Python Transcriptomics

Open-source Python projects categorized as Transcriptomics
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Topics: Bioinformatics Python Machine Learning Genomics Data Science
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Top 3 Python Transcriptomic Projects

  • scanpy

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

    • Project mention: Renaming Genes for Scanpy Plot | /r/bioinformatics | 2023-06-15

  • PyDESeq2

    A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

    • Project mention: DESeq2 Normalization | /r/bioinformatics | 2023-06-09

    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.

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  • enrich_omics

    A python package to explore pathways, diseases and drugs associated to a list of targets (genes, proteins, etc)

NOTE: The open source projects on this list are ordered by number of github stars. The number of mentions indicates repo mentiontions in the last 12 Months or since we started tracking (Dec 2020).

Python Transcriptomics related posts

  • Renaming Genes for Scanpy Plot

    1 project | /r/bioinformatics | 15 Jun 2023

  • [Scanpy] Installation issues related to pytables

    1 project | /r/learnpython | 8 Mar 2022

  • standardize/normalize seq data

    1 project | /r/bioinformatics | 17 Jan 2022

  • Flipping one histogram below the axis.

    1 project | /r/matlab | 2 Sep 2021

Index

What are some of the best open-source Transcriptomic projects in Python? This list will help you:

Project Stars
1 scanpy 1,757
2 PyDESeq2 515
3 enrich_omics 17

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