Scientific Software
Updated 9 months ago

SCIMAP — Peer-reviewed • Rank 15.7 • Science 95%

SCIMAP: A Python Toolkit for Integrated Spatial Analysis of Multiplexed Imaging Data - Published in JOSS (2024)

Sociology Economics Biochemistry, Genetics and Molecular Biology
Scientific Software · Peer-reviewed
Updated 9 months ago

raer • Rank 12.9 • Science 57%

Characterize A-to-I RNA editing in bulk and single-cell RNA sequencing experiments

Updated 9 months ago

DIscBIO • Rank 14.5 • Science 54%

A user-friendly R pipeline for biomarker discovery in single-cell transcriptomics

Updated 9 months ago

https://github.com/arogozhnikov/demuxalot • Rank 7.8 • Science 49%

Reliable, scalable, efficient demultiplexing for single-cell RNA sequencing

Updated 9 months ago

htsimaging • Rank 5.3 • Science 49%

🔬Python package for high-throughput single-cell imaging analysis.

Updated 9 months ago

harmonypy • Rank 16.5 • Science 33%

🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.

Updated 9 months ago

cytotable • Rank 12.2 • Science 36%

Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools.

Updated 9 months ago

celescope • Rank 14.1 • Science 26%

Single Cell Analysis Pipelines

Updated 9 months ago

dyngen • Rank 12.6 • Science 23%

Simulating single-cell data using gene regulatory networks 📠

Updated 9 months ago

mnnpy • Rank 12.1 • Science 20%

An implementation of MNN (Mutual Nearest Neighbors) correct in python.

Updated 9 months ago

nebulosa • Rank 6.5 • Science 13%

R package to visualize gene expression data based on weighted kernel density estimation

Updated 9 months ago

https://github.com/berenslab/umi-normalization • Science 23%

Companion repository to Lause, Berens & Kobak (2021): "Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data", Genome Biology