Skip to content
View sinanugur's full-sized avatar

Organizations

@Gardner-BinfLab @miRTop

Block or report sinanugur

Block user

Prevent this user from interacting with your repositories and sending you notifications. Learn more about blocking users.

You must be logged in to block users.

Please don't include any personal information such as legal names or email addresses. Maximum 100 characters, markdown supported. This note will be visible to only you.
Report abuse

Contact GitHub support about this user’s behavior. Learn more about reporting abuse.

Report abuse
sinanugur/README.md

Hello there 👋

I am a senior bioinformatics research scientist at Department of Pathology, Institute of Clinical Medicine, University of Oslo, Norway and working in the Jahnsen lab. My job profile at Klinmed UiO

  • ⚡ I have been developing open-source bioinformatics tools downloaded by thousands including MirMachine and cellsnake.

  • 🔭 My research interests include biostatistics, bioinformatics, molecular epidemiology, spatial transcriptomics, single-cell and bulk RNA sequencing, early detection of cancer using ML and AI, RNA biology of cancer and RNA-RNA interactions.

  • 🔭 I also have bioinformatics pipelines written in Snakemake (also in Python and R) like a small RNA sequencing pipeline, sncRNA-workflow, or a WGS pipeline for HPV variant detection (TaME-seq)

  • 🌱 I completed my doctoral studies in the fields of Biotechnology and Bioinformatics at the University of Canterbury in New Zealand. My research concentrated on the non-coding RNAs in prokaryotic organisms. The primary emphasis of my dissertation was on the interactions between non-coding RNAs and messenger RNAs within the genomes of bacteria and archaea.

Pinned Loading

  1. MirMachine MirMachine Public

    MirMachine, a command line tool to detect microRNA homologs in genome sequences.

    Python 5 4

  2. cellsnake cellsnake Public

    Cellsnake tool main repo

    Python 33 8

  3. scrna-workflow scrna-workflow Public

    scRNA workflow of Cellsnake

    R 6 1

  4. sncRNA-workflow sncRNA-workflow Public

    A small ncRNA workflow in Snakemake.

    Python 6

  5. LCscripts LCscripts Public

    Lung Cancer scripts for XGBoost training/testing

    Python

  6. RNAseq-variant-calling RNAseq-variant-calling Public

    Python