dmitrymyl / hlpiensemble

A tool for predicting lncRNA-protein interaction probability from sequences.

Hi there 👋

My name's Dmitry, i'm a PhD student at Gerlich lab, Institute of Molecular Biotechnology, Vienna BioCenter.

My interests

• 🧮 Statistics
• 🧑‍💻 NGS data analysis
• 🧫 Nuclear architecture
• 🐈 Pallas's cats
• ☕ Coffee brewing

Highlighted projects here

• 🧬 BaRDIC — Binomial RNA-DNA Interaction Caller
• 🧑‍💻 ortho2align — lncRNA ortholog discovery tool
• 🔢 corgis — a pack of tools for CORrelation analysis of Genomic Intervals and Signals

hlpiensemble's Issues

Test run with RBPs from literature

Hi,
I have used this great package for predicting interactions for my LncRNAs. I got some significant interactions with the 27 proteins used in another such method LPIDF: https://github.com/plhhnu/LPIDF/tree/main/bioseq2vec/data . I was trying to run hlpiensemble with some RBPs associated with cancer genes in literature. However any protein not among the 27 proteins whe run - gives no significant interaction even with genes it has experimentally validated interactions with. I was wondering if this is because there really is no interaction or if it has something to do with the training dataset. Inputs on this would be really useful for my research .

Thanks and regards,
Prakrithi