peterlipan / DE_rpy2

Differential expression analysis: DESeq2, edgeR, limma. Realized in python based on rpy2

DE_rpy2

Differential expression analysis: DESeq2, edgeR, limma.

Realized in python based on rpy2

Download R and required libraries

R: https://www.r-project.org/

Libraries: DESeq2, edgeR, limma

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DESeq2")
BiocManager::install("edgeR")
BiocManager::install("limma")

Download python packages

rpy2, matplotlib_venn, matplotlib

pip install -r requirements.txt

Input data format

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'

example

see example