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updated 1 day ago

Seam Carving with Dijkstra and Dynamic programming by Y Simson

A comparison between two methods (dijkstra, seam carving)

AddSrcAndSink2Graph( G, rows, cols )

calcEnergy(IN , MASK)

calcGradientEnergy(IN , MASK)

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updated 9 days ago

Strand Align App by Turner Conrad

Combine overlapping forward and reverse sequence strands (pcr, sanger, sequence)

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updated 16 days ago

Whole Genome Sequencing Pipeline by Turner Conrad

Automated mapping and indel realignment of WGS FASTQ files (whole genome sequenci..., sequence, sequencing)

WGSPipeline

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updated 16 days ago

A solution to the Maze problem with Dijkstra by Y Simson

Use Dijkstra to find the shortest path to a Maze (dijkstra, maze, graphs)

im2graph(im, varargin)

MazeSolutionWithDijkstra.m

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updated 23 days ago

KEGGParser: parsing and editing KEGG pathway maps in Matlab by Arsen Arakelyan

Matlab graph based tool for KEGG pathway parsing, editing, visualization and analysis (bioinformatics, pathway visualization, graph manipulation an...)

KEGG_parser(varargin)

edge_add(bg,Source, Sink,edge_type)

edge_del(bg, SourceInd, SinkInd)

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updated 1 month ago

Local Reciprocal Blast search by Hengfu Yin

Perform reciprocal blast against two databases to find RBH Orthologs (bioinfromatics recipr...)

RBHsearch.m

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updated 1 month ago

Detection of Period-3 Behavior in F56F11.4 gene Using Singular Value Decomposition by Ismail M. El-Badawy

This code simulates the detection of period-3 behavior in F56F11.4 gene using SVD (genomic signal proces..., dna sequence analysis, singular value decomp...)

[xA xT xC xG]=dna_binary(sample_dna)

main.m

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updated 6 months ago

image connectivity graph - SfM by Bashar Alsadik

This code developed to compute and visualize the connectivity between images in SfM (computer vision, photogrammetry)

H=connectivityplot(W,Tre)

Tre=connectivity(vib,WPK,P)

[vib]=visibilitytesting(Tx,Ty,Tz,w2,p2,k2,P,f,Ro,No)

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updated 6 months ago

Building the component tree in quasi-linear time by Kang Wang

The connected components of the level sets can be organized in a tree structure. (component tree, connected operators, mathematical morpholo...)

buildComponentTree(F)

plotAdjacentTree(nodes, adjs)

demo.m

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updated 7 months ago

Graph-based segmentation of retinal layers in oct images by ted p teng

Demonstration of graph-based segmentation of retinal layers in an optical coherence tomography image (image processing, image segmentation, retina)

octGraphTheorySimplified.m

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updated 8 months ago

Content Based Image Retrieval by Chez

Simple content based image retrieval for demonstration purposes. Either using knn or classification (image retrieval, content based image r..., classification)

L1(numOfReturnedImages, queryImageFeatureVector, dataset)

L2(numOfReturnedImages, queryImageFeatureVector, dataset,...

[obj, overall]=confMatPlot(confMat, opt)

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updated 8 months ago

Significance Analysis of Microarrays (SAM) using Matlab by Eric

SAM is a popular method of finding differentially expressed genes through a microarray experiment. (significance analysis..., sam, gene expression)

bal_perm (seq_samp)

build_dperm (data, cl, type_mt, seq_samp)

d_null (d, type_mt)

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updated 1 year ago

K shortest paths in a graph represented by a sparse matrix (Yen's algorithm) by El-ad David Amir

Determine the K shortest paths from node S to node T. (dijkstra, shortestpath, graph)

graphkshortestpaths.m

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updated 1 year ago

Geometric Gaussian-Kernel Bolstered Error Estimation for Linear Classification by Arsen Arakelyan

This is fast implementation of bolstered error estimation algorithm for linear SVM classification. (linear classification, feature selection, bolstered error estim...)

bolster.m

spherecapbetainc.m

svm(P,T,flag)

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updated 1 year ago

A road to classification in high dimensional space: the regularized optimal affine discriminant by Yang Feng

A powerful method for binary classification in high dimensional space (classification, statistics, optimization)

[Sigma]=eqcor(p,rho)

analyzeReal(traindata, testdata)

lda(x, y, xtest, ytest)

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updated 1 year ago

Multi Class SVM by Cody

Model and classify training/test data sets into more than 2 classes with SVM. (svm, multiclass svm, support vector machin...)

multisvm(TrainingSet,GroupTrain,TestSet)

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updated 1 year ago

Thresholding by Toan

Thresholding for Medical Imaging (thresholding for medi...)

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updated 1 year ago

Primer Design GUI by Brett Shoelson

A GUI for designing primers (primer design, bioinformatics, genbank)

Primer Design GUI

PrimerDesignFcn(sequence,TargetLength,GCRange,TmRange,noS...

PrimerDesignGUI(varargin)

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updated 1 year ago

SCOPE: interactively tabulate SEER excel variables by Rex Cheung

This takes SEER excel column data interactively, tabulate them, write back in table format. (data import, data export, optimization)

output=xls2tabulate2xls(xlsfilename)

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updated almost 2 years ago

Graph manipulation by Arsen Arakelyan

These four files are intended for adding/deleting nodes and edges in biograph object (graphs, graph theory, graph manipulation)

edge_add(bg,Source, Sink, edge_col)

edge_del(bg, SourceInd, SinkInd)

node_add(bg, node_pos, node_size, UserData)

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updated almost 2 years ago

database figure chao heart N°3 for students by Dit Papa Lamine ndao

database figure chao N°3 for students (image processing, signal processing, simulation)

v=pacemaker1VINAIK

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updated almost 2 years ago

Image 3D chao of heart for students by Dit Papa Lamine ndao

database image 3D chao heart (image processing, biotech, signal processing)

v=pacemaker1VI1

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updated almost 2 years ago

NDao's Academic Chao Database figure 1 by Dit Papa Lamine ndao

figures of chao 3D for heart (image processing, signal processing, biotech)

v=pacemaker1VINAIK

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updated 2 years ago

Multi Class Support Vector Machine by Anand Mishra

This function removes out the limitation of MATLAB SVM function of two class and uses more classes. (svm, support vector machin..., multiclass)

multisvm( T,C,test )

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updated 2 years ago

User Defined Constants by John D'Errico

Define your own special constants

Demo for the User Defined Constants capability in MATLAB

defcon(ConstantName,Value,Description)

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updated 2 years ago

Find an ungapped pattern window from a set of protein sequences by Xugang Ye

This program is to find an ungapped pattern window of certain width from a set of protein sequences (bioinformatics, machine learning, dirichlet mixture mod...)

gibbs_script_4_1.m

load_DM_1.m

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updated 2 years ago

MotifCatcher by Phillip Seitzer

a MATLAB GUI platform for determination and evaluation of biologically significant motifs (motif, positionspecific scor..., scoring matrix)

...

MC_CompareOccurrenceAndLocalization(MotifMap)

MC_GetFPDir

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updated almost 3 years ago

Etherneo by Andrey

To run this model you need to download the Ethernet Header Extraction Tool (posted on MATLAB Central (go go)

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updated almost 3 years ago

Exploring Protein-DNA Binding Sites from Paired-End ChIP-Seq Data by Richard Willey

MATLAB code for the "Exploring Protein-DNA Binding Sites from Paired-End ChIP-Seq Data" webinar. (chipseqbioinformatics...)

chipseqdemo.m

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updated almost 3 years ago

periodogram technique by D.K. Ravish Bangre

spectral estimation technique (signal processing)

periodogram.m

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updated 3 years ago

A ODE system associated to PDE Electrical Propagation On Cable by Dit Papa Lamine ndao

PDE electrical propagation (control design, mathematics, optimization)

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updated 3 years ago

Cardiac PDE VI1 And Computing With Matlab-Part1 by Dit Papa Lamine ndao

Cardiac PDE VI1 (control design, mathematics, optimization)

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updated 3 years ago

A Linear Dynamical System Associated To Wave Equation by Dit Papa Lamine ndao

PDE and ODe system (control design, mathematics, optimization)

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updated 3 years ago

Cardiac Chao Vi1 And Strange Attractor-Part1 by Dit Papa Lamine ndao

cardiac chao VI1 and strange attractor (control design, mathematics, optimization)

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updated 3 years ago

Un Système Dynamique Linèaire Associè à l'Equation De La Chaleur by Dit Papa Lamine ndao

PDE et ODE equation (control design, mathematics, optimization)

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updated 3 years ago

Reentrance VI1-file 15 by Dit Papa Lamine ndao

heart VI1 block simulink (biotech, control design)

ReentranceVI115.mdl

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updated 3 years ago

Heart VI1 Block Simulink-file 37 by Dit Papa Lamine ndao

heart VI1 block simulink (biotech, control design)

HEARTVI137.mdl

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updated 3 years ago

Reentrance VI1 Block Simulink-file 14 by Dit Papa Lamine ndao

Heart Vi1 block simulink simulator (biotech, control design)

ReentranceVI114.mdl

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updated 3 years ago

Heart VI1 Block Simulink-file 36 by Dit Papa Lamine ndao

heart Vi1 block simulink (biotech, control design)

HEARTVI136.mdl

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updated 3 years ago

Reentrance VI1 Heart VI1 block simulink-N°13 by Dit Papa Lamine ndao

heart VI1 block simulink (biotech, control design)

ReentranceVI113.mdl

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updated 3 years ago

Heart VI1-block simulink-N°33 by Dit Papa Lamine ndao

heart VI1 block simulink (biotech, control design)

HEARTVI133.mdl

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updated 3 years ago

Reentrance VI1-file 11 by Dit Papa Lamine ndao

heart Vi1 block simulink (control design, biotech, optimization)

ReentranceVI111.mdl

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updated 3 years ago

HeartVI1-31 block simulink investigation by Dit Papa Lamine ndao

heart Vi1 block simulink file 31 (control design, biotech, mathematics)

HEARTVI131.mdl

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updated 3 years ago

Reentrance VI1-10 Heart Vi1 Block Simulink by Dit Papa Lamine ndao

reentrance Vi1-10 heart VI1 block simulink (biotech, control design)

ReentranceVI110.mdl

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updated 3 years ago

HeartVI1-30 Blocks Simulink by Dit Papa Lamine ndao

Heart Vi1 blocks simulink (control design, biotech)

HEARTVI130.mdl

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updated 3 years ago

uidendrogram by Malcolm McLean

Interactive dendrogram viewer using nested boxes (gui, dendrogram, clustering)

drawtree(link, cut, colours, iwidth, iheight)

getleaves( link, id )

testuidendrogram

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updated 3 years ago

intent.m by Peter Cotton

Graphically display mfiles, and naive intent (bioplot, files, functional)

bakery(money)

bioPlot(labels,nodeType,adj)

intent(mfiles)

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updated almost 4 years ago

Heart VI1 simulator simulink Reentrance investigation 8 by Dit Papa Lamine ndao

heart VI1 simulator simulink (biotech, control design)

ReentranceVI18.mdl

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updated almost 4 years ago

HEART VI1 Simulator Simulink Investigation 28 by Dit Papa Lamine ndao

heart VI1 simulink simulator (biotech, control design)

HEARTVI128.mdl

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updated 4 years ago

functor by Peter Cotton

Automated composition of function handles (functional programmin..., function_handle, handle)

bioPlot(labels,nodeType,adj)

function_handle_like

functor

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