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)

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...)

svm(P,T,flag)

svmcoefs(svm_struct)

bolster.m

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)

Segmentation of retinal layers in OCT images with graph theory by ted teng

Demonstrates segmentation of retinal layers in OCT images with graph theory. (image processing, graph theory, ophthalmology)

graphkshortestpaths( G, S, T, K )

octGraphTheoryDemo.m

Multi Class SVM by Cody

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

multisvm(TrainingSet,GroupTrain,TestSet)

Primer Design GUI by Brett Shoelson

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

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

PrimerDesignGUI(varargin)

gbout=getncbidata(accessnum,varargin)

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)

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)

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

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

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

v=pacemaker1VI1

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

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. (multiclass svm, multiclass, support vector machin...)

multisvm( T,C,test )

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

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

uidendrogram by Malcolm McLean

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

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

getleaves( link, id )

testuidendrogram

intent.m by Peter Cotton

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

bakery(money)

bioPlot(labels,nodeType,adj)

intent(mfiles)

functor by Peter Cotton

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

bioPlot(labels,nodeType,adj)

function_handle_like

functor

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)

DNAmusic1 - the life music by Nobuo Munakata by Giuseppe Cardillo

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

DNAmusic1(varargin)

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)

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)

Web Deployment Using MATLAB by Todd Flanagan

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

applyLogRatio

applyThreshold(threshold)

filterGenes;

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

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)

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

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)

Fractal visualisation of genomic sequences by Sam Roberts

Visualise n-mer nucleotide sequences using a fractal visualisation based on a Sierpinski gasket. (pharmaceutical, graphics, biotech)

nmervis(sequence,n,varargin)

nmervisdemo.m

View Class Inheritance Hierarchy by Matt Dunham

View inheritance hierarchy of a Matlab OO project (classdef, oop, inheritance)

viewClassTree(directory)

Objective Image Fusion Performance Measure by Richang Hong

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

Qabf(strA, strB, strF)

Modeling Lung Cancer Diagnosis Using Bayesian Network Inference by Paola Favaretto

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

bnMsgPassCreate(M, values, CPT)

bnMsgPassInitiate(nodes, edges, root)

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

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)

v=model1VI1

EMBLRead by Xindong Song

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

data=emblread(embltext,varargin)

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)

v=model1VI1

plotphytree by Bingley L

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

plotphytree(tr,varargin)

Image Segmenter (tiles) by Nathir Rawashdeh

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

imseg(img,Lseg,F)

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)

natural (Hadamard) and dyadic (Paley) ordered fast Hadamard transform by Gylson Thomas

The function implement the 1D natural(Hadamard) and dyadic (Paley) ordered fast Hadamard transform. (transforms, fast hadamard transfo..., 1d)

x=fhtnat(data)

dbSNP tool by Colin Clarke

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

dbSNP(varargin)

dbsnpTool()

Seri Fourier Gui by SAYED MEYSAM HOSSEINI

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

serifouriergui_export(varargin)

Improved GUI for Affymetrix gene expression analysis by Shailender Nagpal

Log transform, Log ratio, Normalization, Filtering, Visualization, Noise reduction, PCA, Clustering (biotech, pharmaceutical, microarray)

cellarray=vec2cell(vector);

maGUI(varargin)

plotmatrix2(varargin)

Absolute and Comparison Analysis for Affymetrix Data by Abram Jujunashvili

Perform single-array and comparison analysis for Affymetrix data given by CEL and CDF files ... (biotech, pharmaceutical, affymetrix)

[bM,nM]=affyBackgrNoise(intensMatrix,varargin)

[bZ,nZ]=affyZoneBackground(intensMatrix,varargin)

affyCdfCel2chp(celStruct,cdfStruct,theID)

GeneralizedLucas.m by David Terr

GeneralizedLucas(n,a,b) returns the generalized Lucas number with index n and parameters a and b. (symbolic math, lucas number, generalized lucas num...)

GeneralizedLucas(n,a,b)

tau.m by David Terr

Given a nonnegative integer n, tau(n) is the Ramanujan tau function of n. (symbolic math, ramanujan tau functio..., modular)

tau(n)

sigma.m by David Terr

Given nonnegative integers k and n, sigma(k,n) is the sum of the kth powers of the divisors of n. (symbolic math, divisor, factor)

sigma(k,n)