B. Ogan Mancarci

I am a PhD student of bioinformatics in UBC. I work on gene expression in brain cell types and try to extract cell type specific signals from whole brain gene expression data.

Here’s a CV.

Projects

  • NeuroExpresso is my lab’s database cell type specific gene expression. It was released with Mancarci et al. 2017 paper.

  • markerGeneProfile is an R package to infer cell type proportion changes from whole tissue expression profiles. My current work involves improving the reliability of this package and using it on as many whole tissue datasets as I can find.

  • gemmaAPI is an R package that wraps the API for Gemma, our lab’s manually curated gene expression database.

  • ermineR is an R package that wraps ermineJ, our lab’s gene set enrichment tool.

  • allenBrain is an R package that wraps parts of the Allen Brain Atlas API. It focuses on extracting ISH images and syncronization between reference atlases and ISH images.

  • I maintain bunch of other bioinformatics related packages as well. Packages for gene homology and synonym detection, an MRI visualization tool etc. As a bonus, here’s my brain visualized by said tool. Coronal and saggital plane images are inferred using actual images from the axial plane.

Side projects

  • staplr is an R package for PDF manipulation. I contributed its PDF form filling functionality.

  • stockfisher is an R package that allows easy interaction with UCI capable chess engines through R.

  • import5eChar is an R package that reads D&D character data exported from Walter Kammerer’s Fifth Edition Character Sheet and allows automation of character actions and printing PDF character sheets (this is where staplr contributions came from). It also includes a shiny app that acts as an interactive character sheet.

  • printSheetApp is a shiny app that wraps import5eChar’s pdf printing functionality for non-R-users.

  • interactiveSheet is the shiny app that ships with import5eChar package

  • diceSyntax is an R package that supports complex dice rolling syntax such as 10d8d3ro<3. That means roll 10 d8s, reroll anything below 3 once, drop three lowest dice. import5eChar and my other D&D related packages depend on this

  • I wrote this article about statistics of D&D characters submitted to my shiny applications.

  • I maintain other D&D related packages as well.

  • I run a small plumber API. Its main functionality is to create image from texts that are redirected to imgur. Try oganm.com/api/t2img?t=Whatever. Primarily developed for use in Tabletop Simulator.