{ "info": { "author": "Alex Federation", "author_email": "drpolaskijr@gmail.com", "bugtrack_url": null, "classifiers": [], "description": "Coltron\n=======\n\n\nOverview\n--------\n\nColtron is an application designed to build transcriptional regulatory networks.\n\n\nInstallation\n------------\n\nInstallation of Coltron has only been vetted on Ubuntu 12.04 LTS and Ubuntu 14.04 LTS. If you encounter \\\nany errors in the installation process, please contact drpolaskijr@gmail.com for additional help.\n\n**Confirm PIP Installation**::\n\n pip --version \n pip 1.5.6 from /usr/local/lib/python2.7/dist-packages/pip-1.5.6-py2.7.egg (python 2.7)\n\nIf the pip --version command generates a command not found error, you will have to download PIP. Instructions for the installation can be found at the following `location\n`_. \n\nRun the following command to start the module download::\n\n $ sudo pip install coltron\n\nThis command should produce output that looks like this::\n\n $ sudo pip install coltron\n Downloading coltron-1.0.1.tar.gz (8.8MB)\n \t100% |\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 8.8MB 7.3kB/s \n\tBuilding wheels for collected packages: coltron\n \t Running setup.py bdist_wheel for coltron\n \t Stored in directory: /home/name/.cache/pip/wheels/83/8c/26/def2b761371d20e93848a6628662df\n\tSuccessfully built coltron\n\tInstalling collected packages: coltron\n\tSuccessfully installed coltron-1.0.1\n\n\nOnce the PIP installation is complete, the data files that Coltron uses to operate must be downloaded.\n\n**Data Download**\n\nColtron provides a command for downloading its required files. The command can be executed as follows::\n \n $ sudo coltron-get-data\n\nThe required data is downloaded from the web and stored in Coltron's data repository. This process can be time consuming.\n\nUsage\n-----\nThe following command is used to run the main Coltron executable::\n\n$ coltron [options] -e [ENHANCER_FILE] -b [BAM_FILE] -g [GENOME] -o [OUTPUTFOLDER] -n [NAME]\n\nOptions::\n\n -h HELP, --help show this help message and exit\n -e ENHANCERS, --enhancer_file=ENHANCERS\n Provide a ROSE generated enhancer table\n (_AllEnhancers.table.txt)\n -b BAM, --bam=BAM Provide a bam that corresponds to the super enhancer\n table\n -g GENOME, --genome=GENOME\n Provide the build of the genome to be used for the\n analysis. Currently supports HG19, HG18 and MM9\n -o OUTPUT, --output=OUTPUT\n Enter an output folder\n -n NAME, --name=NAME Provide a name for the job\n -s SUBPEAKS, --subpeaks=SUBPEAKS\n Enter a BED file of regions to search for motifs\n -x EXPCUTOFF, --expCutoff=EXPCUTOFF\n Enter the expression cutoff to be used to define\n candidate TFs\n -l EXTENSION, --extension-length=EXTENSION\n Enter the length to extend subpeak regions for motif\n finding\n -a ACTIVITY, --activity=ACTIVITY\n A table with refseq in the first column and activity\n (expression or promoter acetylation) in second\n -E ENUMBER, --enhancer_number=ENUMBER\n Enter the number of top ranked enhancers to include in\n the analysis. Default is all super-enhancers\n --promoter=PROMOTER Enter True if the promoters should be included in the\n analysis\n --motifs=MOTIFS Enter an alternative PWM file for the analysis\n -t TFS, --tfs=TFS Enter additional TFs (comma separated) to be used in\n the bindinf analysis\n -v VALLEY, --valley=VALLEY\n Parameter for valley calling threshold, default = 0.3\n\nDependencies\n------------\n\nColtron has a number of software dependencies for full operation:\n\n`Bamliquidator\n`_ \u2013 version 1.2.0\n\n`Samtools\n`_\n\u2013 version 0.1.19\n\n`FIMO \n`_\n\u2013 version 4.91\n\n`NetworkX \n`_\n\u2013 version 1.8.1\n\nPIP installation will take care of the NetworkX dependency. Installation guides\nfor the remaining dependencies can be found at the links provided.", "description_content_type": null, "docs_url": null, "download_url": "UNKNOWN", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/BradnerLab/pipeline", "keywords": null, "license": "UNKNOWN", "maintainer": null, "maintainer_email": null, "name": "coltron", "package_url": "https://pypi.org/project/coltron/", "platform": "UNKNOWN", "project_url": "https://pypi.org/project/coltron/", "project_urls": { "Download": "UNKNOWN", "Homepage": "https://github.com/BradnerLab/pipeline" }, "release_url": "https://pypi.org/project/coltron/1.0.2/", "requires_dist": null, "requires_python": null, "summary": "Package for generating and analyzing transcription networks", "version": "1.0.2" }, "last_serial": 1675112, "releases": { "1.0.1": [ { "comment_text": "", "digests": { "md5": "97f73a1d4917a32b42a45eb1ad986b89", "sha256": "c3c69aaa22703cd761b1fbbe9d543f84dee25b97f39fa896b70b4713e7c67cd7" }, "downloads": -1, "filename": "coltron-1.0.1.tar.gz", "has_sig": false, "md5_digest": "97f73a1d4917a32b42a45eb1ad986b89", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 8796461, "upload_time": "2015-08-12T18:35:46", "url": "https://files.pythonhosted.org/packages/33/95/41cbb1678be23f797ab1d2d1269c10b65ce7bb397a5667056f7736ed85ba/coltron-1.0.1.tar.gz" } ], "1.0.2": [ { "comment_text": "", "digests": { "md5": "b05849477dd008d54584b2e7fe30bcaa", "sha256": "c8e5d805e3ba66e0fa8840d422ff6f2a3c8a0887eb79eecaa35d81e1544d0fe6" }, "downloads": -1, "filename": "coltron-1.0.2.tar.gz", "has_sig": false, "md5_digest": "b05849477dd008d54584b2e7fe30bcaa", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 8796683, "upload_time": "2015-08-12T20:09:46", "url": "https://files.pythonhosted.org/packages/1a/df/2239781f084a6de2bacf201bb1b0f34fdeefa50fba2ef537b69c6e94df57/coltron-1.0.2.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "b05849477dd008d54584b2e7fe30bcaa", "sha256": "c8e5d805e3ba66e0fa8840d422ff6f2a3c8a0887eb79eecaa35d81e1544d0fe6" }, "downloads": -1, "filename": "coltron-1.0.2.tar.gz", "has_sig": false, "md5_digest": "b05849477dd008d54584b2e7fe30bcaa", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 8796683, "upload_time": "2015-08-12T20:09:46", "url": "https://files.pythonhosted.org/packages/1a/df/2239781f084a6de2bacf201bb1b0f34fdeefa50fba2ef537b69c6e94df57/coltron-1.0.2.tar.gz" } ] }