[{"_1":2,"_161":-5,"_162":-5},"loaderData",{"_3":4,"_17":18,"_25":26,"_140":141},"root",{"_5":-5,"_6":-7,"_7":8,"_9":-7,"_10":11,"_12":-7,"_13":14,"_15":16},"currentUser","primaryEmail","siteVerification","6LeIxAcTAAAAAJcZVRqyHh71UMIEGNQ_MXjiZKhI","toast","enableDev",false,"incidentStatus","theme","system","contrast","normal","routes/_layout",{"_19":-5,"_20":21,"_22":21,"_23":11,"_24":21},"username","isAskGordonEnabled",true,"isUsingNewTemplate","showMinimalLanding","showHoneypotTrap","routes/_layout.r.$namespace.$reponame",{"_27":28,"_29":-5,"_30":11,"_31":11,"_32":33,"_34":35,"_36":-5,"_37":11,"_38":39,"_88":-5,"_89":90,"_129":-5,"_130":11,"_131":21,"_132":11,"_133":-5,"_134":11,"_135":-5,"_136":137,"_138":91,"_139":-7},"canonicalUrl","https://hub.docker.com/r/msauria/hifive/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","msauria","reponame","hifive","cloudBuildSource","isAutobuildsAvailable","repo",{"_40":41,"_42":43,"_45":46,"_47":48,"_49":11,"_50":51,"_52":53,"_54":55,"_57":35,"_32":33,"_58":59,"_60":44,"_61":62,"_63":64,"_65":66,"_67":-5,"_68":62,"_69":70,"_71":11,"_72":33,"_73":74,"_79":21,"_80":81,"_85":33,"_86":87},"categories",[],"content_types",[44],"image","date_registered","2015-09-14T14:37:13.562457Z","description","The HiC and 5C chromatin interaction analysis program HiFive, its requirements, and test data.","is_private","last_updated","2018-11-30T02:42:54.681408Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[56],"application/vnd.docker.container.image.v1+json","name","pull_count",1883,"repository_type","star_count",0,"status",1,"status_description","active","source","collaborator_count","full_description",".. image:: https://readthedocs.org/projects/bxlab-hifive/badge/?version=latest\r\n :target: http://bxlab-hifive.readthedocs.org/en/latest/\r\n :alt: Latest Documentation\r\n \r\n.. image:: https://travis-ci.org/bxlab/hifive.svg?branch=master\r\n :target: https://travis-ci.org/bxlab/hifive\r\n :alt: Latest Build\r\n\r\nThis repository contains code for the hifive package, a set of tools for\r\nhandling HiC and 5C data. This includes managing data from mapped reads, either\r\nin bam, mat, or raw formats. All stages use hdf5 dictionaries for fast access\r\nand minimal memory and storage usage.\r\n\r\nThis package includes methods for normalizing data from either HiC or 5C\r\nexperiments at the fragment-end, or fragment level resolution, respectively.\r\nOnce normalized, data can be used for plotting, binning, or other statistical\r\ntests within the package very quickly.\r\n\r\nThis package makes extensive use of the h5py and numpy packages. In addition, if\r\nmpi4py is installed, several methods are compatible with parallelization,\r\nincluding HiC normalization and heatmap generation.\r\n\r\nDocumentation can be found `here `_.\r\n\r\nThe HiFive binary requires Python 2.7. However, the library can be used by Python 2.6 and 2.7.\r\n\r\nInstalling HiFive\r\n=============================\r\n\r\nThe easiest way to get HiFive is using pip::\r\n\r\n > pip install hifive\r\n\r\nHiFive can also be obtained from `github `_ using the following command::\r\n\r\n > git clone https://github.com/bxlab/hifive.git\r\nor alternatively, download a snapshot of the repository using the following commands::\r\n\r\n > wget https://github.com/bxlab/hifive/tarball/1.0\r\n > tar -xf hifive_v1.0.tar\r\n\r\nHiFive depends on a few packages and has several others that extend its functionality.\r\n\r\nRequired Packages\r\n-----------------\r\n * `Scipy `_\r\n * `Numpy `_\r\n * `Cython `_\r\n * `h5py `_\r\n\r\nRecommended Packages\r\n--------------------\r\n * `Pysam `_\r\n * `Pyx `_\r\n * `PIL `_\r\n * `mpi4py `_\r\n * `mlpy `_\r\n\r\nTo install HiFive, simply enter the directory that the repository was cloned or downloaded to and use the following command::\r\n\r\n > python setup.py install\r\n\r\nIf you wish to install HiFive in a location other than the default, you can use the prefix option::\r\n\r\n > python setup.py install --prefix=/your/desired/path\r\n\r\n.. _installing_docs:\r\n\r\nInstalling Documentation\r\n================================\r\n\r\nIn order to build HiFive's documentation locally, you need to execute the following command::\r\n\r\n > cd doc\r\n > make html\r\n\r\nThis will create the documentation suitable for viewing with a web browser. 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msauria/hifive

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