Mercurial > repos > vimalkumarvelayudhan > riboplot

annotate README.rst @ 28:60bbd8ebe314

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Working install (virtualenv)
author Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
date Wed, 02 Sep 2015 14:25:18 +0100
parents cff63cf0dea8
children fb64b970da25
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
18
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
1 ========
14
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
2 RiboPlot
18
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
3 ========
14
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
4
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
5 .. image:: https://img.shields.io/travis/vimalkumarvelayudhan/riboplot.svg
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
6 :target: https://travis-ci.org/vimalkumarvelayudhan/riboplot
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
7
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
8 .. image:: https://img.shields.io/pypi/v/riboplot.svg
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
9 :target: https://pypi.python.org/pypi/riboplot
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
10
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
11
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
12 RiboPlot includes programs to plot and output Ribo-Seq read counts from an alignment file (BAM format).
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
13
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
14 There are two programs in the package:
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
15
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
16 **riboplot**
18
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
17
14
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
18 Plot and output read counts (csv) for a single transcript.
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
19
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
20 **ribocount**
18
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
21
14
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
22 Output read counts for all transcripts in an alignment.
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
23
18
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
24 Free software: GPL license
14
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
25
18
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
26 Documentation: https://riboplot.readthedocs.org
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
27
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
28 Repository: https://github.com/vimalkumarvelayudhan/riboplot
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
29
28
60bbd8ebe314 Working install (virtualenv)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 18
diff changeset
30
60bbd8ebe314 Working install (virtualenv)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 18
diff changeset
31 .. note::
60bbd8ebe314 Working install (virtualenv)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 18
diff changeset
32
60bbd8ebe314 Working install (virtualenv)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 18
diff changeset
33 RNA coverage plot requires `bedtools <https://github.com/arq5x/bedtools2>`_ to be installed.
14
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
34
28
60bbd8ebe314 Working install (virtualenv)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 18
diff changeset
35 This release of riboplot has been tested with bedtools version ``2.17.0``.
14
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
36
28
60bbd8ebe314 Working install (virtualenv)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 18
diff changeset
37 On Ubuntu and derivatives, bedtools can be installed from the repositories using::
18
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
38
28
60bbd8ebe314 Working install (virtualenv)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 18
diff changeset
39 sudo apt-get install bedtools
18
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
40