├── .gitignore ├── CODE_OF_CONDUCT.md ├── FAQ.md ├── Henry ├── README.md ├── compute.scores.transcriptome.py ├── parsebeta.py └── predflaskapp │ ├── app │ ├── __init__.py │ ├── __init__.pyc │ ├── forms.py │ ├── forms.pyc │ ├── helpfuncs.py │ ├── models.py │ ├── templates │ │ ├── 404.html │ │ ├── 500.html │ │ ├── base.html │ │ ├── cmdgen.html │ │ ├── edit.html │ │ ├── index.html │ │ ├── login.html │ │ ├── multiupload.html │ │ ├── newpost.html │ │ ├── post.html │ │ ├── predict.html │ │ ├── tarupload.html │ │ ├── uploaded_file.html │ │ ├── uploadfile.html │ │ └── user.html │ ├── views.py │ └── views.pyc │ ├── config.py │ ├── config.pyc │ ├── flask │ ├── bin │ │ ├── activate │ │ ├── activate.csh │ │ ├── activate.fish │ │ ├── activate_this.py │ │ ├── easy_install │ │ ├── easy_install-2.7 │ │ ├── pip │ │ ├── pip2 │ │ ├── pip2.7 │ │ ├── python │ │ ├── python2 │ │ └── python2.7 │ ├── include │ │ └── python2.7 │ ├── lib │ │ └── python2.7 │ │ │ ├── UserDict.py │ │ │ ├── UserDict.pyc │ │ │ ├── _abcoll.py │ │ │ ├── _abcoll.pyc │ │ │ ├── _weakrefset.py │ │ │ ├── _weakrefset.pyc │ │ │ ├── abc.py │ │ │ ├── abc.pyc │ │ │ ├── codecs.py │ │ │ ├── codecs.pyc │ │ │ ├── copy_reg.py │ │ │ ├── copy_reg.pyc │ │ │ ├── distutils │ │ │ ├── __init__.py │ │ │ ├── __init__.pyc │ │ │ └── distutils.cfg │ │ │ ├── encodings │ │ │ ├── fnmatch.py │ │ │ ├── fnmatch.pyc │ │ │ ├── genericpath.py │ │ │ ├── genericpath.pyc │ │ │ ├── lib-dynload │ │ │ ├── linecache.py │ │ │ ├── linecache.pyc │ │ │ ├── locale.py │ │ │ ├── locale.pyc │ │ │ ├── no-global-site-packages.txt │ │ │ ├── ntpath.py │ │ │ ├── orig-prefix.txt │ │ │ ├── os.py │ │ │ ├── os.pyc │ │ │ ├── posixpath.py │ │ │ ├── posixpath.pyc │ │ │ ├── re.py │ │ │ ├── re.pyc │ │ │ ├── site-packages │ │ │ ├── _markerlib │ │ │ │ ├── __init__.py │ │ │ │ ├── __init__.pyc │ │ │ │ ├── markers.py │ │ │ │ └── markers.pyc │ │ │ ├── easy_install.py │ │ │ ├── easy_install.pyc │ │ │ ├── pip-1.5.6.dist-info │ │ │ │ ├── DESCRIPTION.rst │ │ │ │ ├── METADATA │ │ │ │ ├── RECORD │ │ │ │ ├── WHEEL │ │ │ │ ├── entry_points.txt │ │ │ │ ├── metadata.json │ │ │ │ └── top_level.txt │ │ │ ├── pip │ │ │ │ ├── __init__.py │ │ │ │ ├── __init__.pyc │ │ │ │ ├── __main__.py │ │ │ │ ├── __main__.pyc │ │ │ │ ├── _vendor │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── __init__.pyc │ │ │ │ │ ├── _markerlib │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ ├── __init__.pyc │ │ │ │ │ │ ├── markers.py │ │ │ │ │ │ └── markers.pyc │ │ │ │ │ ├── colorama │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ ├── __init__.pyc │ │ │ │ │ │ ├── ansi.py │ │ │ │ │ │ ├── ansi.pyc │ │ │ │ │ │ ├── ansitowin32.py │ │ │ │ │ │ ├── ansitowin32.pyc │ │ │ │ │ │ ├── initialise.py │ │ │ │ │ │ ├── initialise.pyc │ │ │ │ │ │ ├── win32.py │ │ │ │ │ │ ├── win32.pyc │ │ │ │ │ │ ├── winterm.py │ │ │ │ │ │ └── winterm.pyc │ │ │ │ │ ├── distlib │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ ├── __init__.pyc │ │ │ │ │ │ ├── _backport │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ ├── __init__.pyc │ │ │ │ │ │ │ ├── misc.py │ │ │ │ │ │ │ ├── misc.pyc │ │ │ │ │ │ │ ├── shutil.py │ │ │ │ │ │ │ ├── shutil.pyc │ │ │ │ │ │ │ ├── sysconfig.cfg │ │ │ │ │ │ │ ├── sysconfig.py │ │ │ │ │ │ │ ├── sysconfig.pyc │ │ │ │ │ │ │ ├── tarfile.py │ │ │ │ │ │ │ └── tarfile.pyc │ │ │ │ │ │ ├── compat.py │ │ │ │ │ │ ├── compat.pyc │ │ │ │ │ │ ├── database.py │ │ │ │ │ │ ├── database.pyc │ │ │ │ │ │ ├── index.py │ │ │ │ │ │ ├── index.pyc │ │ │ │ │ │ ├── locators.py │ │ │ │ │ │ ├── locators.pyc │ │ │ │ │ │ ├── manifest.py │ │ │ │ │ │ ├── manifest.pyc │ │ │ │ │ │ ├── markers.py │ │ │ │ │ │ ├── markers.pyc │ │ │ │ │ │ ├── metadata.py │ │ │ │ │ │ ├── metadata.pyc │ │ │ │ │ │ ├── resources.py │ │ │ │ │ │ ├── resources.pyc │ │ │ │ │ │ ├── scripts.py │ │ │ │ │ │ ├── scripts.pyc │ │ │ │ │ │ ├── t32.exe │ │ │ │ │ │ ├── t64.exe │ │ │ │ │ │ ├── util.py │ │ │ │ │ │ ├── util.pyc │ │ │ │ │ │ ├── version.py │ │ │ │ │ │ ├── version.pyc │ │ │ │ │ │ ├── w32.exe │ │ │ │ │ │ ├── w64.exe │ │ │ │ │ │ ├── wheel.py │ │ │ │ │ │ └── wheel.pyc │ │ │ │ │ ├── html5lib │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ ├── __init__.pyc │ │ │ │ │ │ ├── constants.py │ │ │ │ │ │ ├── constants.pyc │ │ │ │ │ │ ├── filters │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ ├── __init__.pyc │ │ │ │ │ │ │ ├── _base.py │ │ │ │ │ │ │ ├── _base.pyc │ │ │ │ │ │ │ ├── alphabeticalattributes.py │ │ │ │ │ │ │ ├── alphabeticalattributes.pyc │ │ │ │ │ │ │ ├── inject_meta_charset.py │ │ │ │ │ │ │ ├── inject_meta_charset.pyc │ │ │ │ │ │ │ ├── lint.py │ │ │ │ │ │ │ ├── lint.pyc │ │ │ │ │ │ │ ├── optionaltags.py │ │ │ │ │ │ │ ├── optionaltags.pyc │ │ │ │ │ │ │ ├── sanitizer.py │ │ │ │ │ │ │ ├── sanitizer.pyc │ │ │ │ │ │ │ ├── whitespace.py │ │ │ │ │ │ │ └── whitespace.pyc │ │ │ │ │ │ ├── html5parser.py │ │ │ │ │ │ ├── html5parser.pyc │ │ │ │ │ │ ├── ihatexml.py │ │ │ │ │ │ ├── ihatexml.pyc │ │ │ │ │ │ ├── inputstream.py │ │ │ │ │ │ ├── inputstream.pyc │ │ │ │ │ │ ├── sanitizer.py │ │ │ │ │ │ ├── sanitizer.pyc │ │ │ │ │ │ ├── serializer │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ ├── __init__.pyc │ │ │ │ │ │ │ ├── htmlserializer.py │ │ │ │ │ │ │ └── htmlserializer.pyc │ │ │ │ │ │ ├── tokenizer.py │ │ │ │ │ │ ├── tokenizer.pyc │ │ │ │ │ │ ├── treeadapters │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ ├── __init__.pyc │ │ │ │ │ │ │ ├── sax.py │ │ │ │ │ │ │ └── sax.pyc │ │ │ │ │ │ ├── treebuilders │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ ├── __init__.pyc │ │ │ │ │ │ │ ├── _base.py │ │ │ │ │ │ │ ├── _base.pyc │ │ │ │ │ │ │ ├── dom.py │ │ │ │ │ │ │ ├── dom.pyc │ │ │ │ │ │ │ ├── etree.py │ │ │ │ │ │ │ ├── etree.pyc │ │ │ │ │ │ │ ├── etree_lxml.py │ │ │ │ │ │ │ └── etree_lxml.pyc │ │ │ │ │ │ ├── treewalkers │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ ├── __init__.pyc │ │ │ │ │ │ │ ├── _base.py │ │ │ │ │ │ │ ├── _base.pyc │ │ │ │ │ │ │ ├── dom.py │ │ │ │ │ │ │ ├── dom.pyc │ │ │ │ │ │ │ ├── etree.py │ │ │ │ │ │ │ ├── etree.pyc │ │ │ │ │ │ │ ├── genshistream.py │ │ │ │ │ │ │ ├── genshistream.pyc │ │ │ │ │ │ │ ├── lxmletree.py │ │ │ │ │ │ │ ├── lxmletree.pyc │ │ │ │ │ │ │ ├── pulldom.py │ │ │ │ │ │ │ └── pulldom.pyc │ │ │ │ │ │ ├── trie │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ ├── __init__.pyc │ │ │ │ │ │ │ ├── _base.py │ │ │ │ │ │ │ ├── _base.pyc │ │ │ │ │ │ │ ├── datrie.py │ │ │ │ │ │ │ ├── datrie.pyc │ │ │ │ │ │ │ ├── py.py │ │ │ │ │ │ │ └── py.pyc │ │ │ │ │ │ ├── utils.py │ │ │ │ │ │ └── utils.pyc │ │ │ │ │ ├── pkg_resources.py │ │ │ │ │ ├── pkg_resources.pyc │ │ │ │ │ ├── re-vendor.py │ │ │ │ │ ├── re-vendor.pyc │ │ │ │ │ ├── requests │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ ├── __init__.pyc │ │ │ │ │ │ ├── adapters.py │ │ │ │ │ │ ├── adapters.pyc │ │ │ │ │ │ ├── api.py │ │ │ │ │ │ ├── api.pyc │ │ │ │ │ │ ├── auth.py │ │ │ │ │ │ ├── auth.pyc │ │ │ │ │ │ ├── cacert.pem │ │ │ │ │ │ ├── certs.py │ │ │ │ │ │ ├── certs.pyc │ │ │ │ │ │ ├── compat.py │ │ │ │ │ │ ├── compat.pyc │ │ │ │ │ │ ├── cookies.py │ │ │ │ │ │ ├── cookies.pyc │ │ │ │ │ │ ├── exceptions.py │ │ │ │ │ │ ├── exceptions.pyc │ │ │ │ │ │ ├── hooks.py │ │ │ │ │ │ ├── hooks.pyc │ │ │ │ │ │ ├── models.py │ │ │ │ │ │ ├── models.pyc │ │ │ │ │ │ ├── packages │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ ├── __init__.pyc │ │ │ │ │ │ │ ├── chardet │ │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ │ ├── __init__.pyc │ │ │ │ │ │ │ │ ├── big5freq.py │ │ │ │ │ │ │ │ ├── big5freq.pyc │ │ │ │ │ │ │ │ ├── big5prober.py │ │ │ │ │ │ │ │ ├── big5prober.pyc │ │ │ │ │ │ │ │ ├── chardetect.py │ │ │ │ │ │ │ │ ├── chardetect.pyc │ │ │ │ │ │ │ │ ├── chardistribution.py │ │ │ │ │ │ │ │ ├── chardistribution.pyc │ │ │ │ │ │ │ │ ├── charsetgroupprober.py │ │ │ │ │ │ │ │ ├── charsetgroupprober.pyc │ │ │ │ │ │ │ │ ├── charsetprober.py │ │ │ │ │ │ │ │ ├── charsetprober.pyc │ │ │ │ │ │ │ │ ├── codingstatemachine.py │ │ │ │ │ │ │ │ ├── codingstatemachine.pyc │ │ │ │ │ │ │ │ ├── compat.py │ │ │ │ │ │ │ │ ├── compat.pyc │ │ │ │ │ │ │ │ ├── constants.py │ │ │ │ │ │ │ │ ├── constants.pyc │ │ │ │ │ │ │ │ ├── cp949prober.py │ │ │ │ │ │ │ │ ├── cp949prober.pyc │ │ │ │ │ │ │ │ ├── escprober.py │ │ │ │ │ │ │ │ ├── escprober.pyc │ │ │ │ │ │ │ │ ├── escsm.py │ │ │ │ │ │ │ │ ├── escsm.pyc │ │ │ │ │ │ │ │ ├── eucjpprober.py │ │ │ │ │ │ │ │ ├── eucjpprober.pyc │ │ │ │ │ │ │ │ ├── euckrfreq.py │ │ │ │ │ │ │ │ ├── euckrfreq.pyc │ │ │ │ │ │ │ │ ├── euckrprober.py │ │ │ │ │ │ │ │ ├── euckrprober.pyc │ │ │ │ │ │ │ │ ├── euctwfreq.py │ │ │ │ │ │ │ │ ├── euctwfreq.pyc │ │ │ │ │ │ │ │ ├── euctwprober.py │ │ │ │ │ │ │ │ ├── euctwprober.pyc │ │ │ │ │ │ │ │ ├── gb2312freq.py │ │ │ │ │ │ │ │ ├── gb2312freq.pyc │ │ │ │ │ │ │ │ ├── gb2312prober.py │ │ │ │ │ │ │ │ ├── gb2312prober.pyc │ │ │ │ │ │ │ │ ├── hebrewprober.py │ │ │ │ │ │ │ │ ├── hebrewprober.pyc │ │ │ │ │ │ │ │ ├── jisfreq.py │ │ │ │ │ │ │ │ ├── jisfreq.pyc │ │ │ │ │ │ │ │ ├── jpcntx.py │ │ │ │ │ │ │ │ ├── jpcntx.pyc │ │ │ │ │ │ │ │ ├── langbulgarianmodel.py │ │ │ │ │ │ │ │ ├── langbulgarianmodel.pyc │ │ │ │ │ │ │ │ ├── langcyrillicmodel.py │ │ │ │ │ │ │ │ ├── langcyrillicmodel.pyc │ │ │ │ │ │ │ │ ├── langgreekmodel.py │ │ │ │ │ │ │ │ ├── langgreekmodel.pyc │ │ │ │ │ │ │ │ ├── langhebrewmodel.py │ │ │ │ │ │ │ │ ├── langhebrewmodel.pyc │ │ │ │ │ │ │ │ ├── langhungarianmodel.py │ │ │ │ │ │ │ │ ├── langhungarianmodel.pyc │ │ │ │ │ │ │ │ ├── langthaimodel.py │ │ │ │ │ │ │ │ ├── langthaimodel.pyc │ │ │ │ │ │ │ │ ├── latin1prober.py │ │ │ │ │ │ │ │ ├── latin1prober.pyc │ │ │ │ │ │ │ │ ├── mbcharsetprober.py │ │ │ │ │ │ │ │ ├── mbcharsetprober.pyc │ │ │ │ │ │ │ │ ├── mbcsgroupprober.py │ │ │ │ │ │ │ │ ├── mbcsgroupprober.pyc │ │ │ │ │ │ │ │ ├── mbcssm.py │ │ │ │ │ │ │ │ ├── mbcssm.pyc │ │ │ │ │ │ │ │ ├── sbcharsetprober.py │ │ │ │ │ │ │ │ ├── sbcharsetprober.pyc │ │ │ │ │ │ │ │ ├── sbcsgroupprober.py │ │ │ │ │ │ │ │ ├── sbcsgroupprober.pyc │ │ │ │ │ │ │ │ ├── sjisprober.py │ │ │ │ │ │ │ │ ├── sjisprober.pyc │ │ │ │ │ │ │ │ ├── universaldetector.py │ │ │ │ │ │ │ │ ├── universaldetector.pyc │ │ │ │ │ │ │ │ ├── utf8prober.py │ │ │ │ │ │ │ │ └── utf8prober.pyc │ │ │ │ │ │ │ └── urllib3 │ │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ │ ├── __init__.pyc │ │ │ │ │ │ │ │ ├── _collections.py │ │ │ │ │ │ │ │ ├── _collections.pyc │ │ │ │ │ │ │ │ ├── connection.py │ │ │ │ │ │ │ │ ├── connection.pyc │ │ │ │ │ │ │ │ ├── connectionpool.py │ │ │ │ │ │ │ │ ├── connectionpool.pyc │ │ │ │ │ │ │ │ ├── contrib │ │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ │ ├── __init__.pyc │ │ │ │ │ │ │ │ ├── ntlmpool.py │ │ │ │ │ │ │ │ ├── ntlmpool.pyc │ │ │ │ │ │ │ │ ├── pyopenssl.py │ │ │ │ │ │ │ │ └── pyopenssl.pyc │ │ │ │ │ │ │ │ ├── exceptions.py │ │ │ │ │ │ │ │ ├── exceptions.pyc │ │ │ │ │ │ │ │ ├── fields.py │ │ │ │ │ │ │ │ ├── fields.pyc │ │ │ │ │ │ │ │ ├── filepost.py │ │ │ │ │ │ │ │ ├── filepost.pyc │ │ │ │ │ │ │ │ ├── packages │ │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ │ ├── __init__.pyc │ │ │ │ │ │ │ │ ├── ordered_dict.py │ │ │ │ │ │ │ │ ├── ordered_dict.pyc │ │ │ │ │ │ │ │ ├── six.py │ │ │ │ │ │ │ │ ├── six.pyc │ │ │ │ │ │ │ │ └── ssl_match_hostname │ │ │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ │ │ ├── __init__.pyc │ │ │ │ │ │ │ │ │ ├── _implementation.py │ │ │ │ │ │ │ │ │ └── _implementation.pyc │ │ │ │ │ │ │ │ ├── poolmanager.py │ │ │ │ │ │ │ │ ├── poolmanager.pyc │ │ │ │ │ │ │ │ ├── request.py │ │ │ │ │ │ │ │ ├── request.pyc │ │ │ │ │ │ │ │ ├── response.py │ │ │ │ │ │ │ │ ├── response.pyc │ │ │ │ │ │ │ │ └── util │ │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ │ ├── __init__.pyc │ │ │ │ │ │ │ │ ├── connection.py │ │ │ │ │ │ │ │ ├── connection.pyc │ │ │ │ │ │ │ │ ├── request.py │ │ │ │ │ │ │ │ ├── request.pyc │ │ │ │ │ │ │ │ ├── response.py │ │ │ │ │ │ │ │ ├── response.pyc │ │ │ │ │ │ │ │ ├── ssl_.py │ │ │ │ │ │ │ │ ├── ssl_.pyc │ │ │ │ │ │ │ │ ├── timeout.py │ │ │ │ │ │ │ │ ├── timeout.pyc │ │ │ │ │ │ │ │ ├── url.py │ │ │ │ │ │ │ │ └── url.pyc │ │ │ │ │ │ ├── sessions.py │ │ │ │ │ │ ├── sessions.pyc │ │ │ │ │ │ ├── status_codes.py │ │ │ │ │ │ ├── status_codes.pyc │ │ │ │ │ │ ├── structures.py │ │ │ │ │ │ ├── structures.pyc │ │ │ │ │ │ ├── utils.py │ │ │ │ │ │ └── utils.pyc │ │ │ │ │ ├── six.py │ │ │ │ │ └── six.pyc │ │ │ │ ├── backwardcompat │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── __init__.pyc │ │ │ │ ├── basecommand.py │ │ │ │ ├── basecommand.pyc │ │ │ │ ├── baseparser.py │ │ │ │ ├── baseparser.pyc │ │ │ │ ├── cmdoptions.py │ │ │ │ ├── cmdoptions.pyc │ │ │ │ ├── commands │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── __init__.pyc │ │ │ │ │ ├── bundle.py │ │ │ │ │ ├── bundle.pyc │ │ │ │ │ ├── completion.py │ │ │ │ │ ├── completion.pyc │ │ │ │ │ ├── freeze.py │ │ │ │ │ ├── freeze.pyc │ │ │ │ │ ├── help.py │ │ │ │ │ ├── help.pyc │ │ │ │ │ ├── install.py │ │ │ │ │ ├── install.pyc │ │ │ │ │ ├── list.py │ │ │ │ │ ├── list.pyc │ │ │ │ │ ├── search.py │ │ │ │ │ ├── search.pyc │ │ │ │ │ ├── show.py │ │ │ │ │ ├── show.pyc │ │ │ │ │ ├── uninstall.py │ │ │ │ │ ├── uninstall.pyc │ │ │ │ │ ├── unzip.py │ │ │ │ │ ├── unzip.pyc │ │ │ │ │ ├── wheel.py │ │ │ │ │ ├── wheel.pyc │ │ │ │ │ ├── zip.py │ │ │ │ │ └── zip.pyc │ │ │ │ ├── download.py │ │ │ │ ├── download.pyc │ │ │ │ ├── exceptions.py │ │ │ │ ├── exceptions.pyc │ │ │ │ ├── index.py │ │ │ │ ├── index.pyc │ │ │ │ ├── locations.py │ │ │ │ ├── locations.pyc │ │ │ │ ├── log.py │ │ │ │ ├── log.pyc │ │ │ │ ├── pep425tags.py │ │ │ │ ├── pep425tags.pyc │ │ │ │ ├── req.py │ │ │ │ ├── req.pyc │ │ │ │ ├── runner.py │ │ │ │ ├── runner.pyc │ │ │ │ ├── status_codes.py │ │ │ │ ├── status_codes.pyc │ │ │ │ ├── util.py │ │ │ │ ├── util.pyc │ │ │ │ ├── vcs │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── __init__.pyc │ │ │ │ │ ├── bazaar.py │ │ │ │ │ ├── bazaar.pyc │ │ │ │ │ ├── git.py │ │ │ │ │ ├── git.pyc │ │ │ │ │ ├── mercurial.py │ │ │ │ │ ├── mercurial.pyc │ │ │ │ │ ├── subversion.py │ │ │ │ │ └── subversion.pyc │ │ │ │ ├── wheel.py │ │ │ │ └── wheel.pyc │ │ │ ├── pkg_resources.py │ │ │ ├── pkg_resources.pyc │ │ │ ├── setuptools-3.6.dist-info │ │ │ │ ├── DESCRIPTION.rst │ │ │ │ ├── METADATA │ │ │ │ ├── RECORD │ │ │ │ ├── WHEEL │ │ │ │ ├── dependency_links.txt │ │ │ │ ├── entry_points.txt │ │ │ │ ├── pydist.json │ │ │ │ ├── requires.txt.orig │ │ │ │ ├── top_level.txt │ │ │ │ └── zip-safe │ │ │ └── setuptools │ │ │ │ ├── __init__.py │ │ │ │ ├── __init__.pyc │ │ │ │ ├── archive_util.py │ │ │ │ ├── archive_util.pyc │ │ │ │ ├── cli-32.exe │ │ │ │ ├── cli-64.exe │ │ │ │ ├── cli-arm-32.exe │ │ │ │ ├── cli.exe │ │ │ │ ├── command │ │ │ │ ├── __init__.py │ │ │ │ ├── __init__.pyc │ │ │ │ ├── alias.py │ │ │ │ ├── alias.pyc │ │ │ │ ├── bdist_egg.py │ │ │ │ ├── bdist_egg.pyc │ │ │ │ ├── bdist_rpm.py │ │ │ │ ├── bdist_rpm.pyc │ │ │ │ ├── bdist_wininst.py │ │ │ │ ├── bdist_wininst.pyc │ │ │ │ ├── build_ext.py │ │ │ │ ├── build_ext.pyc │ │ │ │ ├── build_py.py │ │ │ │ ├── build_py.pyc │ │ │ │ ├── develop.py │ │ │ │ ├── develop.pyc │ │ │ │ ├── easy_install.py │ │ │ │ ├── easy_install.pyc │ │ │ │ ├── egg_info.py │ │ │ │ ├── egg_info.pyc │ │ │ │ ├── install.py │ │ │ │ ├── install.pyc │ │ │ │ ├── install_egg_info.py │ │ │ │ ├── install_egg_info.pyc │ │ │ │ ├── install_lib.py │ │ │ │ ├── install_lib.pyc │ │ │ │ ├── install_scripts.py │ │ │ │ ├── install_scripts.pyc │ │ │ │ ├── launcher manifest.xml │ │ │ │ ├── register.py │ │ │ │ ├── register.pyc │ │ │ │ ├── rotate.py │ │ │ │ ├── rotate.pyc │ │ │ │ ├── saveopts.py │ │ │ │ ├── saveopts.pyc │ │ │ │ ├── sdist.py │ │ │ │ ├── sdist.pyc │ │ │ │ ├── setopt.py │ │ │ │ ├── setopt.pyc │ │ │ │ ├── test.py │ │ │ │ ├── test.pyc │ │ │ │ ├── upload_docs.py │ │ │ │ └── upload_docs.pyc │ │ │ │ ├── compat.py │ │ │ │ ├── compat.pyc │ │ │ │ ├── depends.py │ │ │ │ ├── depends.pyc │ │ │ │ ├── dist.py │ │ │ │ ├── dist.pyc │ │ │ │ ├── extension.py │ │ │ │ ├── extension.pyc │ │ │ │ ├── gui-32.exe │ │ │ │ ├── gui-64.exe │ │ │ │ ├── gui-arm-32.exe │ │ │ │ ├── gui.exe │ │ │ │ ├── lib2to3_ex.py │ │ │ │ ├── lib2to3_ex.pyc │ │ │ │ ├── package_index.py │ │ │ │ ├── package_index.pyc │ │ │ │ ├── py26compat.py │ │ │ │ ├── py26compat.pyc │ │ │ │ ├── py27compat.py │ │ │ │ ├── py27compat.pyc │ │ │ │ ├── py31compat.py │ │ │ │ ├── py31compat.pyc │ │ │ │ ├── sandbox.py │ │ │ │ ├── sandbox.pyc │ │ │ │ ├── script template (dev).py │ │ │ │ ├── script template (dev).pyc │ │ │ │ ├── script template.py │ │ │ │ ├── script template.pyc │ │ │ │ ├── site-patch.py │ │ │ │ ├── site-patch.pyc │ │ │ │ ├── ssl_support.py │ │ │ │ ├── ssl_support.pyc │ │ │ │ ├── svn_utils.py │ │ │ │ ├── svn_utils.pyc │ │ │ │ ├── tests │ │ │ │ ├── __init__.py │ │ │ │ ├── __init__.pyc │ │ │ │ ├── doctest.py │ │ │ │ ├── doctest.pyc │ │ │ │ ├── environment.py │ │ │ │ ├── environment.pyc │ │ │ │ ├── py26compat.py │ │ │ │ ├── py26compat.pyc │ │ │ │ ├── script-with-bom.py │ │ │ │ ├── script-with-bom.pyc │ │ │ │ ├── server.py │ │ │ │ ├── server.pyc │ │ │ │ ├── test_bdist_egg.py │ │ │ │ ├── test_bdist_egg.pyc │ │ │ │ ├── test_build_ext.py │ │ │ │ ├── test_build_ext.pyc │ │ │ │ ├── test_develop.py │ │ │ │ ├── test_develop.pyc │ │ │ │ ├── test_dist_info.py │ │ │ │ ├── test_dist_info.pyc │ │ │ │ ├── test_easy_install.py │ │ │ │ ├── test_easy_install.pyc │ │ │ │ ├── test_egg_info.py │ │ │ │ ├── test_egg_info.pyc │ │ │ │ ├── test_find_packages.py │ │ │ │ ├── test_find_packages.pyc │ │ │ │ ├── test_markerlib.py │ │ │ │ ├── test_markerlib.pyc │ │ │ │ ├── test_packageindex.py │ │ │ │ ├── test_packageindex.pyc │ │ │ │ ├── test_resources.py │ │ │ │ ├── test_resources.pyc │ │ │ │ ├── test_sandbox.py │ │ │ │ ├── test_sandbox.pyc │ │ │ │ ├── test_sdist.py │ │ │ │ ├── test_sdist.pyc │ │ │ │ ├── test_svn.py │ │ │ │ ├── test_svn.pyc │ │ │ │ ├── test_test.py │ │ │ │ ├── test_test.pyc │ │ │ │ ├── test_upload_docs.py │ │ │ │ └── test_upload_docs.pyc │ │ │ │ ├── version.py │ │ │ │ └── version.pyc │ │ │ ├── site.py │ │ │ ├── site.pyc │ │ │ ├── sre.py │ │ │ ├── sre_compile.py │ │ │ ├── sre_compile.pyc │ │ │ ├── sre_constants.py │ │ │ ├── sre_constants.pyc │ │ │ ├── sre_parse.py │ │ │ ├── sre_parse.pyc │ │ │ ├── stat.py │ │ │ ├── stat.pyc │ │ │ ├── types.py │ │ │ ├── types.pyc │ │ │ ├── warnings.py │ │ │ └── warnings.pyc │ └── local │ │ ├── bin │ │ ├── include │ │ └── lib │ ├── predictX.py │ ├── prediction.py │ └── run.py ├── LICENSE ├── Paper-Scripts ├── Eric │ ├── GEO.replication.RA.r │ ├── QC.sh │ ├── createDGNExprTable.r │ ├── createDGNSNPTables.r │ ├── extract.pl │ ├── gene_location_info │ ├── mapeQTLs.r │ ├── merge.WTCCC.sh │ ├── parseAmbig.sh │ ├── peer.r │ ├── run_mapeQTLs.sh │ └── splitchrom.replication.RA.sh ├── Figures │ ├── Fig1-PrediXcan-Mechanism.pdf │ ├── Fig2-PrediXcan-Framework.pdf │ ├── Fig3_compareR2_h2_en.png │ ├── Fig3_compareR2_h2_en_poly_top.png │ ├── Fig4_DGN_to_GEU_qqR2_R2h2.png │ ├── Fig5_DGNtoGEU_examples.png │ ├── Fig6.png │ ├── Fig7.pdf │ ├── FigS2_ggpairs_DGN-WB_10-fCV_en_SNPplatforms.png │ ├── FigS3_DGN-EN_to_GTEx-pilot.png │ ├── FigS4_cis_v_trans.png │ ├── FigS5.png │ ├── FigS6.png │ ├── FigS7.png │ └── genetically-determined.pdf ├── Files │ └── gencode.v18.genes.patched_contigs.summary.protein ├── Heather │ ├── DGN-calc-weights │ │ ├── 01_imputedDGN-WB_CV_elasticNet.r │ │ ├── 02_imputedDGN-WB_CV_polyscore.r │ │ ├── 03_imputedDGN-WB_calc_topSNP_R2.r │ │ ├── make_run_scripts_01.pl │ │ ├── make_run_scripts_02.pl │ │ └── make_run_scripts_03.py │ ├── DGN-imputation │ │ ├── 01_DGN_pre-impute_QC.sh │ │ ├── 02_DGN-WB_imputation.sh │ │ ├── 03_DGN_vcf2mach.dosage_hapmapSNPs.pl │ │ ├── match_ids.pl │ │ ├── pull_het_outliers.r │ │ └── vcf.filelist.for.sftp │ └── make-figures │ │ ├── Fig3_compareR2_h2_en_poly_top.png │ │ ├── Fig3_compareR2_h2_en_poly_top.tiff │ │ ├── Fig4_DGN_to_GEU_qqR2_R2h2.png │ │ ├── Fig4_DGN_to_GEU_qqR2_R2h2.tiff │ │ ├── Fig5.DGNtoGEU.examples.png │ │ ├── Fig5.DGNtoGEU.examples.tiff │ │ ├── FigS1_ggpairs_DGN-WB_10-fCV_with_topSNP.png │ │ ├── FigS1_ggpairs_DGN-WB_10-fCV_with_topSNP.tiff │ │ ├── FigS2_ggpairs_DGN-WB_10-fCV_en_SNPplatforms.png │ │ ├── FigS2_ggpairs_DGN-WB_10-fCV_en_SNPplatforms.tiff │ │ ├── FigS3_DGN-EN_to_GTEx-pilot.png │ │ ├── FigS3_DGN-EN_to_GTEx-pilot.tiff │ │ ├── PrediXcan_paper_plots.Rmd │ │ ├── PrediXcan_paper_plots.html │ │ ├── calc_GTEx-pilot_obs_pred_R2.r │ │ ├── multiplot.R │ │ └── updatedFigs.tar.gz ├── Kaanan │ ├── PrediXcan_readme.txt │ ├── PrediXcan_with_DGN_WTCCC.pl │ ├── WTCCC_PrediXcan_metaanalysis_overlap.pl │ ├── WTCCC_Summaries.R │ ├── WTCCC_Summaries2.R │ ├── WTCCC_imputation_QCcheck.pl │ ├── prediXcanAssociation_jointimpute.r │ ├── runGWAS2.pl │ ├── runPrediXcan3.pl │ └── vcf_to_dose_hapmap2.pl ├── Keston │ └── PrediX_NHGRI │ │ ├── NHGRI_Bipolar_disorder_noWTCCC.txt │ │ ├── NHGRI_Coronary_heart_disease_noWTCCC.txt │ │ ├── NHGRI_Crohn's_disease_noWTCCC.txt │ │ ├── NHGRI_Hypertension_noWTCCC.txt │ │ ├── NHGRI_Rheumatoid_arthritis_noWTCCC.txt │ │ ├── NHGRI_Type_1_diabetes_noWTCCC.txt │ │ ├── NHGRI_Type_2_diabetes_noWTCCC.txt │ │ └── PrediX_NHGRI.R └── README.md ├── README.md └── Software ├── PrediXcan.py ├── PrediXcanAssociation.R ├── README.md ├── convert_plink_to_dosage.py ├── deprecated ├── R_versions │ ├── predict_gene_expression---datatable.R │ ├── predict_gene_expression---hash.R │ └── predict_gene_expression---iterators.R └── SNP2GReX.pl ├── predict_gene_expression.py 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