Skip to content

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

License

Notifications You must be signed in to change notification settings

peterlipan/DE_rpy2

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

21 Commits
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

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

About

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

Topics

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published