scanpy
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Single-cell analysis in Python. Scales to >100M cells.
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Mar 17, 2025 - Python
Annotated data.
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Mar 17, 2025 - Python
An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
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May 21, 2024 - R
muon is a multimodal omics Python framework
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Feb 28, 2025 - Python
Cell type annotation with local Large Language Models (LLMs) - Ensuring privacy and speed with extensive customized reports
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Oct 25, 2024 - R
Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.
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Mar 14, 2025 - Jupyter Notebook
Convert between AnnData and SingleCellExperiment
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Mar 10, 2025 - Python
Learning cell communication from spatial graphs of cells
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Jan 15, 2024 - Python
Bring your single-cell data to life
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Mar 3, 2025 - JavaScript
pseudobulking on an AnnData object
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Mar 14, 2025 - Python
This repository extends scanpy to handle flow and mass cytometry data.
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Aug 5, 2022 - Jupyter Notebook
Notes and studies about single-cell RNA-Seq analysis
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Jul 5, 2022 - Python
MiCV is a python dash-based web-application that enables researchers to upload raw scRNA-seq data and perform filtering, analysis, and manual annotation.
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Jan 23, 2023 - CSS
An easy-to-use PyTorch implementation of Automatic Cell-Types Identification of single-cell RNA sequencing using Neural Networks (ACTINN)
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Jan 23, 2023 - Python
orthomap is a python package to extract orthologous maps (in other words the evolutionary age of a given orthologous group) from OrthoFinder/eggNOG results. Orthomap results (gene ages per orthogroup) can be further used to calculate weigthed expression data (transcriptome evolutionary index) from scRNA sequencing objects.
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Nov 20, 2023 - Python
Sobolev alignment of deep probabilistic models for comparing single cell profiles
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Mar 10, 2025 - Python
Python pipelines for analysis of adipocyte scRNA-seq data
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Feb 20, 2025 - Jupyter Notebook
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