PyDESeq2 VS diffexpr

Compare PyDESeq2 vs diffexpr and see what are their differences.

PyDESeq2

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA. (by owkin)
Bioinformatics differential-expression Python rna-seq Transcriptomics
Source Code
pydeseq2.readthedocs.io
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diffexpr

Porting DESeq2 into python via rpy2 (by wckdouglas)
rna-seq Python differential-expression
Source Code
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PyDESeq2 diffexpr
2 1
515 68
3.5% -
8.4 2.7
8 days ago 11 months ago
Python Python
MIT License MIT License
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
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PyDESeq2

Posts with mentions or reviews of PyDESeq2. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2023-02-07.
  • DESeq2 Normalization
    1 project | /r/bioinformatics | 9 Jun 2023
    https://github.com/owkin/PyDESeq2/blob/main/pydeseq2/preprocessing.py I'm not sure but only a normalized count matrix seems not enough to do differential expression analysis. For example, in this script, it gathers also the size factor from the raw read count matrix. Maybe you could find it somewhere or recalculate it.
  • When would you use R instead of Python?
    2 projects | /r/bioinformatics | 7 Feb 2023
    PyDESeq2? https://github.com/owkin/PyDESeq2

diffexpr

Posts with mentions or reviews of diffexpr. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2022-02-23.

What are some alternatives?

When comparing PyDESeq2 and diffexpr you can also consider the following projects:

rnaseq - RNA-seq analyses.

rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

scanpy - Single-cell analysis in Python. Scales to >1M cells.

zarp - The Zavolab Automated RNA-seq Pipeline

py-shiny - Shiny for Python

PyDESeq2 vs rnaseq diffexpr vs rnaseq PyDESeq2 vs scanpy PyDESeq2 vs zarp PyDESeq2 vs py-shiny