Deconvolution Python Packages

chatspatial

MCP server for spatial transcriptomics analysis through natural language interfaces.

spxtacular

Chainable Spectrum API for MS processing: denoising, isotope deconvolution, matching, scoring, plotting

deeppeak

Python toolkit for peak detection and analysis in 1D signals, with classical methods, neural deconvolution, and synthetic data generation.

pyspfm

Blind sparse hemodynamic deconvolution methods for fMRI data

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.

flashdeconv

Fast, deterministic cell-type deconvolution for million-bin spatial transcriptomics

deconversation

DECONVersation is a tool designed for the deconvolution of bulk RNA-seq data using embeddings derived from large-scale, LLM-based foundation models. DECONVersation produces robust cell type proportions by leveraging these high-dimensional embeddings to eschew explicit marker selection and mitigate batch effects typically present in single-cell reference signature matrices.

iobrx

Bit-exact, multithreaded Python+Rust acceleration layer for IOBRpy — CIBERSORT, signature scoring, TPM, EPIC, quanTIseq, MCP-counter, ESTIMATE at 23–26× speed with bit-identical outputs

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.

pyunfold

Iterative unfolding for Python

deconvolawrence

Automated deconvolution of Bruker mass spectra datasets using UniDec

scaden

Deep Learning based cell composition analysis with Scaden.

magnetstein

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

acscend

Comprehensive Enumeration of Cancer Stem-like Cell Heterogeneity Using Deep Neural Network

bafpipe

Automated deconvolution of Bruker mass spectra datasets using UniDec

mumfordshah2d

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

abundancematching

A Python package for subhalo abundance matching (SHAM) with scatter.

tpxlab

Reproducible analysis and global deconvolution of TPR, TPD and TPO data.

hrm-omero

A connector between OMERO and a Huygens Remote Manager (HRM) server. [ARCHIVED]

declust

A cluster-based cell-type deconvolution of spatial transcriptomic data

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

faim-huygens

Tools to interact with SVI Huygens from Python

splora

Sparse and Low-Rank Paradigm Free Mapping.