bioconductor-condiments

name	bioconductor-condiments
description	This package encapsulate many functions to conduct a differential topology analysis. It focuses on analyzing an 'omic dataset with multiple conditions. While the package is mostly geared toward scRNASeq, it does not place any restriction on the actual input format.

condiments

Workflows

Standard Workflow

Perform differential topology, progression, and fate selection analysis on single-cell data across multiple conditions.

library(condiments)
library(slingshot)
library(dplyr)

# Load toy dataset
data("toy_dataset", package = "condiments")
df <- toy_dataset$sd

# 1. Compute imbalance scores
scores <- imbalance_score(
  Object = df %>% select(Dim1, Dim2) %>% as.matrix(),
  conditions = df$conditions
)
dfscores  scoresscores
dfscaled_scores  scoresscaled_scores


rd  as.matrixdf  
sds  slingshotrd dfcl


top_res  topologyTestsds  sds conditions  dfconditions   


prog_res  progressionTestsds conditions  dfconditions global   lineages  


dif_res  fateSelectionTestsds conditions  dfconditions global   pairwise