README.md

In hmumme/finalProjectMUMME: What the Package Does (One Line, Title Case)

finalProjectMUMME

Final Project for BMI585-Spring2022

Hope Mumme ([e-mail])

Provides functions to predict transcription factor and target activities using Seurat (CITE) and ArchR (ATAC)

Installation:

devtools::install_github("hmumme/finalProjectMUMME")

Required Libraries: - Seurat - ArhcR - dplyr - fgsea

Functions:

buildCITE(rna, adt)
getTFs(object, rna.markers, tf.db, num = all)
tfEnrichment(atac.markers, db.filt)
plotEn(atac.markers, db.filt, TF.name)
getProteins(adt.markers, db.filt)
getScale(object, ident)
estProtein(x, object, db.filt, TF.name, ident)
tfBar(est, TF.name)

Demo:

See demo folder with demo.Rmd, demo.html, and demo.pdf for an example workthrough of analysis.

The following data is needed to run the demo: - Gene Set Library ENCODE Transcription Factor Targets Dataset from the Harmonizome portal - fragments files and rds files for BMMC_D1T1, BMMC_D1T2, MPAL1_T1, MPAL1_T2, MPAL2_T1, and MPAL2_T2 samples from GSE139369 on the GEO accession viewer

hmumme/finalProjectMUMME documentation built on April 22, 2022, 12:43 a.m.