scanpy
There are 62 repositories under scanpy topic.
scverse/scanpy
Single-cell analysis in Python. Scales to >100M cells.
scverse/anndata
Annotated data.
zhanghao-njmu/SCP
An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
scverse/muon
muon is a multimodal omics Python framework
CelVoxes/ceLLama
Cell type annotation with local Large Language Models (LLMs) - Ensuring privacy and speed with extensive customized reports
interactivereport/cellxgene_VIP
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.
theislab/anndata2ri
Convert between AnnData and SingleCellExperiment
theislab/ncem
Learning cell communication from spatial graphs of cells
lilab-bcb/cirrocumulus
Bring your single-cell data to life
noamteyssier/adpbulk
pseudobulking on an AnnData object
stefanpeidli/mousipy
Translates an AnnData object with mouse gene symbols into one with human gene symbols by mapping orthologs from biomart.
buettnerlab/pytometry_legacy
This repository extends scanpy to handle flow and mass cytometry data.
ebi-gene-expression-group/scanpy-workflow
Workflow leveraging the scanpy-scripts package to run Scanpy in a Nextflow workflow
gozsari/Single-Cell-Data-Analysis
Notes and studies about single-cell RNA-Seq analysis
Cai-Lab-at-University-of-Michigan/MiCV
MiCV is a python dash-based web-application that enables researchers to upload raw scRNA-seq data and perform filtering, analysis, and manual annotation.
kullrich/orthomap
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.
SindiLab/ACTINN-PyTorch
An easy-to-use PyTorch implementation of Automatic Cell-Types Identification of single-cell RNA sequencing using Neural Networks (ACTINN)
NKI-CCB/sobolev_alignment
Sobolev alignment of deep probabilistic models for comparing single cell profiles
theislab/scanpy-demo-czbiohub
single-cell scanpy teaching
viktormiok/scRNAseq_AdipocyteSubtyping
Python pipelines for analysis of adipocyte scRNA-seq data
gambalab/scRNAseq_chapter
Review on Single Cell RNA-sequencing
becavin-lab/checkatlas
One liner tool to check the quality of your single-cell atlases.
connerlambden/Cube
Intuitive Nonparametric Gene Network Search Algorithm
luglilab/NaCl-enhances-CD8-T-cell-effector-functions-in-cancer-immunotherapy
Integration analysis with Scanpy and scRNAseq TME from blueprint
Nuwa-genomics/Nuwa
A bioinformatics web app for single cell RNA seq analysis.
YosefLab/treedata
anndata with trees
AseenaSulthana/Cyber-Archive
Recon Automation Tool is a Python-based toolkit designed for web penetration testing and reconnaissance. It features IP and port scanning, barcode and QR code generation, password and wordlist creation, phone number information gathering, subdomain checking, and even a DDoS attack simulation tool. Ideal for security professionals.
liekevandehaar/Dev_Hb_mouse
Transcriptomic analysis of the developing mouse habenula
lisafournier/GenomicsProject
Analysis of a .loom file containing single-cell RNA-sequencing data. Clustering & UMAP embedding using Scanpy, followed by RNA velocity analysis using scVelo.
mcrewcow/BaranovLab
Main projects during my current position in Petr Baranov Lab | Schepens Eye Research Institute, Mass General Hospital, Harvard Medical School
mhbsiam/cafe
Cell Analyzer for Flow Experiment
milescsmith/s2a
Seurat to AnnData conversion
PMBio/mudatasets
Multimodal datasets, in MuData format
theislab/HPA_reproducibility
Reproducible code for the scRNA-seq analyses in the paper 'The neuroendocrine response to stress at single-cell resolution" by Lopez et al. 2020.
zehua0417/Juscan.jl
Single-cell data analysis toolkit built with Julia and inspired by Scanpy.