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updated 1 month ago

3DSpectra by Sara Nasso

A 3-dimensional quantification algorithm for LC–MS labeled profile data (proteomics, lcms, quantification)

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updated 1 month ago

Management of Accession Numbers and sequences by José Luis Ruiz

A GUI designed to management of big amount of accession numbers. (bioinformatics)

FASTA_MULTIFASTA(varargin)

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updated 1 month ago

MGraph by junbai wang

Probabilistic graphical models for reconstruction of genetic regulatory networks using DNA microarra (statistics, probability, graphical models for ...)

G=MGraph_add_best_edge_to_pat(d,G,sigma,alpha,L,T0,TL)

G=MGraph_remove_worst_edge_in_pat(d,G,sigma,alpha,L,T0,TL)

MGraph_BGscore(d,G)

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updated 5 months ago

Information-based Similarity Toolbox by Albert Yang

Information-based similarity index is an analysis of measuring distance between symbolic sequences (statistical physics, information theory, distance)

binmapping(signal)

checkfiletype(filename)

ibs(wrf1,wrf2)

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updated 5 months ago

Characteristic path length, global and local efficiency, and clustering coefficient of a graph by Nathan Cahill

Computes various graph-theoretic properties related to network connectivity (graph theory, characteristic path l..., global efficiency)

graphProperties( varargin )

exampleScript.m

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updated 6 months ago

shortest_distance_Dijkstra_algorithm.m by Alok Patel

Finds Shortest Distance between nodes using Dijkstra Algorithm. (shortest distance, distance algorithm, dijkstra algorithm)

shortestdistalgo(Weight_matrix,startterminal_matrix,endte...

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updated 6 months ago

Whole Genome Resequencing Pipeline v2.0 by Turner Conrad

Automated mapping and indel realignment of resequencing data (whole genome sequenci..., sequence, sequencing)

WGRSPipeline(reads_file,ref_file)

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updated 6 months 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 7 months 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 7 months 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 8 months 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 12 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 1 year 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 1 year 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 1 year 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 almost 2 years 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 2 years ago

Primer Design GUI by Brett Shoelson

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

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

PrimerDesignGUI(varargin)

gbout=getncbidata(accessnum,varargin)

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updated 2 years 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 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 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 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 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

defcon(ConstantName,Value,Description)

Demo for the User Defined Constants capability in MATLAB

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updated almost 3 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 4 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 4 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 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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updated 4 years ago

SeqLogoFig by Will Dampier

This is a wrapper around the bioinformatics SeqLogo function that creates a REAL matlab figure. (bioinformatics, seqlogo, figure)

SeqLogoFig(SEQ, varargin)

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updated almost 5 years ago

DNAmusic1 - the life music by Nobuo Munakata by Giuseppe Cardillo

convert a mRNA and coded protein sequences into music (data exploration, game)

DNAmusic1(varargin)

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updated almost 5 years ago

DNAmusic2 - The life music by King and Angus by Giuseppe Cardillo

convert a mRNA and coded protein sequences into music (game, data exploration)

DNAmusic2(varargin)

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updated almost 5 years ago

DNAmusic3 - The life music by Takahashi and Miller by Giuseppe Cardillo

convert a mRNA and coded protein sequences into music (data exploration, game)

DNAmusic3(varargin)

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updated almost 5 years ago

Web Deployment Using MATLAB by Todd Flanagan

A web-based gene analysis demonstration using MATLAB Builder for COM (biotech, pharmaceutical, webinar)

applyLogRatio

applyThreshold(threshold)

filterGenes;

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updated almost 5 years ago

M File Computing Rational Coefficiant For Heart VI1 Simulink by Dit Papa Lamine ndao

computing rational coefficiants for heart VI1 simulink-Mfile (biotech, control design, mathematics)

v=pacemaker1VI1

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updated 5 years ago

RefineAlignments by Will Dampier

A tool which can refine a set of multiple alignments to reduce the global alignment score. (bioinformatics, sequence alignment, multialign)

RefineAlignments(IN_ALIGN, varargin)

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updated 5 years ago

Edmonds algorithm by Ashish Choudhary

An implementation of Edmond's algorithm to obtain the maximum spanning weight tree from a graph. (edmonds algorithm, maximum weight tree, maximum branching)

edmonds.m

incidence_to_3n.m

reconstruct_2.m

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updated 6 years ago

View Class Inheritance Hierarchy by Matt Dunham

View inheritance hierarchy of a Matlab OO project (development environme..., class, inheritance)

viewClassTree(directory)

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updated almost 7 years ago

Objective Image Fusion Performance Measure by Richang Hong

Objective Image Fusion Performance Measure (image analysis, image fusion objectiv...)

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updated almost 7 years ago

Modeling Lung Cancer Diagnosis Using Bayesian Network Inference by Paola Favaretto

Pearl's message passing algorithm implementation and application to lung cancer diagnosis (biotech, pharmaceutical, bayes nets)

bnMsgPassCreate(M, values, CPT)

bnMsgPassInitiate(nodes, edges, root)

bnMsgPassNetUpdate(nodes, edges, A, ahat, V, vhat)

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updated 7 years ago

M-File Comput N°1 Of Model Pacemaker VI1 Of All The Cardiac Cells With R2007a by Dit Papa Lamine NDao

it is M-file computing with runge kutta 4 model pacemaker VI1 for all the cardiac cells (simulation, edo, periodic solution)

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updated 7 years ago

EMBLRead by Xindong Song

A modified version of EMBLRead for Reading a EMBL file into a Matlab structure much faster (biotech, pharmaceutical, embl)

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updated 7 years ago

M-File Application OF Model Pcemaker VI1 of Cardiac Cells With Runge Kutta 4 by Dit Papa Lamine NDao

it is M-file of runge kutta 4 of model pacemaker VI1 for all the cardiac cells parametrized (simulation, runge kutta 4, ode)

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updated 7 years ago

plotphytree by Bingley L

PLOTPHYTREE(TREE) renders a phylogenetic tree object into a MATLAB figure as a phylogram. (biotech, pharmaceutical, phylogenetic tree)

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updated 7 years ago

Image Segmenter (tiles) by Nathir Rawashdeh

A simple function to segment an image into square tiles (geometric transformat..., image registration, image segmentation ti...)

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updated almost 8 years ago

Homogeneous Transformation Matrix Function Set by Alessandro Formaglio

A set of 9 functions to extend and simplify usage of Robotics Toolbox by Peter Corke (matrices, roboticsc, kinaematics)

M=sk(vett)

h2r(H)

h2t(H)

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updated 8 years ago

dbSNP tool by Colin Clarke

GUI for the retrieval of single nucleotide polymorphism data from dbSNP (biotech, pharmaceutical, dbsnp)

dbSNP(varargin)

dbsnpTool()

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updated 9 years ago

Seri Fourier Gui by SAYED MEYSAM HOSSEINI

This figure display aspect of seri fourier. (gui tools, example, seri fourier gui)

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