Python rna-seq

Open-source Python projects categorized as rna-seq
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Topics: differential-expression Snakemake Bioinformatics single-cell Python
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Top 7 Python rna-seq Projects

  • RNA-seq-analysis

    RNAseq analysis notes from Ming Tang

  • 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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  • COVID-19-RNA-Seq-datasets

    A repository for sharing information on available COVID-19 RNA-Seq datasets

  • cellSNP

    Pileup biallelic SNPs from single-cell and bulk RNA-seq data

  • diffexpr

    Porting DESeq2 into python via rpy2

  • rna-seq-kallisto-sleuth

    A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

  • zarp

    The Zavolab Automated RNA-seq Pipeline (by zavolanlab)

    • Project mention: Any links to R-scripts for common NGS pipelines? | /r/bioinformatics | 2023-05-11

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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 rna-seq related posts

  • DESeq2 Normalization

    1 project | /r/bioinformatics | 9 Jun 2023

  • How to create VCFs for scRNA-Seq data sets

    1 project | /r/bioinformatics | 16 Mar 2023

  • Pipeline to analyze ATAC seq

    3 projects | /r/bioinformatics | 25 Feb 2023

  • Generate GUIs and deploy bioinformatics workflows with python

    3 projects | /r/bioinformatics | 7 Sep 2022

  • I've been really frustrated with picking the right tools for bulk RNA-seq, so I did a long literature review and wrote this workflow

    3 projects | /r/bioinformatics | 4 Aug 2022

  • What's so special about covid that it needs multiple vaccines and boosters and all these mandates and passports ?

    2 projects | /r/conspiracy | 30 Oct 2021

  • Project ideas

    1 project | /r/bioinformatics | 29 Mar 2021
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    www.influxdata.com | 2 May 2024
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Index

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

Project Stars
1 RNA-seq-analysis 809
2 PyDESeq2 515
3 COVID-19-RNA-Seq-datasets 75
4 cellSNP 69
5 diffexpr 68
6 rna-seq-kallisto-sleuth 63
7 zarp 28

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