Differential expression analysis: DESeq2, edgeR, limma.
Realized in python based on rpy2
Libraries: DESeq2, edgeR, limma
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DESeq2")
BiocManager::install("edgeR")
BiocManager::install("limma")rpy2, matplotlib_venn, matplotlib
pip install -r requirements.txt
count matrix:
pandas.DataFrame object. 'id' is a column not index.
| id | sample1 | sample2 | sample3 | sample4 | sample5 | sample6 |
|---|---|---|---|---|---|---|
| gene1 | 808.77 | 878.44 | 1017.81 | 626.82 | 535.66 | 569.03 |
| gene2 | 26.72 | 39.76 | 41.99 | 61.06 | 54.86 | 57.74 |
| gene3 | 46.1 | 64.35 | 74.96 | 67.84 | 63.18 | 66.24 |
design matrix:
sample name as index.
It's OK not to contain this index as you give the conditions in the same order of the samples in count matrix's columns.
| condition | |
|---|---|
| sample1 | treated |
| sample2 | treated |
| sample3 | treated |
| sample4 | untreated |
| sample5 | untreated |
| sample6 | untreated |
design formula:
string. Default= column name of design matrix.
'~ condition'
see example