GitHub

mnnpy - MNN-correct in python!

An implementation of MNN correct in python featuring low memory usage, full multicore support and compatibility with the scanpy framework. Batch effect correction by matching mutual nearest neighbors ...
PNAS

Light controls mesophyll-specific post-transcriptional splicing of photoregulatory genes by AtPRMT5

Photomorphogenesis is a pivotal stage in early seedling growth that begins when the shoot first emerges from the soil and is exposed to light. Here, we investigated the role of post-transcriptional ...
Frontiers

Deciphering tissue heterogeneity from spatially resolved transcriptomics by the autoencoder-assisted graph convolutional neural network

Spatially resolved transcriptomics (SRT) technologies, such as spatial transcriptomics (ST) (Ståhl et al., 2016), 10x Visium, and Slide-seqV2 (Stickels et al., 2021), can measure the transcript ...
Frontiers

scMODD: A model-driven algorithm for doublet identification in single-cell RNA-sequencing data

The input data is preprocessed with the Scanpy package in Python. Starting from the raw gene-cell count matrix, library size normalization is performed to scale the total counts of each cell to be ...
GitHub

SCeptre is a python package that extends the functionalities of Scanpy to analyze multiplexed single-cell proteomics data.

Replication of Schoof et al. Usage is exemplified in the notebooks for the analysis from the mansucript "Quantitative Single-Cell Proteomics as a Tool to Characterize Cellular Hierarchies". The ...
Europe PMC

SCANPY: large-scale single-cell gene expression data analysis.

SCANPY is a scalable toolkit for analyzing single-cell gene expression data. It includes methods for preprocessing, visualization, clustering, pseudotime and trajectory inference, differential ...