org.Mm.egPFAM is defunct. Please use select() if you need access to PFAM or PROSITE accessions.

jaleesr / BITFAM

BITFAM is a Bayesian approach and platform to infer transcription factor activities within individual cells using single cell RNA-sequencing data. Please see Gao S et al., Genome Research (2021) https://genome.cshlp.org/content/31/7/1296 for details.

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org.Mm.egPFAM is defunct. Please use select() if you need access to PFAM or PROSITE accessions. #13

Open Roger-GOAT opened 1 year ago

Roger-GOAT commented 1 year ago

Hi, great package! I run this:

data_matrix_normalized <- BITFAM_preprocess(raw_data = seurat@assays$RNA@counts)
BITFAM_res <- BITFAM(data = data_matrix_normalized, species = "mouse", scATAC_obj = NA, 
                     ncores = 30)

Error in (function ()  : 
  org.Mm.egPFAM is defunct. Please use select() if you need access to PFAM or PROSITE accessions.

I search they said: "Using this form PACKAGE::select() (within rstan) should solve this problem for biology-focused users" , But how to do that? thanks!

gaoshang1102 commented 11 months ago

It seems like a conflict of function names between org.Mm.eg.db and rstan. Please try without import library(org.Mm.eg.db).