## splicekit: an integrative toolkit for splicing analysis from short-read RNA-seq
<b>splicekit</b> is a modular platform for splicing analysis from short-read RNA-seq datasets. The platform also integrates an JBrowse2 instance, [pybio](https://github.com/grexor/pybio) for genomic operations and [scanRBP](https://github.com/grexor/scanRBP) for RNA-protein binding studies. The whole analysis is self-contained (one single folder) and the platform is written in Python, in a modular way.
Check a short video presentation about splicekit (poster) at ECCB 2023 on Youtube:
[<img src="media/splicekit_youtube.jpg" width=300>](https://youtu.be/P1m73usZ3lc?si=HBJxWOkUajObFpu1)
## Quick start
The easiest way to install splicekit is to simply run:
`$ pip install splicekit`
Note that on some systems, pip is installing the executable scripts under `~/.local/bin`. However this folder is not in the PATH which will result in `command not found` if you try to run `$ splicekit` on the command line. To fix this, please execute:
`export PATH="$PATH:~/.local/bin"`
Another suggestion is to install inside a virtual environment (using `virtualenv`).
<details>
<summary>Installing splicekit directly from the GitHub repository</summary>
```
pip install git+https://github.com/bedapub/splicekit.git@main
```
</details>
<details>
<summary>If you already have aligned reads in BAM files</summary>
All you need is `samples.tab` (note that this is a <b>TAB delimited file</b>) and `splicekit.config` in one folder (check [datasets](datasets) for examples).
You can easily download and prepare the reference genome (e.g. `$ pybio genome homo_sapiens`).
Finally run `$ splicekit process` (inside the folder with `samples.tab` and `splicekit.config`).
Easiest is to check [datasets](datasets) examples to see how the above files look like and also to check scripts if you need to map reads from FASTQ files with `pybio`.
</details>
## Documentation
* [PDF reference manual](https://github.com/bedapub/splicekit/raw/main/docs/splicekit_docs.pdf)
* [Google docs](https://docs.google.com/document/d/15ZRCeK8xyg3klLktZSHZ9k__Xw_BZRn_Q-J4W35JNnQ/edit?usp=sharing) of the above PDF (comment if you like)
## Changelog<a name="changelog"></a>
**v0.6**: released in April 2024
* updated reports
* JUNE analysis (junction-events to classify skipped and mutually exclusive exons)
<details>
<summary>Past changenotes (click to view)</summary>
<b>v0.4.9</b>: released in November 2023
* added rMATS analysis for splicing events
* added Docker container that can be directly imported to singularity via ghcr.io
* fixed dependencies
* other small fixes
<b>v0.4</b>: released in May 2023
* added singularity container with all dependencies
* added local integrated JBrowse2
* cluster or desktop runs
* scanRBP and bootstrap analysis of RNA-protein binding
* further development and integration with pybio
* extended documentation of concepts, analysis and results
<b>v0.3</b>: released in January 2023 (click to show details)
* re-coded junction analysis
* independent junctions parsing from provided bam files
* master table of all junctions in the samples of the analyzed project, including novel junctions (refseq/ensembl non-annotated)
* clustering by logFC of pairwise-comparisons with dendrogram: junction, exon and gene levels (clusterlogfc module)
* added *first_exon* annotation for junctions touching annotated first exons of transcripts
* extended documentation of concepts, analysis and results
<b>v0.2</b>: released in October 2022
* software architecture restructure with python modules
* filtering of lowly expressed features by edgeR
* DonJuan analysis (junction-anchor analysis)
* more advanced motif analysis with DREME
* filtering regulated junctions with regulated donors
<b>v0.1</b>: released in July 2022
* initial version of splicekit
* parsing of junction and exon counts
* computing edgeR analysis from count tables and producing a results file with direct links to JBrowse2
* basic motif analysis
</details>
## Citing and Contact<a name="citation"></a>
If you find **splicekit** useful in your work and research, please cite:
Gregor Rot, Arne Wehling, Roland Schmucki, Nikolaos Berntenis, Jitao David Zhang, Martin Ebeling<br>
<a href='https://www.biorxiv.org/content/10.1101/2023.05.25.542256v1' target='_biorxiv'>splicekit: a comprehensive toolkit for splicing analysis from short-read RNA-seq</a><br>
bioRxiv, 2023.05. 25.542256
In case of questions, issues and other ideas, please use the <a href='https://github.com/bedapub/splicekit/issues'>GitHub Issues</a> or write directly to <a href='mailto:gregor.rot@gmail.com'>Gregor Rot</a>.
Raw data
{
"_id": null,
"home_page": "https://github.com/bedapub/splicekit",
"name": "splicekit",
"maintainer": null,
"docs_url": null,
"requires_python": null,
"maintainer_email": null,
"keywords": "splicekit, splicing, transcriptomics, bioinformatics",
"author": "Roche, PMDA Spliceosome team",
"author_email": "gregor.rot@gmail.com",
"download_url": "https://files.pythonhosted.org/packages/7c/99/343adbab1466dcca1d03ad2151c5204f08117f29c004fceda02f710efad9/splicekit-0.6.tar.gz",
"platform": null,
"description": "## splicekit: an integrative toolkit for splicing analysis from short-read RNA-seq\n\n<b>splicekit</b> is a modular platform for splicing analysis from short-read RNA-seq datasets. The platform also integrates an JBrowse2 instance, [pybio](https://github.com/grexor/pybio) for genomic operations and [scanRBP](https://github.com/grexor/scanRBP) for RNA-protein binding studies. The whole analysis is self-contained (one single folder) and the platform is written in Python, in a modular way.\n\nCheck a short video presentation about splicekit (poster) at ECCB 2023 on Youtube:\n\n[<img src=\"media/splicekit_youtube.jpg\" width=300>](https://youtu.be/P1m73usZ3lc?si=HBJxWOkUajObFpu1)\n\n## Quick start\n\nThe easiest way to install splicekit is to simply run:\n\n`$ pip install splicekit`\n\nNote that on some systems, pip is installing the executable scripts under `~/.local/bin`. However this folder is not in the PATH which will result in `command not found` if you try to run `$ splicekit` on the command line. To fix this, please execute:\n\n`export PATH=\"$PATH:~/.local/bin\"`\n\nAnother suggestion is to install inside a virtual environment (using `virtualenv`).\n\n<details>\n<summary>Installing splicekit directly from the GitHub repository</summary>\n\n```\npip install git+https://github.com/bedapub/splicekit.git@main\n```\n</details>\n\n<details>\n<summary>If you already have aligned reads in BAM files</summary>\n\nAll you need is `samples.tab` (note that this is a <b>TAB delimited file</b>) and `splicekit.config` in one folder (check [datasets](datasets) for examples).\n\nYou can easily download and prepare the reference genome (e.g. `$ pybio genome homo_sapiens`).\n\nFinally run `$ splicekit process` (inside the folder with `samples.tab` and `splicekit.config`).\n\nEasiest is to check [datasets](datasets) examples to see how the above files look like and also to check scripts if you need to map reads from FASTQ files with `pybio`.\n</details>\n\n## Documentation\n\n* [PDF reference manual](https://github.com/bedapub/splicekit/raw/main/docs/splicekit_docs.pdf)\n* [Google docs](https://docs.google.com/document/d/15ZRCeK8xyg3klLktZSHZ9k__Xw_BZRn_Q-J4W35JNnQ/edit?usp=sharing) of the above PDF (comment if you like)\n\n## Changelog<a name=\"changelog\"></a>\n\n**v0.6**: released in April 2024\n\n* updated reports\n* JUNE analysis (junction-events to classify skipped and mutually exclusive exons)\n\n<details>\n<summary>Past changenotes (click to view)</summary>\n\n<b>v0.4.9</b>: released in November 2023\n\n* added rMATS analysis for splicing events\n* added Docker container that can be directly imported to singularity via ghcr.io\n* fixed dependencies\n* other small fixes\n\n<b>v0.4</b>: released in May 2023\n\n* added singularity container with all dependencies\n* added local integrated JBrowse2\n* cluster or desktop runs\n* scanRBP and bootstrap analysis of RNA-protein binding\n* further development and integration with pybio\n* extended documentation of concepts, analysis and results\n\n<b>v0.3</b>: released in January 2023 (click to show details)\n\n* re-coded junction analysis\n * independent junctions parsing from provided bam files\n * master table of all junctions in the samples of the analyzed project, including novel junctions (refseq/ensembl non-annotated)\n* clustering by logFC of pairwise-comparisons with dendrogram: junction, exon and gene levels (clusterlogfc module)\n* added *first_exon* annotation for junctions touching annotated first exons of transcripts\n* extended documentation of concepts, analysis and results\n\n<b>v0.2</b>: released in October 2022\n\n* software architecture restructure with python modules\n* filtering of lowly expressed features by edgeR\n* DonJuan analysis (junction-anchor analysis)\n* more advanced motif analysis with DREME\n* filtering regulated junctions with regulated donors\n\n<b>v0.1</b>: released in July 2022\n\n* initial version of splicekit\n* parsing of junction and exon counts\n* computing edgeR analysis from count tables and producing a results file with direct links to JBrowse2\n* basic motif analysis\n\n</details>\n\n## Citing and Contact<a name=\"citation\"></a>\n\nIf you find **splicekit** useful in your work and research, please cite:\n\nGregor Rot, Arne Wehling, Roland Schmucki, Nikolaos Berntenis, Jitao David Zhang, Martin Ebeling<br>\n<a href='https://www.biorxiv.org/content/10.1101/2023.05.25.542256v1' target='_biorxiv'>splicekit: a comprehensive toolkit for splicing analysis from short-read RNA-seq</a><br>\nbioRxiv, 2023.05. 25.542256\n\nIn case of questions, issues and other ideas, please use the <a href='https://github.com/bedapub/splicekit/issues'>GitHub Issues</a> or write directly to <a href='mailto:gregor.rot@gmail.com'>Gregor Rot</a>.\n",
"bugtrack_url": null,
"license": null,
"summary": "splicekit: comprehensive toolkit for splicing analysis from short-read RNA-seq",
"version": "0.6",
"project_urls": {
"Homepage": "https://github.com/bedapub/splicekit"
},
"split_keywords": [
"splicekit",
" splicing",
" transcriptomics",
" bioinformatics"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "c70b66a0aa6c40d6ef504c4d1296ca2e5bc04828e866c683667619e3938c0993",
"md5": "282410c8e5f609911e2991e50c867aa2",
"sha256": "a7070b628841b673e024f2d0a5ba8df4429eeaeef47ec449dc29f0f47617d418"
},
"downloads": -1,
"filename": "splicekit-0.6-py3-none-any.whl",
"has_sig": false,
"md5_digest": "282410c8e5f609911e2991e50c867aa2",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": null,
"size": 71157,
"upload_time": "2024-04-25T08:54:30",
"upload_time_iso_8601": "2024-04-25T08:54:30.248231Z",
"url": "https://files.pythonhosted.org/packages/c7/0b/66a0aa6c40d6ef504c4d1296ca2e5bc04828e866c683667619e3938c0993/splicekit-0.6-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "7c99343adbab1466dcca1d03ad2151c5204f08117f29c004fceda02f710efad9",
"md5": "a0c0844c90c9ca9beab881f684b41999",
"sha256": "66aae79b707255bd148c733b6cefa0408619f88619658e824c85cd4a34d83b67"
},
"downloads": -1,
"filename": "splicekit-0.6.tar.gz",
"has_sig": false,
"md5_digest": "a0c0844c90c9ca9beab881f684b41999",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 59989,
"upload_time": "2024-04-25T08:54:31",
"upload_time_iso_8601": "2024-04-25T08:54:31.799171Z",
"url": "https://files.pythonhosted.org/packages/7c/99/343adbab1466dcca1d03ad2151c5204f08117f29c004fceda02f710efad9/splicekit-0.6.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-04-25 08:54:31",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "bedapub",
"github_project": "splicekit",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"lcname": "splicekit"
}
JSON
