Package: imfusion
IM-FusionIM-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.DocumentationIM-Fusion’s documentation is available atnki-ccb.github.io/imfusion.Referencesde Ruiter J.R., Kas S.M.et al.“Identifying transposon insertions and their
effects from RNA-sequencing data”Nucleic Acids Research 2017,in press.LicenseThis software is released under the MIT license.History0.3.2 (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 theimfusion.externalmodule.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.