{ "info": { "author": "Julian de Ruiter", "author_email": "julianderuiter@gmail.com", "bugtrack_url": null, "classifiers": [], "description": "IM-Fusion\n=========\n\nIM-Fusion is a tool for identifying transposon insertion sites in\ninsertional mutagenesis screens using single- and paired-end RNA-sequencing\ndata. It essentially identifies insertion sites from gene-transposon fusions\nin the RNA-sequencing data, which represent splicing events between the\ntransposon and endogeneous genes.\n\nIM-Fusion also identifies candidate genes for a given screen using a\nstatistical test (based on the Poisson distribution) that identifies Commonly\nTargeted Genes (CTGs) -- genes that are more frequently affected by insertions\nthan would be expected by chance. To further narrow down a list of CTGs, which\nmay contain hundreds of genes, IM-Fusion also tests if insertions in a CTG have\na significant effect on the expression of the gene, which is a strong indicator\nof them having an actual biological effect.\n\nIM-Fusion has the following key features:\n\n- It identifies transposon insertion sites from both single- and paired-end\n RNA-sequencing data, without having any special sequencing requirements.\n- It uses a gene-centric approach -- both for the identification of insertions\n and for testing of differential expression for identified candidate genes --\n which greatly reduces the number of false positive candidate genes.\n- It implements several exon-level and gene-level differential expression\n tests, which provide detailed insight into the effects of insertions on\n the expression of their target gene(s). By providing both a group-wise and\n a single-sample version of the test, IM-Fusion can identify effects for a\n single insertion in a specific sample, or determine the general\n effect of insertions on a given gene within the tumor cohort.\n\nFor more details on the approach and a comparison with existing methods,\nplease see our manuscript.\n\nDocumentation\n=============\n\nIM-Fusion's documentation is available at\n`nki-ccb.github.io/imfusion `_.\n\nReferences\n==========\n\nde Ruiter J.R., Kas S.M. *et al.* **\"Identifying transposon insertions and their\neffects from RNA-sequencing data\"** Nucleic Acids Research 2017, *in press*.\n\n\nLicense\n=======\n\nThis software is released under the MIT license.\n\n\n=======\nHistory\n=======\n\n0.3.2 (2017-05-11)\n------------------\n\n* Properly added star-fusion support to star aligner (was previously not\n fully merged).\n* Changed documentation URLs to new repository.\n\n0.3.1 (2017-05-09)\n------------------\n\n* Several small fixes for Python 2.7 compatibility.\n* Fixed issue in CTG test that occurs when no insertions are within the\n gene windows.\n* Replaced usage of deprecated .ix indexer for pandas DataFrames.\n* Updated documentation.\n\n0.3.0 (2017-05-04)\n------------------\n\n* Refactored external tools into the ``imfusion.external`` module.\n* Use docker/tox for testing against multiple Python versions locally.\n* Added additional checks for inputs and improved error messages.\n* Added support for DataFrame insertion inputs to DE testing functions.\n* Added building of exon gtf as part of imfusion-build.\n* Added identification of endogenous fusions using STAR-Fusion as part\n of imfusion-insertions (using STAR). Also adds script for building\n (murine) STAR-Fusion references.\n* Made matplotlib/seaborn lazy imports that are only required when actually\n using the plotting functions. This makes IM-Fusion easier to use on\n headless servers/HPCs.\n\n0.2.0 (2017-03-09)\n------------------\n\n* Added support for the STAR aligner.\n* Added detection of novel transcripts using StringTie.\n* Changed reference building to generate a self-contained reference.\n* Refactored differential expression tests + added gene-level test.\n\n0.1.0 (2016-03-26)\n------------------\n\n* First release on GitHub.", "description_content_type": null, "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/nki-ccb/imfusion", "keywords": "", "license": "MIT license", "maintainer": "", "maintainer_email": "", "name": "imfusion", "package_url": "https://pypi.org/project/imfusion/", "platform": "UNKNOWN", "project_url": "https://pypi.org/project/imfusion/", "project_urls": { "Homepage": "https://github.com/nki-ccb/imfusion" }, "release_url": "https://pypi.org/project/imfusion/0.3.2/", "requires_dist": [ "future", 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