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Linear regression classifier development and application scripts

software
posted on 11.04.2022, 19:49 authored by David Stern, Clair HanClair Han

Code used in the development of the gene-structure based bicycle classifier from H. cornu and it's application to all 22 species from Figure 1 of "Gene structure-based homology search identifies highly divergent putative effector gene family", Stern and Han, BioRxiv https://doi.org/10.1101/2021.09.24.461719.


Classifier development from H. cornu data: Hcor_bicycle_classifier.Rmd

All other files in this folder are input files for this script.

Generates all panels in Fig S2


Application to all 22 species:

bicycle_classifier_outgroup_species.Rmd

All annotation input files can be found on Janelia Figshare at https://doi.org/10.25378/janelia.17777888

Generates classifier bicycle counts in column 3 of Fig 1.


classifier_exon_numVsLength_v5.5.6_revised.Rmd

Generates all panels of Fig S3, whole transcriptome exon counts vs median exon lengths.

Input files available on Janelia Figshare at https://doi.org/10.25378/janelia.17783336 and

https://doi.org/10.25378/janelia.17777888.


Please contact Clair Han at hanc@janelia.hhmi.org with questions.

See related materials in collection at https://doi.org/10.25378/janelia.c.5778905.

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