Deconvolution Python Packages

hide-deconv

HIDE-Deconv: Interactive command line tool and python package for hierarchical cell type deconvolution and analysis of bulk RNA-seq data.

chatspatial

MCP server for spatial transcriptomics analysis through natural language interfaces.

pyspfm

Blind sparse hemodynamic deconvolution methods for fMRI data

bafpipe

Automated deconvolution of Bruker mass spectra datasets using UniDec

lls-core

Napari plugin for custom analysis and visualization of lattice lightsheet and Oblique Plane Microscopy data. The plugin is optimized for data from the Zeiss lattice lightsheet microscope.

magnetstein

Tools for quantitative analysis of nuclear magnetic resonance (NMR) spectra using the Wasserstein metric.

pyunfold

Iterative unfolding for Python

deconvolawrence

Automated deconvolution of Bruker mass spectra datasets using UniDec

napari-lattice

Napari plugin for custom analysis and visualization of lattice lightsheet and Oblique Plane Microscopy data. The plugin is optimized for data from the Zeiss lattice lightsheet microscope.

flashdeconv

Fast spatial deconvolution via leverage-score sketching — scales to million-spot datasets while preserving rare cell type signals.

scaden

Deep Learning based cell composition analysis with Scaden.

mumfordshah2d

Algorithms for edge preserving smoothing based on the Mumford-Shah model

acscend

A deep learning tool for bulk RNA-seq deconvolution and Stem Cells Sub-Class prediction.

deconversation

DECONVersation uses LLM-derived embeddings to deconvolve bulk RNA-seq data into robust cell type proportions, mitigating batch effects inherent to single-cell reference matrices.

declust

A cluster-based cell-type deconvolution of spatial transcriptomic data (DECLUST)

abundancematching

A Python package for subhalo abundance matching (SHAM) with scatter. It creates abundance functions and runs Peter Behroozi's fiducial deconvolution code.

covidxai

Implementation of explainability algorithms (layer-wise relevance propagation, local interpretable model-agnostic explanations, gradient-weighted class activation mapping) on computer vision architectures to identify and explain regions of COVID 19 pneumonia in chest X-ray and CT scans.

birfi

Blind instrument response function identification from fluorescence decays

hrm-omero

A connector between the Huygens Remote Manager (HRM) and OMERO.

faim-huygens

Tools to interact with SVI Huygens from Python

pydeconv

Python implementation of bulk RNAseq deconvolution algorithms

splora

Sparse and Low-Rank Paradigm Free Mapping.

jolideco

A Python package for Poisson joint likelihood deconvolution