Hello guys! I am a student who recently got into bioinformatics and doing a small project! I am trying to do DEGs of >4 clusters and rank genes by logFC and perform GSEA with Hallmark pathways but I am not sure where to start. If there are any good resources or advice, I would really appreciate it! Thank you!
Hi bioinformatics experts!
I am doing a project but i am struggling with finding parameters to lower the numbers of clusters. I am trying different parameters such as lowering resolution, lambda, and k_geom.
I tried a total of three so far and they all look similar so I decided to make this post to get some ideas of how i can lower the numbers of clusters and make it clear.
Trial1: K_geom 30 and resolution = 0.5
Trial 2: K_geom 30 and resolution = 0.1
Trial3: K_geom10 and resolution = 0.5
Parameters I was told to adjust:
Before running BANKSY, there are two important model parameters that users should consider:
k_geom : Local neighborhood size. Larger values will yield larger domainslambda : Influence of the neighborhood. Larger values yield more spatially coherent domainsI ended up having 44 clusters and I would love to get some insights!
Thank you!