GitHub topics: deconvolution

Repositories

SciComp8/NGSOmics_Programming

Computational biology/bioinformatics workflows, codes, and concept notes on NGS data

Language: HTML - Size: 8.3 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 6 - Forks: 0

bdsc-tds/SPLIT

Profile purification of single-cell spatial transcriptomics data

Language: R - Size: 2.97 MB - Last synced at: about 23 hours ago - Pushed at: 1 day ago - Stars: 7 - Forks: 0

Qingyueee/DECLUST

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

Language: Jupyter Notebook - Size: 18.1 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 2 - Forks: 0

BDomzal/magnetstein_x_chemical_reactions

Employing Magnetstein for the analysis of chemical reactions.

Language: Jupyter Notebook - Size: 1.55 GB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 0

unfoldtoolbox/Unfold.jl

Neuroimaging (EEG, fMRI, pupil ...) regression analysis in Julia

Language: Julia - Size: 66.7 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 56 - Forks: 12

smith6jt-cop/KINTSUGI

Jupyter notebook based multiplex image processing pipeline.

Language: Jupyter Notebook - Size: 518 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 7 - Forks: 0

sof202/HyLoRD

A Hybrid Approach for Cell Type Deconvolution in Long-Read (ONT) Methylation Data

Language: C++ - Size: 436 KB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 0 - Forks: 0

sashielvagus/Multimodal-Deconvolution-of-Zebrafish-Gene-Expression-Using-MuSiC-Project

Multimodal project: MuSiC used to process gene expression data using a signature matrix built from single-cell RNA-seq data that defines gene profiles for each cell type. The goal of this project is to use multimodal to quantify how environmental exposures alter gene expression in zebrafish.

Language: R - Size: 9.77 KB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 0 - Forks: 0

WireCell/wire-cell-toolkit Fork of brettviren/wire-cell-toolkit

Toolkit for Liquid Argon TPC Simulation and Reconstruction

Language: C++ - Size: 73 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 7 - Forks: 24

SKYL2R/cleanfm

Implementation of the Dirichlet Kernel Deconvolution algorithm for precise FFT parameter estimation and near-perfect elimination of spectral leakage. Additionally includes the "Cleaned" STFT and the Frequency Modulation Transform. Repository for code contained in Matthew McQuistion's Applied Mathematics Honors Thesis at Brown University

Language: C - Size: 18.8 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 0 - Forks: 0

Lukeli0425/Galaxy-Deconv

Official code for Galaxy Image Deconvolution for Weak Gravitational Lensing with Unrolled Plug-and-Play ADMM

Language: Jupyter Notebook - Size: 4.91 GB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 54 - Forks: 5

Papatheodorou-Group/CATD_snakemake

Snakemake pipeline for benchmarking cell-type deconvolution methods and deconvolving real bulk RNA-seq data with the use of scRNA-seq datasets

Language: R - Size: 27.5 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 15 - Forks: 3

BioimageAnalysisCoreWEHI/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.

Language: Jupyter Notebook - Size: 181 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 13 - Forks: 4

flatironinstitute/CaImAn

Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.

Language: Python - Size: 571 MB - Last synced at: 4 days ago - Pushed at: 15 days ago - Stars: 659 - Forks: 379

matthewmcq/cleanfm

Implementation of the Dirichlet Kernel Deconvolution algorithm for precise FFT parameter estimation and spectral leakage elimination. Repository for code contained in Matthew McQuistion's Applied Mathematics Honors Thesis at Brown University

Language: C - Size: 256 KB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 1 - Forks: 0

HelmchenLabSoftware/Cascade

Calibrated inference of spiking from calcium ΔF/F data using deep networks

Language: Jupyter Notebook - Size: 462 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 140 - Forks: 39

LieberInstitute/DeconvoBuddies

Helper Functions for LIBD Deconvolution

Language: R - Size: 63.3 MB - Last synced at: 3 days ago - Pushed at: about 2 months ago - Stars: 5 - Forks: 1

roflmaostc/DeconvOptim.jl

A multi-dimensional, high performance deconvolution framework written in Julia Lang for CPUs and GPUs.

Language: Julia - Size: 21.1 MB - Last synced at: 5 days ago - Pushed at: 17 days ago - Stars: 64 - Forks: 6

MsMatias/MixturePy

Language: Python - Size: 110 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 0 - Forks: 1

WeisongZhao/Sparse-SIM

Official MATLAB implementation of the "Sparse deconvolution" -v1.0.3

Language: MATLAB - Size: 15.1 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 85 - Forks: 14

SteamedFish6/NextVpower

Next V-Power is a tool for multi-virus lineage demixing from amplicon sequencing data.

Language: Python - Size: 85.1 MB - Last synced at: 23 days ago - Pushed at: 23 days ago - Stars: 0 - Forks: 1

kalidouBA/DICEPRO

Semi-Supervise cellular deconvolution of Bulk RnaSeq using NMF and CiberSortx, DCQ or others

Language: R - Size: 42.2 MB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 2 - Forks: 0

pashtari/deconver

Official PyTorch Implementation of "Deconver: A Deconvolutional Network for Medical Image Segmentation"

Language: Python - Size: 20.5 KB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 4 - Forks: 0

kpreveza/Stimulated-Luminescence

Python scripts to perform deconvolution of stimulated luminescence curves and fitting analysis of dose responce curves.

Language: Python - Size: 319 KB - Last synced at: 2 days ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 1

hjhaghshenas/SMND

Skip-connected autoencoder semi-blind multichannel nonstationary deconvolution (SMND) for seismic data

Language: Python - Size: 17.3 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

vgkavin/Deconvolution--BayesPrism

Deconvolution of bulk RNA seq data using annotated single cell RNA seq dataset as reference

Language: R - Size: 1000 Bytes - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

NathanSkene/EWCE

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

Language: R - Size: 38.3 MB - Last synced at: 27 days ago - Pushed at: 3 months ago - Stars: 57 - Forks: 25

CompEpigen/methylbert

A Transformer-based model for read-level DNA methylation pattern identification and tumour deconvolution

Language: Jupyter Notebook - Size: 3.02 MB - Last synced at: 24 days ago - Pushed at: about 2 months ago - Stars: 27 - Forks: 4

KnutOlaD/Deconv_code_data

Deconvolution of the growth law equation. Theory and experiments published at https://doi.org/10.5194/gi-11-293-2022

Language: Python - Size: 1.35 MB - Last synced at: 29 days ago - Pushed at: 12 months ago - Stars: 3 - Forks: 1

agarnung/image-deblurring-exploration

An attempt to make my mobile phone's camera work

Language: Jupyter Notebook - Size: 29.6 MB - Last synced at: 25 days ago - Pushed at: about 2 months ago - Stars: 2 - Forks: 0

itserphun/CyclicVoltammetryDeconvolution

Language: Jupyter Notebook - Size: 12.7 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

unfoldtoolbox/unfold

A matlab EEG toolbox to perform overlap correction and non-linear & linear regression.

Language: MATLAB - Size: 38.3 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 60 - Forks: 16

msacchi/SeismicLab

Matlab research tools to read, write and process seismic data

Language: MATLAB - Size: 20.8 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 82 - Forks: 20

elgw/deconwolf

Deconvolution of widefield microscopy images and generation of point spread functions

Language: C - Size: 8.74 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 45 - Forks: 2

jolideco/jolideco

A Python package for Poisson joint likelihood deconvolution

Language: Python - Size: 4.14 MB - Last synced at: 14 days ago - Pushed at: 23 days ago - Stars: 8 - Forks: 2

Biomedical-Imaging-Group/DeconvolutionLab2

Java (ImageJ/Fiji) software package for 3D deconvolution microscopy

Language: Java - Size: 2.3 MB - Last synced at: about 1 month ago - Pushed at: about 6 years ago - Stars: 55 - Forks: 15

takushim/momomagick

Python toolkit for 2D/3D image processing using CPU or GPU

Language: Python - Size: 23 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 4 - Forks: 0

Liuy12/SCdeconR

Deconvolution of bulk RNA-seq data using single-cell RNA-seq data as reference

Language: HTML - Size: 38.8 MB - Last synced at: 9 days ago - Pushed at: 10 months ago - Stars: 4 - Forks: 0

alcarbone/S5P_SISR_Toolbox

Sentinel-5P Single-Image Super-Resolution Toolbox

Language: Python - Size: 361 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 6 - Forks: 3

VladKarpushin/out_of_focus_deblur

You will learn how to recover an out-of-focus image by Wiener filter

Language: C++ - Size: 9.83 MB - Last synced at: about 1 month ago - Pushed at: over 6 years ago - Stars: 41 - Forks: 13

manyaafonso/pySENS

Python implementation of optimization methods for inverse problems in imaging.

Language: Jupyter Notebook - Size: 3.32 MB - Last synced at: about 1 month ago - Pushed at: about 2 years ago - Stars: 2 - Forks: 1

KevinMenden/scaden

Deep Learning based cell composition analysis with Scaden.

Language: Python - Size: 1020 KB - Last synced at: about 2 months ago - Pushed at: 6 months ago - Stars: 76 - Forks: 27

yymao/abundancematching

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

Language: Python - Size: 39.1 KB - Last synced at: 26 days ago - Pushed at: 3 months ago - Stars: 6 - Forks: 0

SML-CompBio/ACSCEND

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

Language: Jupyter Notebook - Size: 14.9 MB - Last synced at: 13 days ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

WeisongZhao/SACD

Source code of SACD(Super-resolution with Auto-Correlation two-step Deconvolution)

Language: MATLAB - Size: 27 MB - Last synced at: 27 days ago - Pushed at: over 2 years ago - Stars: 11 - Forks: 4

imcf/hrm_containerization 📦

:crystal_ball::microscope: Installation scripts for setting up the HRM in containers. :truck: :construction: :whale:

Language: Shell - Size: 25.4 KB - Last synced at: 2 months ago - Pushed at: almost 6 years ago - Stars: 1 - Forks: 0

diegommcc/SpatialDDLS

Deconvolution of spatial transcriptomics data based on Deep Learning

Language: R - Size: 131 MB - Last synced at: 3 days ago - Pushed at: 6 months ago - Stars: 5 - Forks: 1

Marzi-lab/CHAS

Cell type-specific Histone Acetylation Score

Language: R - Size: 169 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 3 - Forks: 1

broadinstitute/temporal-rna-seq-deconvolution

Package for temporal deconvolution of bulk RNA-seq samples using SVI

Language: Jupyter Notebook - Size: 22.1 MB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0

eonurk/seAMLess

A single cell transcriptomics based deconvolution pipeline for Leukemia

Language: R - Size: 93 MB - Last synced at: 21 days ago - Pushed at: 5 months ago - Stars: 2 - Forks: 1

LieberInstitute/TREG

Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data

Language: R - Size: 24.1 MB - Last synced at: 3 days ago - Pushed at: 5 months ago - Stars: 4 - Forks: 2

ChristianOrr/feature-attribution-methods-jax

Suite of methods that create attribution maps from image classification models.

Language: Jupyter Notebook - Size: 1.72 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 6 - Forks: 1

jrbourbeau/pyunfold

Iterative unfolding for Python

Language: Python - Size: 6.82 MB - Last synced at: 8 days ago - Pushed at: over 4 years ago - Stars: 27 - Forks: 13

eurunuela/phd

A website version of my PhD dissertation.

Language: JavaScript - Size: 228 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 1 - Forks: 0

bguo068/posseleff_empirical

Nextflow pipeline for analyzing empirical WGS data for the effect of positive selection on IBD-based inference

Language: Nextflow - Size: 2.15 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 0

vgkavin/Deconvolution--ImmuCellAI-Mouse

Deconvoluting mouse Immune cell fractions from Bulk RNAseq data with ImmuCell-AI_mouse

Language: R - Size: 384 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

code-instable/ENSAI-2A-stage-FGAM

ENSAI : Stage 2A - modèles additifs fonctionnels & déconvolution

Language: TeX - Size: 6.44 MB - Last synced at: 4 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 0

XWangLabTHU/ARIC

Accurate and robust inference of cell type proportions from bulk gene expression or DNA methylation data

Language: Python - Size: 820 KB - Last synced at: 21 days ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 3

IHB-IBR-department/BOLD_deconvolution

BOLD signal deconvolution based on ridge regression. Can be used to calculate psycho-physiological interaction (PPI) at the neuronal level. Python and MATLAB functions recover neuronal time series, similar to the Parametric Empirical Bayes (PEB) approach implemented in SPM12 (spm_peb_ppi.m).

Language: Jupyter Notebook - Size: 2.77 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

abarton51/Hyperspectral-Deep-Deconvolution

Project on using deep models for deconvolution of hyperspectral images with chromatic aberration.

Language: TeX - Size: 142 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 1 - Forks: 0

alex-lechner/PyTorch-GAN

Creating artificial images with a Generative Adversarial Network written in PyTorch.

Language: Python - Size: 304 MB - Last synced at: about 1 month ago - Pushed at: over 6 years ago - Stars: 8 - Forks: 8

micsthepick/REAPERDenoiser Fork of Nbickford/REAPERDenoiser

A JSFX denoiser for REAPER based on Norbert Weiner's deconvolution algorithm.

Language: Shell - Size: 22 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 11 - Forks: 0

mdtanker/RIS_basement_sediment

Ross Ice Shelf basement depths and sediment thickness

Language: Jupyter Notebook - Size: 682 MB - Last synced at: 25 days ago - Pushed at: almost 3 years ago - Stars: 9 - Forks: 3

hyeonsangjeon/disparity-based-space-vagriant-image-deblurring

“Disparitybased space-variant image deblurring,” Signal Processing: Image Communication, vol. 28, no. 7, pp. 792–808, 2013.

Size: 20.5 MB - Last synced at: 2 months ago - Pushed at: 8 months ago - Stars: 14 - Forks: 0

mkizilov/TCSPC-Reconvolution

Language: AGS Script - Size: 1.62 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

jebard/ACED

ACED

Language: R - Size: 239 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

Masharipov/TMFC_simulations

Repository for Masharipov, Knyazeva, Korotkov, Cherednichenko & Kireev: "Comparison of whole-brain task-modulated functional connectivity methods for fMRI task connectomics"

Language: Jupyter Notebook - Size: 1.96 GB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 1

jiaweih14/DeepDecon

DeepDecon accurately estimates cancer cell fractions in bulk RNA-seq data

Language: Jupyter Notebook - Size: 846 KB - Last synced at: 9 months ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 1

EliasFink122/Surface_SAXS

Simulate and analyse surface probe small angle xray scattering experiments.

Language: Python - Size: 27.1 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

theislab/hadge

Comprehensive pipeline for donor demultiplexing in single cell

Language: Nextflow - Size: 8.34 MB - Last synced at: 4 months ago - Pushed at: 11 months ago - Stars: 24 - Forks: 6

Paradigm-Free-Mapping/pySPFM

Python version of 3dPFM and 3dMEPFM

Language: Python - Size: 374 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 1 - Forks: 4

Honchkrow/Deconer

Deconer: A Comprehensive and Systematic Cell Type Deconvolution Evaluator

Language: R - Size: 69.5 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

FerreolS/tipi4icy

tipi4icy is a collection of Icy plugins based on TiPi

Language: Java - Size: 2.2 MB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 11 - Forks: 2

LieberInstitute/deconvo_lute-paper

Contains analysis for the lute software paper

Language: HTML - Size: 548 MB - Last synced at: about 2 months ago - Pushed at: 9 months ago - Stars: 1 - Forks: 0

bwmeyers/tauclean

Python implementation of pulse profile scattering deconvolution

Language: Python - Size: 1.09 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 1

csgroen/deconverse

Bulk RNA-seq deconvolution and benchmarking using single-cell reference profiles

Language: R - Size: 581 MB - Last synced at: 10 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0

compneuro-da/rsHRF

rsHRF: A Toolbox for Resting State HRF Deconvolution and Connectivity Analysis (MATLAB)

Language: MATLAB - Size: 104 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 47 - Forks: 15

denniepatton/Keraon

As a tool for cancer subtype prediction, Keraon uses features derived from cell-free DNA (cfDNA) in conjunction with PDX reference models to perform both classification and heterogenous phenotype fraction estimation.

Language: Python - Size: 1.82 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 3 - Forks: 2

cansysbio/ConsensusTME

ConsensusTME Gene Sets and R Script

Language: R - Size: 4.4 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 36 - Forks: 17

pawbz/FocusedBlindDecon.jl

FBD: Multi-channel blind deconvolution with focusing constraints

Language: Julia - Size: 1.52 MB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 7 - Forks: 2

bposantos/Circular_Dichroism_Analysis

Analysis of circular dichroism spectra - deconvolution and plotting

Language: Jupyter Notebook - Size: 32.2 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

danilexn/deCU

Fluorescence microscopy deconvolution scripts, using CUDA. DeltaVision and Zeiss Spinning-Disk formats supported.

Language: Python - Size: 150 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

purbayankar/DeepDeconvResUNet

Landslide segmentation using Deep Deconvolutional Residual UNet

Language: Jupyter Notebook - Size: 144 KB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 9 - Forks: 2

zhampel/pyunfold Fork of jrbourbeau/pyunfold

Iterative unfolding in Python

Language: Python - Size: 2.56 MB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0

Related Keywords

deconvolution 218 image-processing 23 deep-learning 19 deblurring 14 python 13 inverse-problems 12 tensorflow 11 microscopy 11 single-cell 10 single-cell-rna-seq 10 rna-seq 9 convolutional-neural-networks 9 computer-vision 9 neural-network 9 methylation 8 matlab 8 bulk-rna-seq 8 signal-processing 8 fmri 7 pytorch 6 convolution 6 transcriptomics 6 image-restoration 6 r 6 opencv 6 machine-learning 6 calcium-imaging 5 non-negative-matrix-factorization 5 scrna-seq 5 gpu 5 cnn 5 spatial-transcriptomics 5 generative-adversarial-network 5 autoencoder 5 segmentation 5 unet 5 bioinformatics 5 rna-seq-analysis 4 tumor 4 regularization 4 gene-expression 4 imaging 4 immune 4 blind-deconvolution 4 genomics 4 fmri-data-analysis 4 denoising 4 wiener 3 frequency-analysis 3 fft 3 interferometry 3 richardson-lucy 3 bioconductor 3 audio 3 sparse 3 fluorescence 3 super-resolution 3 vgg16 3 classification 3 admm 3 matrix-factorization 3 image-reconstruction 3 blind-source-separation 3 optimization 3 data-analysis 3 jupyter-notebook 3 spectroscopy 3 immunology 3 clustering 3 statistics 3 image 3 psf 3 gan 3 transpose-convolution 3 restoration 3 dataflow 2 uv-vis 2 dnn 2 wiener-filter 2 spectral-unmixing 2 systolic-arrays 2 huygens 2 nmf 2 rnaseq 2 biology 2 nmf-matrix-factorization 2 whole-genome-sequencing 2 registration 2 mcmc 2 noise 2 python3 2 eeg 2 cell-type-deconvolution 2 event-related-potentials 2 julia 2 fluorescence-microscopy-imaging 2 proteomics 2 deep-neural-networks 2 linear-regression 2 edge-detection 2