SCIMAP
SCIMAP: A Python Toolkit for Integrated Spatial Analysis of Multiplexed Imaging Data - Published in JOSS (2024)
raer
Characterize A-to-I RNA editing in bulk and single-cell RNA sequencing experiments
DIscBIO
A user-friendly R pipeline for biomarker discovery in single-cell transcriptomics
pycomplexheatmap
PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)
https://github.com/arogozhnikov/demuxalot
Reliable, scalable, efficient demultiplexing for single-cell RNA sequencing
harmonypy
🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.
cytotable
Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools.
nebulosa
R package to visualize gene expression data based on weighted kernel density estimation
https://github.com/berenslab/umi-normalization
Companion repository to Lause, Berens & Kobak (2021): "Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data", Genome Biology