#BioinFormAtics

Hi everyone, I am a 4-5th-year Bioinformatics PhD student in the US, and I am currently feeling quite stuck with my dissertation project. I am hoping to get advice from people who have experience in cancer genomics, somatic mutation analysis, normal…

Hello everyone, I have been using LIANA plus for cell cell communication inference, however i am finding the visualisation toolkit/functions quite lacking, specially for chord circular plots.…

hey everyone.. I was just wondering if anyone here working on ML/DL/AI + drug discovery.. how are you actually doing large scale virtual screening?…

I’ve been wanting to do some bioinformatic analyses for my project, since I think it would make sense. I’m not a bioinformatician at all but I do know how to code a decent bit (although python mostly) and I have read a lot about specific methods,…

I wanted ask if anyone else is getting error 500 when accessing WormBase ParaSite? I have a project on Schistosomes and from what I can tell WBPS is the only repository of the (maybe formerly) up to date genomic bioinformatics on this and related…

Hi, I’m working as a bioinformatician in genetics, and one of my colleagues asked me about creating publication-quality figures for a paper. I haven’t seen the data yet, but I’d also like to start making figures for other colleagues in the future, so I’m…

I am currently work on a manuscript which is about an R package focusing on cancer molecular subtyping and prediction. Besides well-known journals like Bioinformatics, BMC Bioinformatics and Computational and Structural Biotechnology Journal, are there…

Hello everyone! I am reading and diving into single cell foundation models, and have struglling to wrap up my head between masked objective and Next Token Objective in single cell foundation.…

Hi! I want to use AutoDockTools on macOS M series for a molecular docking project, however I cannot manage to load the scripps website, https://autodock.scripps.edu and https://ccsb.scripps.edu/mgltools/downloads/, to access and download/install the…

Hi, I have run harmony (and all pre-normalizing steps) and when I get to RunUmap, my umap is essentially split by seq type. I have ran this data before in different subsets and the flex and sc data has clustered well together.…

Hello! I have been provided with proteomic / phosphoproteomic / scRNA data from various KOs from my lab and was asked to a) provide a clue of what’s happening in the KO b) what are the possible mechanisms explaining the change.…

I got a side project to design qPCR printer sets for several human genome targets, and I already finished designing the primer sets themselves and tested for specificity etc. What I just need is to visualize them in the context of gene structures.…

Hi, I'm a bioinformatician at a research institute processing in-house generated 10X Visium-HD datasets. I've noticed that the microscopy images sometimes have tissue structures that are completely absent from the Cytassist image (including inside the…

Hello guys, I am working in a pharmacy lab in Korea, and we don't have a computer cluster. PI needs me to give her the spec. of a computer that can run protein and antibody in silicon design software locally (such as Boltzgen, RFantibody, RFdiffusion) I…

I love Bioinformatics and computational biology. However, R always drives me nuts. I always face some sort of dependency issue and although I make conda environment in the server but while using my Rstudio in my personal computer, I dont make conda.…

Hello, I'm a third year undergrad, I was accepted as a research intern to a prominent lab at the uni I attend. They told me they needed help with handling some data, I was immediately thrown into the world of bioinformatic transcriptome analysis.…

I followed a 2-part molecular docking tutorial on YouTube by Sanket Bapat exactly protein prep by removing H2O, adding hydrogen and kollman charges grid box is in its automatic state…

Hi everyone, I'd like to predict a protein complex involving a target protein and polyubiquitin chains with covalent linkage. However, our lab does not currently have access to HPC resources or local servers capable of running AlphaFold3.…

What are the salary opportunities after u do bsc in biotechnology and then msc in bio informatics + technology ? submitted by /u/lavishio_ [link] [comments]

I was wondering if anybody here has experience with doing HLA typing from WES BAM data using optitype and how to verify the HLA calls by visualising on IGV? submitted by /u/ZooplanktonblameFun8 [link] [comments]