Merge pull request #51 from cmatKhan/develop

adding citations and updating changelog

CHANGELOG

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+# 0.3.0
+
+This is the result of the 2023 hackathon. Current features:
+
+1. The [Coordinate submodule](src/isocomp/Coordinates/) creates windows based 
+on overlapping transcripts in the concatenated set of input sequences
+2. The [Compare submodule](src/isocomp/Compare/) outputs unique transcripts 
+based on first whether they are individual transcripts in a given overlap 
+bin, next whether they have the exact same start/end points, and finally 
+those transcripts which do have the same start/end are pair-wise compared
+3. the command line tools function. On a 16 core machine on DNAnexus, runtime 
+is ~15 minutes with less than 7GB on 16 CPU
+
+## Caveats
+
+1. The output should be considered an intermediate result. It is unparsed and
+not immediately useful to anyone. However, there is good information there
+
+2. We are not conducting exon level coordinate matching on the transcripts. We 
+are therefore doing sequence comparison on transcripts which are not actually 
+the same (eg, transcripts form the same individual with different exon usage), 
+and we are not reporting the wealth of information that we could using the
+interval data alone.
+
+## Future directions
+
+1. The Coordinate submodule should create an interval tree structure from the
+input gtf files using exon coordinates. Exons should be labelled with the 
+transcript and gene IDs
+2. The interval tree can then be used to more finely compare intervals and
+label different TSS/TTS, exon usage, intron retention, etc
+3. The output format(s) must be refined

CITATIONS.md

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+# If you use this repo, please cite:
+
+>Qiu, Y., Liew, C. S., Mateusiak, C., Kesharwani, R., Gu, B., Raza, M. S., Biederstedt, E., Yaman, U., Al Nahid, A., Tat, T., Modha, S., & Kubica, J. (2023). Isocomp. Carnegie Mellon, University of Nebraska-Lincoln, Washington University, Baylor College of Medicine, University of Southern California, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, HMS, UK Dementia Research Institute, University College London, Shahjalal University of Science and Technology, Houston Methodist Research Institute, Theolytics Limited, University of Warsaw. https://github.com/collaborativebioinformatics/isocomp
+
+## Significant dependencies
+
+### BioPython
+
+> Cock, P.J.A. et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 2009 Jun 1; 25(11) 1422-3 https://doi.org/10.1093/bioinformatics/btp163 pmid:19304878
+
+### edlib
+
+>Martin Šošić, Mile Šikić; Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance. Bioinformatics 2017 btw753. doi: 10.1093/bioinformatics/btw753
+
+### PyRanges
+
+> Endre Bakken Stovner , Pål Sætrom, PyRanges: efficient comparison of genomic intervals in Python, Bioinformatics, Volume 36, Issue 3, February 2020, Pages 918–919, https://doi.org/10.1093/bioinformatics/btz615