scanpy | Topic | Ecosyste.ms: Repos

Topic: "scanpy"

scverse/scanpy

Single-cell analysis in Python. Scales to >100M cells.

Language: Python - Size: 41 MB - Last synced at: 7 days ago - Pushed at: 8 days ago - Stars: 2,082 - Forks: 629

scverse/anndata

Annotated data.

Language: Python - Size: 5.71 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 623 - Forks: 164

cafferychen777/mLLMCelltype

An iterative multi-LLM consensus framework for accurate cell type annotation in single-cell RNA-seq data

Language: Python - Size: 57.9 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 474 - Forks: 43

zhanghao-njmu/SCP

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.

Language: R - Size: 788 MB - Last synced at: 11 months ago - Pushed at: 12 months ago - Stars: 315 - Forks: 66

scverse/muon

muon is a multimodal omics Python framework

Language: Python - Size: 5.05 MB - Last synced at: 3 days ago - Pushed at: 3 months ago - Stars: 235 - Forks: 31

CelVoxes/ceLLama

Cell type annotation with local Large Language Models (LLMs) - Ensuring privacy and speed with extensive customized reports

Language: R - Size: 84.9 MB - Last synced at: 10 days ago - Pushed at: 7 months ago - Stars: 147 - Forks: 6

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.

Language: Jupyter Notebook - Size: 162 MB - Last synced at: 29 days ago - Pushed at: 30 days ago - Stars: 146 - Forks: 49

theislab/anndata2ri

Convert between AnnData and SingleCellExperiment

Language: Python - Size: 241 KB - Last synced at: 1 day ago - Pushed at: 5 days ago - Stars: 132 - Forks: 19

theislab/ncem

Learning cell communication from spatial graphs of cells

Language: Python - Size: 40.8 MB - Last synced at: 17 days ago - Pushed at: over 1 year ago - Stars: 110 - Forks: 13

lilab-bcb/cirrocumulus

Bring your single-cell data to life

Language: JavaScript - Size: 223 MB - Last synced at: 7 days ago - Pushed at: 3 months ago - Stars: 80 - Forks: 17

noamteyssier/adpbulk

pseudobulking on an AnnData object

Language: Python - Size: 21.5 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 29 - Forks: 1

stefanpeidli/mousipy

Translates an AnnData object with mouse gene symbols into one with human gene symbols by mapping orthologs from biomart.

Language: Jupyter Notebook - Size: 14.9 MB - Last synced at: 7 days ago - Pushed at: 7 months ago - Stars: 22 - Forks: 5

buettnerlab/pytometry_legacy

This repository extends scanpy to handle flow and mass cytometry data.

Language: Jupyter Notebook - Size: 282 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 9 - Forks: 1

gozsari/Single-Cell-Data-Analysis

Notes and studies about single-cell RNA-Seq analysis

Language: Python - Size: 9.45 MB - Last synced at: 5 days ago - Pushed at: 29 days ago - Stars: 8 - Forks: 4

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.

Language: Python - Size: 59.1 MB - Last synced at: 26 days ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 1

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.

Language: CSS - Size: 9.3 MB - Last synced at: 5 months ago - Pushed at: over 2 years ago - Stars: 6 - Forks: 0

ebi-gene-expression-group/scanpy-workflow

Workflow leveraging the scanpy-scripts package to run Scanpy in a Nextflow workflow

Language: Nextflow - Size: 53.7 KB - Last synced at: about 1 year ago - Pushed at: about 6 years ago - Stars: 6 - Forks: 1

NKI-CCB/sobolev_alignment

Sobolev alignment of deep probabilistic models for comparing single cell profiles

Language: Python - Size: 3.61 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 5 - Forks: 2

theislab/scanpy-demo-czbiohub

single-cell scanpy teaching

Language: HTML - Size: 9.82 MB - Last synced at: 5 months ago - Pushed at: over 5 years ago - Stars: 5 - Forks: 5

mhbsiam/cafe

Cell Analyzer for Flow Experiment

Language: Python - Size: 4.68 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 4 - Forks: 2

zehua0417/Juscan.jl

Single-cell data analysis toolkit built with Julia and inspired by Scanpy.

Language: Julia - Size: 875 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 4 - Forks: 0

viktormiok/scRNAseq_AdipocyteSubtyping

Python pipelines for analysis of adipocyte scRNA-seq data

Language: Jupyter Notebook - Size: 543 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 4 - Forks: 4

SindiLab/ACTINN-PyTorch

An easy-to-use PyTorch implementation of Automatic Cell-Types Identification of single-cell RNA sequencing using Neural Networks (ACTINN)

Language: Python - Size: 44.5 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 4 - Forks: 3

YosefLab/treedata

anndata with trees

Language: Python - Size: 614 KB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 3 - Forks: 3

becavin-lab/checkatlas

One liner tool to check the quality of your single-cell atlases.

Language: HTML - Size: 51.9 MB - Last synced at: 9 days ago - Pushed at: 6 months ago - Stars: 3 - Forks: 1

Iwo-K/genespector

Language: Python - Size: 4.65 MB - Last synced at: 4 days ago - Pushed at: almost 3 years ago - Stars: 3 - Forks: 2

connerlambden/Cube

Intuitive Nonparametric Gene Network Search Algorithm

Language: Python - Size: 9.72 MB - Last synced at: about 1 month ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 3

NygenAnalytics/CyteType

Agentic Cell type annotation for Anndata objects

Language: Python - Size: 55.7 KB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 2 - Forks: 0

PMBio/mudatasets

Multimodal datasets, in MuData format

Language: Python - Size: 66.4 KB - Last synced at: 29 days ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 1

liekevandehaar/Dev_Hb_mouse

Transcriptomic analysis of the developing mouse habenula

Language: Jupyter Notebook - Size: 57.4 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0

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.

Language: Jupyter Notebook - Size: 1.3 MB - Last synced at: 7 months ago - Pushed at: almost 4 years ago - Stars: 2 - Forks: 0

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.

Language: Jupyter Notebook - Size: 120 MB - Last synced at: 5 months ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 1

kn-bibs/biofuzje-single-cell

Biofuzje Single Cell Workshop

Size: 3.91 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0

GiatrasKon/Gastric-Cancer-scRNAseq-Analysis

Recreation and enrichment of the gastric (GC) cancer single-cell RNA-seq (scRNA-seq) data analysis pipeline described in the "Comprehensive analysis of metastatic gastric cancer tumour cells using single‑cell RNA‑seq" by Wang B. et. al, using the raw counts matrix they provide.

Language: Jupyter Notebook - Size: 19.1 MB - Last synced at: about 2 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 1

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"

Language: Jupyter Notebook - Size: 142 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 0

luglilab/SP025_Analysis

Integration analysis with Scanpy and scRNAseq TME from blueprint

Language: Jupyter Notebook - Size: 256 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0

milescsmith/s2a

Seurat to AnnData conversion

Language: Python - Size: 5.58 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

mcrewcow/BaranovLab

Main projects during my current position in Petr Baranov Lab | Schepens Eye Research Institute, Mass General Hospital, Harvard Medical School

Language: Jupyter Notebook - Size: 64.9 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 1

mouzkolit/NeuroBeginner

Data Science Beginner Course teached Jan 23

Language: Jupyter Notebook - Size: 47.3 MB - Last synced at: 2 months ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

Harsheen98/scRNA-seq-CWGPM-22

scRNA-seq data analysis using scanpy

Language: Jupyter Notebook - Size: 15.7 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 1

stefanie-baerthel/combinatorial_treatment_analysis

KRAS-mutant pancreatic ductal adenocarcinoma (PDAC) is highly immunosuppressive and resistant to targeted therapies, immune checkpoint blockade and engineered T cells. In this study, we performed a systematic high throughput combinatorial drug screen and identified a synergistic interaction between the MEK inhibitor trametinib and the multi- kinase inhibitor nintedanib. Using single cell RNA sequencing and immunophenotyping, we show that the combination therapy reprograms the immunosuppressive microenvironment and primes cytotoxic and memory T cells to infiltrate the tumors, thereby sensitizing mesenchymal PDAC to PD-L1 inhibition.

Language: Jupyter Notebook - Size: 70.7 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

FASTGenomics/fgread-py

Python readers for different data formats for FASTGenomics.

Language: Python - Size: 107 KB - Last synced at: 19 days ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 1

gambalab/scRNAseq_chapter

Review on Single Cell RNA-sequencing

Size: 17.1 MB - Last synced at: almost 2 years ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 2

mcrewcow/Yizhen_microglia

collab | DFC

Language: Jupyter Notebook - Size: 4.85 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 0 - Forks: 1

malbiruk/plotly_for_scanpy

A collection of Plotly-based functions to visualize Scanpy data mimicking functions from scanpy.pl package.

Language: Python - Size: 94.7 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

YosefLab/pycea

scverse lineage tracing analysis toolkit

Language: Python - Size: 601 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 1

kris96tian/scRNA-WebApp

Interactive web application for analyzing scRNA-seq data using Scanpy

Language: Python - Size: 12.7 KB - Last synced at: 13 days ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

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.

Language: Python - Size: 3.91 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

kris96tian/sc-RNAseq_analysis

Single-cell RNA data analysis using R (Seurat) , Python (Scanpy), and Julia.

Language: Jupyter Notebook - Size: 4.53 MB - Last synced at: 13 days ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

kaderhoussein/sc_oop

Interactive diffusion map for Single-Cell Data Analysis

Language: Python - Size: 2.55 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

Nuwa-genomics/Nuwa

A bioinformatics web app for single cell RNA seq analysis.

Language: Python - Size: 431 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

ch1ru/Nuwa

A bioinformatics web app for single cell RNA seq analysis.

Language: Python - Size: 429 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

mcrewcow/Sun_Ye_microglia_macrophages_paper

Socs3/Spp1 Project on Microglia in OIR | Ye Sun Lab Collaboration Project | Boston Children's Hospital

Language: Jupyter Notebook - Size: 9.85 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 1

karan-nanda/SquidPy

Explore spatial organization of a mouse brain coronal section with Scanpy and Squidpy in this GitHub repository. Analyze cell interactions, visualize distributions, and uncover patterns using various data exploration and spatial analysis techniques.

Language: Jupyter Notebook - Size: 15.5 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

karan-nanda/Spatial-RNA-Analysis

This project employs Scanpy in Python for analyzing spatial transcriptomics data, encompassing preprocessing, quality control, clustering, and marker gene identification, resulting in informative visualizations to reveal gene expression patterns and cellular interactions within tissue samples.

Language: Jupyter Notebook - Size: 2.9 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0