Isotools

Latest version: v0.3.4

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0.0.2

* Change: refactored SpliceGraph to SegmentGraph to better comply with common terms in literature
* New: added a basic implementation of an actual SpliceGraph (as commonly defined in literature)
* based on sorted dict
* not used so far, but maybe useful in importing the long read bam files since it can be extended easily
* New: added decorators "experimental" and "deprecated" to mark unsafe functions
* Change: in differential splicing changed the alternative fraction, to match the common PSI (% spliced in) definition
* Change: narrowed definition of mutually exclusive exons: the alternatives now need to to feature exactly one ME exon and rejoin at node C
* Change: for ME exons now the beginning of node C is returned as "end" of the splice bubble
* New: differential splicing result contains "novel", indicating that the the alternative is in the annotation
* New: added alternative TSS/alternative PAS to the differential splicing test
* Change: removed obsolete weights from splice graph and added strand
* Change: unified parameters and column names of results of Transcriptome.find_splice_bubbles() and Transcriptome.altsplice_test()
* Fix: add_short_read_coverage broken if short reads are already there.

0.0.1

* first shared version
* New: added option to export alternative splicing events for MISO and rMATS
* New: added change log

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