Mercurial > repos > vimalkumarvelayudhan > riboplot

annotate README.rst @ 29:fb64b970da25

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Use latest version (0.1.1) from PyPI
author Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
date Fri, 11 Sep 2015 10:19:58 +0100
parents 60bbd8ebe314
children b26c8f3b5aa6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
14
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
1 RiboPlot
18
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
2 ========
14
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
3 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
4
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
5 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
6
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
7 **riboplot**
18
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
8
14
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
9 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
10
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
11 **ribocount**
18
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
12
14
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
13 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
14
18
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
15 Free software: GPL license
14
628f82e72d72 Version as released on PyPI 0.1.0
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 7
diff changeset
16
18
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
17 Documentation: https://riboplot.readthedocs.org
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
18
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
19 Repository: https://github.com/vimalkumarvelayudhan/riboplot
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
20
28
60bbd8ebe314 Working install (virtualenv)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 18
diff changeset
21
60bbd8ebe314 Working install (virtualenv)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 18
diff changeset
22 .. note::
60bbd8ebe314 Working install (virtualenv)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 18
diff changeset
23
60bbd8ebe314 Working install (virtualenv)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 18
diff changeset
24 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
25
28
60bbd8ebe314 Working install (virtualenv)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 18
diff changeset
26 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
27
28
60bbd8ebe314 Working install (virtualenv)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 18
diff changeset
28 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
29
28
60bbd8ebe314 Working install (virtualenv)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents: 18
diff changeset
30 sudo apt-get install bedtools
18
cff63cf0dea8 Update tool_dependencies to install package from pip
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents: 15
diff changeset
31