imfusion 0.3.2
Tool for identifying transposon insertions in Insertional Mutagenesis screens from gene-transposon fusions using single- and paired-end RNA-sequencing data.
License: MIT license

IM-Fusion
=========

IM-Fusion is a tool for identifying transposon insertion sites in
insertional mutagenesis screens using single- and paired-end RNA-sequencing
data. It essentially identifies insertion sites from gene-transposon fusions
in the RNA-sequencing data, which represent splicing events between the
transposon and endogeneous genes.

IM-Fusion also identifies candidate genes for a given screen using a
statistical test (based on the Poisson distribution) that identifies Commonly
Targeted Genes (CTGs) -- genes that are more frequently affected by insertions
than would be expected by chance. To further narrow down a list of CTGs, which
may contain hundreds of genes, IM-Fusion also tests if insertions in a CTG have
a significant effect on the expression of the gene, which is a strong indicator
of them having an actual biological effect.

IM-Fusion has the following key features:

- It identifies transposon insertion sites from both single- and paired-end
  RNA-sequencing data, without having any special sequencing requirements.
- It uses a gene-centric approach -- both for the identification of insertions
  and for testing of differential expression for identified candidate genes --
  which greatly reduces the number of false positive candidate genes.
- It implements several exon-level and gene-level differential expression
  tests, which provide detailed insight into the effects of insertions on
  the expression of their target  gene(s). By providing both a group-wise and
  a single-sample version of the test, IM-Fusion can identify effects for a
  single insertion in a specific sample, or determine the general
  effect of insertions on a given gene within the tumor cohort.

For more details on the approach and a comparison with existing methods,
please see our manuscript.

Documentation
=============

IM-Fusion's documentation is available at
`nki-ccb.github.io/imfusion <http://nki-ccb.github.io/imfusion>`_.

References
==========

de Ruiter J.R., Kas S.M. *et al.* **"Identifying transposon insertions and their
effects from RNA-sequencing data"** Nucleic Acids Research 2017, *in press*.


License
=======

This software is released under the MIT license.


=======
History
=======

0.3.2 (2017-05-11)
------------------

* Properly added star-fusion support to star aligner (was previously not
  fully merged).
* Changed documentation URLs to new repository.

0.3.1 (2017-05-09)
------------------

* Several small fixes for Python 2.7 compatibility.
* Fixed issue in CTG test that occurs when no insertions are within the
  gene windows.
* Replaced usage of deprecated .ix indexer for pandas DataFrames.
* Updated documentation.

0.3.0 (2017-05-04)
------------------

* Refactored external tools into the ``imfusion.external`` module.
* Use docker/tox for testing against multiple Python versions locally.
* Added additional checks for inputs and improved error messages.
* Added support for DataFrame insertion inputs to DE testing functions.
* Added building of exon gtf as part of imfusion-build.
* Added identification of endogenous fusions using STAR-Fusion as part
  of imfusion-insertions (using STAR). Also adds script for building
  (murine) STAR-Fusion references.
* Made matplotlib/seaborn lazy imports that are only required when actually
  using the plotting functions. This makes IM-Fusion easier to use on
  headless servers/HPCs.

0.2.0 (2017-03-09)
------------------

* Added support for the STAR aligner.
* Added detection of novel transcripts using StringTie.
* Changed reference building to generate a self-contained reference.
* Refactored differential expression tests + added gene-level test.

0.1.0 (2016-03-26)
------------------

* First release on GitHub.