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Single Cell Analysis Python Packages

Python packages with the GitHub topic single-cell-analysis. Sorted by relevance, with stars and monthly downloads.
slowkow
harmonypy

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

43K 268 27
labsyspharm
scimap

Spatial Single-Cell Analysis Toolkit

9K 111 36
DingWB
pycomplexheatmap

PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)

8K 383 36
RI-imaging
qpsphere

Python library for spheres in quantitative phase imaging

4K 6 2
singleron-RD
celescope

Single Cell Analysis Pipelines

4K 119 36
EinarOlafsson
spacr

Spatial phenotype analysis of crisp screens (SpaCr)

3K 6 1
cytomining
cytotable

Harmonize high-content image analysis tool outputs for processing with Pycytominer and other Cytomining tools.

3K 19 6
EinarOlafsson
spacr-nightly

Spatial phenotype analysis of crisp screens (SpaCr)

1K 6 0
nadeemlab
spatialprofilingtoolbox

Spatial Multiomics Profiler for Spatial Characterization of Tissue Microenvironment (https://smprofiler.io)

1K 23 2
MannLabs
scportrait

scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images

1K 109 8
rfechtner
pypairs

PyPairs - A python scRNA-Seq classifier

710 3 4
genecell
piaso-tools

Precise Integrative Analysis of Single-cell Omics.

648 6 2
poseidonchan
sctape

deep learning tools for bulk RNA-seq deconvolution and gene expression analysis

599 61 11
genecell
cosg

Accurate and fast cell marker gene identification with COSG

564 59 7
Risitop
transmorph

A unifying data integration framework.

554 11 2
chriscainx
mnnpy

Mutual nearest neighbors correction in python.

424 77 34
genecell
emergene

EMERGENE for individual cell-based differential transcriptomic analysis across conditions.

422 4 0
YYT1002
featuremap

FeatureMAP (Feature-preserving Manifold Approximation and Projection) is an interpratable dimensionality reduction tool.

381 15 1
jhu99
vipcca

single cell integration

344 9 3
xinglab-ai
ccsf

Leveraging cell-cell similarity from gene expression data for high-performance spatial and temporal cellular mappings.

337 1 2
gao-lab
scslat

A graph deep learning based tool to align single cell spatial omics data

206 92 8
genecell
laris

LARIS enables accurate and efficient ligand and receptor interaction analysis in spatial transcriptomics

203 14 1
jfaccioni
scouts

Single Cell Outlier Selector

200 3 0
poseidonchan
sckinetics

Biological prior guided single-cell kinetics inference.

194 7 0
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