{
"info": {
"author": "Mette Bentsen",
"author_email": "mette.bentsen@mpi-bn.mpg.de",
"bugtrack_url": null,
"classifiers": [
"Intended Audience :: Science/Research",
"License :: OSI Approved :: MIT License",
"Programming Language :: Python :: 3",
"Topic :: Scientific/Engineering :: Bio-Informatics"
],
"description": "TOBIAS - Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal \n=======================================\n\n[](https://pypi.org/project/tobias/)\n[](http://bioconda.github.io/recipes/tobias/README.html)\n\nIntroduction \n------------\n\nATAC-seq (Assay for Transposase-Accessible Chromatin using high-throughput sequencing) is a sequencing assay for investigating genome-wide chromatin accessibility. The assay applies a Tn5 Transposase to insert sequencing adapters into accessible chromatin, enabling mapping of regulatory regions across the genome. Additionally, the local distribution of Tn5 insertions contains information about transcription factor binding due to the visible depletion of insertions around sites bound by protein - known as _footprints_. \n\n**TOBIAS** is a collection of command-line bioinformatics tools for performing footprinting analysis on ATAC-seq data, and includes:\n\n![](\"/figures/tobias.png\")
\n\n- Correction of Tn5 insertion bias\n- Calculation of footprint scores within regulatory regions\n- Estimation of bound/unbound transcription factor binding sites\n- Visualization of footprints within and across different conditions\n\nFor information on each tool, please see the [wiki](https://github.molgen.mpg.de/loosolab/TOBIAS/wiki/).\n\nInstallation\n------------\nTOBIAS is written as a python package and can be quickly installed via pip:\n```bash\npip install tobias\n```\n\nor directly from github using:\n```bash\n$ git clone https://github.molgen.mpg.de/loosolab/TOBIAS\n$ cd TOBIAS\n$ python setup.py install\n```\nPlease see the [installation](https://github.molgen.mpg.de/loosolab/TOBIAS/wiki/installation) page for more info.\n\nUsage\n------------\nAll tools are available through the command-line as ```TOBIAS ```, for example:\n``` \n$ TOBIAS ATACorrect\n__________________________________________________________________________________________\n\n TOBIAS ~ ATACorrect\n__________________________________________________________________________________________\n\nATACorrect corrects the cutsite-signal from ATAC-seq with regard to the underlying\nsequence preference of Tn5 transposase.\n\nUsage:\nTOBIAS ATACorrect --bam --genome --peaks \n\nOutput files:\n- /_uncorrected.bw\n- /_bias.bw\n- /_expected.bw\n- /_corrected.bw\n- /_atacorrect.pdf\n\n(...)\n```\n\nCommand-line examples\n-------------\n\nThese examples use the test data provided in the [TOBIAS/test_data](https://github.molgen.mpg.de/loosolab/TOBIAS/tree/master/test_data) directory, so please make sure you are in the upper TOBIAS/ directory when running the commands.\n\n**ATACorrect: Bias correction of ATAC-seq reads in open chromatin** \n```\n$ TOBIAS ATACorrect --bam test_data/Bcell_chr4.bam --genome test_data/genome_chr4.fa.gz --peaks test_data/merged_peaks.bed --blacklist test_data/blacklist_chr4.bed --outdir atacorrect_test --prefix Bcell --cores 8\n```\n\n**FootprintScores: Calculate footprint scores from corrected cutsites**\n```\n$ TOBIAS FootprintScores --signal test_data/Bcell_corrected.bw --regions test_data/merged_peaks.bed --output Bcell_footprints.bw --cores 8\n```\n\n**BINDetect: Estimation of differentially bound motifs based on scores, sequence and motifs** \n```\n$ TOBIAS BINDetect --motifs test_data/example_motifs.txt --signals test_data/Bcell_footprints.bw test_data/Tcell_footprints.bw --genome test_data/genome_chr4.fa.gz --peaks test_data/annotated_peaks.bed --peak_header test_data/annotated_peaks_header.txt --outdir bindetect_output --cond_names Bcell Tcell --cores 8\n```\n\n**PlotAggregate: Plot aggregated ATAC-seq signals in combinations of .bed/.bw to visualize footprints** \n\nVisualize the difference in footprints between two conditions for all accessible sites: \n```\n$ TOBIAS PlotAggregate --TFBS test_data/BATFJUN_all.bed --signals test_data/Bcell_corrected.bw test_data/Tcell_corrected.bw --output BATFJUN_footprint_comparison_all.pdf --share_y both --plot_boundaries\n```\n\nVisualize the difference in footprints between two conditions exclusively for bound sites: \n```\n$ TOBIAS PlotAggregate --TFBS test_data/BATFJUN_Bcell_bound.bed test_data/BATFJUN_Tcell_bound.bed --signals test_data/Bcell_corrected.bw test_data/Tcell_corrected.bw --output BATFJUN_footprint_comparison_subsets.pdf --share_y both --plot_boundaries\n```\n\nVisualize the split of bound/unbound sites for one condition: \n```\n$ TOBIAS PlotAggregate --TFBS test_data/IRF1_all.bed test_data/IRF1_bound.bed test_data/IRF1_unbound.bed --signals test_data/Bcell_uncorrected.bw test_data/Bcell_expected.bw test_data/Bcell_corrected.bw --output IRF1_footprint.pdf --share_y sites --plot_boundaries\n```\n\n**PlotHeatmap: Plot heatmaps and aggregates of ATAC-seq signals in combinations of .bed/.bw to visualize footprints** \n```\n$ TOBIAS PlotHeatmap --TFBS test_data/BATFJUN_Bcell_bound.bed test_data/BATFJUN_Bcell_unbound.bed --TFBS test_data/BATFJUN_Tcell_bound.bed test_data/BATFJUN_Tcell_unbound.bed --signals test_data/Bcell_corrected.bw test_data/Tcell_corrected.bw --output BATFJUN_heatmap.pdf --signal_labels Bcell Tcell --share_colorbar\n```\n\n**FormatMotifs: A utility to convert and join/split across different motif-file formats** \nJoin individual motif files to one: \n```\n$ TOBIAS FormatMotifs --input test_data/individual_motifs/* --format pfm --task join --output example_motifs.txt\n```\n\nSplit a motif file containing several motifs: \n```\n$ TOBIAS FormatMotifs --input test_data/example_motifs.txt --format pfm --task split --output split_motifs\n```\n\nFilter a larger motif file using TF names:\n```\n$ echo 'MAFK CTCF JUNB' > TF_names.txt\n$ FormatMotifs --input test_data/example_motifs.txt --output filtered_motifs.txt --filter TF_names.txt\n```\n\nSnakemake pipeline\n------------\n\nYou can run each TOBIAS tool independently or as part of a pipeline. We provide a pre-set snakemake workflow which is found [here](https://github.molgen.mpg.de/loosolab/TOBIAS_snakemake).\n\nLicense\n------------\nThis project is licensed under the [MIT license](LICENSE). \n\n\nContact\n------------\nMette Bentsen (mette.bentsen (at) mpi-bn.mpg.de)",
"description_content_type": "text/markdown",
"docs_url": null,
"download_url": "",
"downloads": {
"last_day": -1,
"last_month": -1,
"last_week": -1
},
"home_page": "https://github.molgen.mpg.de/loosolab/TOBIAS",
"keywords": "",
"license": "MIT",
"maintainer": "",
"maintainer_email": "",
"name": "tobias",
"package_url": "https://pypi.org/project/tobias/",
"platform": "",
"project_url": "https://pypi.org/project/tobias/",
"project_urls": {
"Homepage": "https://github.molgen.mpg.de/loosolab/TOBIAS"
},
"release_url": "https://pypi.org/project/tobias/0.8.0/",
"requires_dist": null,
"requires_python": "",
"summary": "Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal",
"version": "0.8.0"
},
"last_serial": 5780222,
"releases": {
"0.3.0": [
{
"comment_text": "",
"digests": {
"md5": "02ca0c379b4887edf6e172b63240d22d",
"sha256": "7c7de1efc97352b6fb7bc21a692c901dc7a8ab270a850445577ae1aa4155d0fc"
},
"downloads": -1,
"filename": "tobias-0.3.0.tar.gz",
"has_sig": false,
"md5_digest": "02ca0c379b4887edf6e172b63240d22d",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 301566,
"upload_time": "2019-03-17T16:39:54",
"url": "https://files.pythonhosted.org/packages/7f/1f/035e1cb139b520e17d79c316d2701a29485bacc6bb5374f9d1705f4225fb/tobias-0.3.0.tar.gz"
}
],
"0.4.0": [
{
"comment_text": "",
"digests": {
"md5": "45a19a6f8f969cb7028b5ddbcea35d51",
"sha256": "995d28dfb4d441bf28c009dcd83c28da0084ccc6ea9ff60afadd42d3da54a30c"
},
"downloads": -1,
"filename": "tobias-0.4.0.tar.gz",
"has_sig": false,
"md5_digest": "45a19a6f8f969cb7028b5ddbcea35d51",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 305607,
"upload_time": "2019-04-29T12:39:07",
"url": "https://files.pythonhosted.org/packages/d8/ba/f414832512ca0971e304a625161ee0ad3de3c93315e48901b80a5eedc8d7/tobias-0.4.0.tar.gz"
}
],
"0.5.0": [
{
"comment_text": "",
"digests": {
"md5": "1591bc9a6d9475fe303bbf6bec49029b",
"sha256": "ae14018c6992c6e8f415e142ee8bbcb3b0932927203fe2061a6ac87169631fef"
},
"downloads": -1,
"filename": "tobias-0.5.0.tar.gz",
"has_sig": false,
"md5_digest": "1591bc9a6d9475fe303bbf6bec49029b",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 305646,
"upload_time": "2019-05-14T10:10:22",
"url": "https://files.pythonhosted.org/packages/d9/57/1debedf1e3be79b3a9789b4317f1091641b106da85b5961b5698bc8cda8e/tobias-0.5.0.tar.gz"
}
],
"0.5.1": [
{
"comment_text": "",
"digests": {
"md5": "bcc82d4171cbe154287924c997636a65",
"sha256": "cba810798019ae3ae0115653edc772538ce29003ea59f3c62bb840f385d246fa"
},
"downloads": -1,
"filename": "tobias-0.5.1.tar.gz",
"has_sig": false,
"md5_digest": "bcc82d4171cbe154287924c997636a65",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 306309,
"upload_time": "2019-05-16T07:52:21",
"url": "https://files.pythonhosted.org/packages/d6/27/96ececd4d286730468a91951f620d711dd66268a9116b1576961d7a5fe47/tobias-0.5.1.tar.gz"
}
],
"0.5.2": [
{
"comment_text": "",
"digests": {
"md5": "3645642976102fe0c3a10f53d2770898",
"sha256": "2253b48436a3d13a8089a31909b05e3c953505b7e0f5766031c6f0564cc70f3f"
},
"downloads": -1,
"filename": "tobias-0.5.2.tar.gz",
"has_sig": false,
"md5_digest": "3645642976102fe0c3a10f53d2770898",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 306461,
"upload_time": "2019-05-16T09:16:54",
"url": "https://files.pythonhosted.org/packages/c9/00/173069a1d9f0d2b35d7fb16917a258a92d909947725fe63f39ab23bc7e85/tobias-0.5.2.tar.gz"
}
],
"0.6.0": [
{
"comment_text": "",
"digests": {
"md5": "b40c45cdc3f0e5d3c199f8a9576c466d",
"sha256": "eb29c1782be7ff7fa9a39050ddeb9e531f98ac491c604e42f636d498e7b7800b"
},
"downloads": -1,
"filename": "tobias-0.6.0.tar.gz",
"has_sig": false,
"md5_digest": "b40c45cdc3f0e5d3c199f8a9576c466d",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 307188,
"upload_time": "2019-05-29T13:50:23",
"url": "https://files.pythonhosted.org/packages/81/07/d837f4cbcb999962fd732c65068f89d083259d86e4d3e80aa84034ce9dfe/tobias-0.6.0.tar.gz"
}
],
"0.6.1": [
{
"comment_text": "",
"digests": {
"md5": "3b994ac17aa9f8c6534f6170eba9e091",
"sha256": "2afda6d73bbfab2f1a77ec14a3780e54c5f2b7aa0cb1cb25194a3ece16ddfbf5"
},
"downloads": -1,
"filename": "tobias-0.6.1.tar.gz",
"has_sig": false,
"md5_digest": "3b994ac17aa9f8c6534f6170eba9e091",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 307882,
"upload_time": "2019-06-10T15:00:53",
"url": "https://files.pythonhosted.org/packages/03/42/bbe7e94a468a3069d0bd984b47d02c2213bc27600b50238cf48477ba923c/tobias-0.6.1.tar.gz"
}
],
"0.6.4": [
{
"comment_text": "",
"digests": {
"md5": "656f515b4f8caca30080ba0f015d1c4c",
"sha256": "6107d978f80e76479f1750291ecc5af470045747208d9f8ce09b3247a8227414"
},
"downloads": -1,
"filename": "tobias-0.6.4.tar.gz",
"has_sig": false,
"md5_digest": "656f515b4f8caca30080ba0f015d1c4c",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 307603,
"upload_time": "2019-08-07T08:11:39",
"url": "https://files.pythonhosted.org/packages/63/c9/ba2e4fae5adeb1e87b347ef978ab60de9597ce73762a27351816e0e16561/tobias-0.6.4.tar.gz"
}
],
"0.7.0": [
{
"comment_text": "",
"digests": {
"md5": "54ef83d90aef92c445e35a62be84851d",
"sha256": "a21b0cb403523ea9522e06cff3dea5b5e0b8be7f83b77c1408d12bbe498d7b52"
},
"downloads": -1,
"filename": "tobias-0.7.0.tar.gz",
"has_sig": false,
"md5_digest": "54ef83d90aef92c445e35a62be84851d",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 307807,
"upload_time": "2019-08-13T09:12:42",
"url": "https://files.pythonhosted.org/packages/9b/3c/6fb653fe7dfe928631927e291f5d6e643477092a17375fb9bb819c484115/tobias-0.7.0.tar.gz"
}
],
"0.8.0": [
{
"comment_text": "",
"digests": {
"md5": "cedfce2ebe4c5b35b75518cbf905b7a3",
"sha256": "27f3d51bd7e5f75323450139a0132fc512bf5a4616afb23ce8f2d53345445aaa"
},
"downloads": -1,
"filename": "tobias-0.8.0.tar.gz",
"has_sig": false,
"md5_digest": "cedfce2ebe4c5b35b75518cbf905b7a3",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 310708,
"upload_time": "2019-09-04T09:28:05",
"url": "https://files.pythonhosted.org/packages/c2/f6/ff9d6ad39ffc73a2462867415353a444d4768ef05d4c45a329816049c8e9/tobias-0.8.0.tar.gz"
}
]
},
"urls": [
{
"comment_text": "",
"digests": {
"md5": "cedfce2ebe4c5b35b75518cbf905b7a3",
"sha256": "27f3d51bd7e5f75323450139a0132fc512bf5a4616afb23ce8f2d53345445aaa"
},
"downloads": -1,
"filename": "tobias-0.8.0.tar.gz",
"has_sig": false,
"md5_digest": "cedfce2ebe4c5b35b75518cbf905b7a3",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 310708,
"upload_time": "2019-09-04T09:28:05",
"url": "https://files.pythonhosted.org/packages/c2/f6/ff9d6ad39ffc73a2462867415353a444d4768ef05d4c45a329816049c8e9/tobias-0.8.0.tar.gz"
}
]
}