scanpy
There are 57 repositories under scanpy topic.
scverse/scanpy
Single-cell analysis in Python. Scales to >1M 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.
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.
ebi-gene-expression-group/scanpy-workflow
Workflow leveraging the scanpy-scripts package to run Scanpy in a Nextflow workflow
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
gambalab/scRNAseq_chapter
Review on Single Cell RNA-sequencing
gozsari/Single-Cell-Data-Analysis
Notes and studies about single-cell RNA-Seq analysis
viktormiok/scRNAseq_AdipocyteSubtyping
Python pipelines for analysis of adipocyte scRNA-seq data
becavin-lab/checkatlas
One liner tool to check the quality of your single-cell atlases.
connerlambden/Cube
Intuitive Nonparametric Gene Network Search Algorithm
PMBio/mudatasets
Multimodal datasets, in MuData format
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.
luglilab/NaCl-enhances-CD8-T-cell-effector-functions-in-cancer-immunotherapy
Integration analysis with Scanpy and scRNAseq TME from blueprint
mcrewcow/BaranovLab
Main projects during my current position in Petr Baranov Lab | Schepens Eye Research Institute, Mass General Hospital, Harvard Medical School
Nuwa-genomics/Nuwa
A bioinformatics web app for single cell RNA seq analysis.
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.
adamatasi/IP-Scanner-Ping-
IP Scanner (Ping All IP Addresses in the network)
Harsheen98/scRNA-seq-CWGPM-22
scRNA-seq data analysis using scanpy
KyriakosPsa/BreastCancer-SingleCell
Replication and extension of the single cell RNA-seq analysis paper "Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer"
mouzkolit/NeuroBeginner
Data Science Beginner Course teached Jan 23
YosefLab/treedata
anndata with trees