, December 2015. doi: 10.12688/f1000research.7563.1 ## License diff --git a/docs/source/start.md b/docs/source/start.md index 1674f02..1147d76 100755 --- a/docs/source/start.md +++ b/docs/source/start.md @@ -15,6 +15,11 @@ `pytximport` is a Python package for efficient (gene-)count estimation from transcript quantification files produced by pseudoalignment/quasi-mapping tools such as `salmon`, `kallisto`, `rsem` and others. `pytximport` is a port of the popular [tximport Bioconductor R package](https://bioconductor.org/packages/release/bioc/html/tximport.html). +## Manuscript & Documentation + +The pytximport manuscript can be accessed at: [https://doi.org/10.1093/bioinformatics/btae700](https://doi.org/10.1093/bioinformatics/btae700). +Detailled documentation is made available at: [https://pytximport.readthedocs.io](https://pytximport.readthedocs.io/en/latest/start.html). + ## Installation The recommended way to install `pytximport` is through Bioconda: @@ -65,10 +70,6 @@ Common options are: - `-tx`: Provide this flag to return transcript-level instead of gene-summarized data. Incompatible with gene-level input and `counts_from_abundance=length_scaled_tpm`. - `--help`: Display all configuration options. -## Documentation - -Detailled documentation is made available at: [https://pytximport.readthedocs.io](https://pytximport.readthedocs.io/en/latest/start.html). - ## Development status `pytximport` is still in development and has not yet reached version 1.0.0 in the [SemVer](https://semver.org/) versioning scheme. While it should work for almost all use cases and we regularly compare outputs against the R implementation, breaking changes between minor versions may occur. If you encounter any problems, please open a GitHub issue. If you are a Python developer, we welcome pull requests implementing missing features, adding more extensive unit tests and bug fixes. @@ -82,7 +83,7 @@ The `tximport` package has become a main stay in the bulk RNA sequencing communi Please cite both the original publication as well as this Python implementation: -- Kuehl, M., & Puelles, V. (2024). pytximport: Gene count estimation from transcript quantification files in Python (Version 0.10.0) [Computer software]. https://github.com/complextissue/pytximport +- Kuehl, M., Wong, M. N., Wanner, N., Bonn, S., & Puelles, V. G. (2024). Gene count estimation with pytximport enables reproducible analysis of bulk RNA sequencing data in Python. Bioinformatics, btae700. https://doi.org/10.1093/bioinformatics/btae700 - Charlotte Soneson, Michael I. Love, Mark D. Robinson. Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences, F1000Research, 4:1521, December 2015. doi: 10.12688/f1000research.7563.1 ## License