There are 3 repositories under scanpy topic.
An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
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.
Convert between AnnData and SingleCellExperiment
Bring your single-cell data to life
pseudobulking on an AnnData object
Translates an AnnData object with mouse gene symbols into one with human gene symbols by mapping orthologs from biomart.
This repository extends scanpy to handle flow and mass cytometry data.
Workflow leveraging the scanpy-scripts package to run Scanpy in a Nextflow workflow
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.
An easy-to-use PyTorch implementation of Automatic Cell-Types Identification of single-cell RNA sequencing using Neural Networks (ACTINN)
MiCV is a python dash-based web-application that enables researchers to upload raw scRNA-seq data and perform filtering, analysis, and manual annotation.
Sobolev alignment of deep probabilistic models for comparing single cell profiles
Review on Single Cell RNA-sequencing
Notes and studies about single-cell RNA-Seq analysis
One liner tool to check the quality of your single-cell atlases.
Intuitive Nonparametric Gene Network Search Algorithm
Multimodal datasets, in MuData format
Python pipelines for analysis of adipocyte scRNA-seq data
Transcriptomic analysis of the developing mouse habenula
Reproducible code for the scRNA-seq analyses in the paper 'The neuroendocrine response to stress at single-cell resolution" by Lopez et al. 2020.
IP Scanner (Ping All IP Addresses in the network)
Python readers for different data formats for FASTGenomics.
scRNA-seq data analysis using scanpy
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"
Analysis of a .loom file containing single-cell RNA-sequencing data. Clustering & UMAP embedding using Scanpy, followed by RNA velocity analysis using scVelo.
Integration analysis with Scanpy and scRNAseq TME from blueprint
Main projects during my current position in Petr Baranov Lab | Schepens Eye Research Institute, Mass General Hospital, Harvard Medical School
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.
A bioinformatics web app for single cell RNA seq analysis.