Top 9 Transcriptomic Open-Source Projects

• scanpy

  5 1,768 9.3 Python

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

  

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

• PyDESeq2

  2 518 8.4 Python

  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.

• InfluxDB

  www.influxdata.com featured

  Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

  

• pagoda2

  2 191 5.3 JavaScript

  R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets

  

• bambu

  1 163 5.7 R

  Reference-guided transcript discovery and quantification for long read RNA-Seq data

  

• alevin-fry

  3 153 7.2 Rust

  🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

  

• DNAnalyzer

  4 123 8.1 Java

  Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools

Project mention: I'm approaching 1000 followers! | dev.to | 2023-06-13

P.S. If you haven't checked out my latest project, DNAnalyzer, please do so! It's a groundbreaking open source tool that brings the power of machine learning to DNA analysis. You can find it on GitHub or read more about it here on dev.to. I would love to hear your feedback and suggestions on how to make it better and more useful for everyone.

• cosmosR

  1 53 6.3 R

  COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.

  

• SaaSHub

  www.saashub.com featured

  SaaSHub - Software Alternatives and Reviews. SaaSHub helps you find the best software and product alternatives

  

• enrich_omics

  2 17 3.6 Python

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

• drugfindR

  1 7 9.4 R

  Repository holding the code for the drugfindR R package

  

Transcriptomics related posts

• Renaming Genes for Scanpy Plot

  1 project | /r/bioinformatics | 15 Jun 2023

• RNA VELOCITY

  2 projects | /r/bioinformatics | 1 Dec 2022

• GOterm analysis in Seurat

  1 project | /r/bioinformatics | 6 Aug 2022

• "Surpassing" Go & the near-future of Rust: in what domains will Rust succeed?

  2 projects | /r/rust | 3 Apr 2022

• [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
• A note from our sponsor - SaaSHub
  www.saashub.com | 15 May 2024

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