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

Primer Design GUI by Brett Shoelson

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

Primer Design GUI

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

PrimerDesignGUI(varargin)

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)

MSKCC CGDS Cancer Genomics Toolbox by Erik Larsson

Functions for retrieving data from the Cancer Genomics Data Server (CGDS) at MSKCC cBio. (biology, genomics, medical)

cgdstutorial

getcancerstudies(cgdsURL, varargin)

getcaselists(cgdsURL, cancerTypeId, varargin)

a fast method of reading data from PDB files by Evan

This file is a blazingly fast method of reading PDB files (biotech, pharmaceutical, protein data bank)

fastPDBRead(readFile)

Hunt For Local Maxima, Minima, Plateau by Michael Chan

Illustrates identification of local maxima, minima or plateau, for exit criteria for long processes. (bioinformatics, image processing, intensive)

benchmarkSampleFunction (thresholdInitial_Trial)

determineLocationsOfMaximaMinimaPlateauFromProclivityFeatur...

determineProclivity( currentInput, previousInput )

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

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

GSEA2 by Wei Keat Lim

Gene Set Enrichment Analysis (GSEA) for 2 complementary gene sets (bioinformatics)

gsea2(rk,rs,gs1,gs2,np,w)

The Spherical K-means algorithm by Xuan Vinh Nguyen

Clustering on the hypersphere with the Spherical K-means algorithm (kmeans, spherical kmeans, clustering)

[best_x,best_f,best_membership,empty,loop]=SPKmeans(a,K,n_r...

b=normalize_norm(a)

b=normalize_norm_mean(a)

dnaTranslate by Alexander Wallar

This function translates DNA nucleotides into Amino Acids (bio, biology, biotech)

dnaTranslate(dnaVec)

Generate Exhaustive Permutations by Michael Chan

Illustrates generation of exhaustive permutation of symbols given the symbolic bases. (bioinformatics, permutation, combinatorics)

computePermutationSeqForSpecificIndex (bases, lengthOfPermu...

convertIndexRepresentedPermutationsToSymbolPermutations (ma...

generateExhaustivePermutation(bases, lengthOfPermutation)

Calculate Time Interval/ Difference by Michael Chan

To compute time interval, taking into account leap days that are subsumed within that interval. (time, bioinformatics, utility)

DateDiff(T1, T2)

adjustUnits2(upperUnit, lowerUnit, base)

daysinmonth(varargin)

Motif Finding by Michael Chan

Illustrates Combinatorial and Viterbi-akin motif finding. (bioinformatics, probabilistic, combinatorics)

PWM( alignmentSetMatrix )

computeNewPWM_GivenSeqBasedOnPWM (alignmentSetMatrix, motif...

computeProbabilityOfSubsequence(sequenceToBeChecked, probab...

Compute Position Weight Matrix (PWM) and display SequenceLogo in terms of frequency by Michael Chan

Illustrates computation of best match scoring with PWM and constructs sequence logo. (bioinformatics, position weight matri..., match)

PWM( alignmentSetMatrix )

change1colorOnRGBToAnother(rgbImage, FromColor, ToColor)

computeProbabilityOfSubsequence(sequenceToBeChecked, probab...

Burrows-Wheeler Matrix (BWM) Transform by Michael Chan

Illustrates the Burrows-Wheeler Matrix (BWM) Transform. (bioinformatics, string, sort)

BWT (shortGeneStr)

cell2str(c,n,mode)

cell2string( cellString )

Suffix Array by Michael Chan

The objective is to illustrate suffix array computation. This does not include the search operation. (bioinformatics, string, sort)

determineSuffixArray( stringTarget )

usage_determineSuffixArray.m

seqlogo generator by Malcolm McLean

Generates a sequence logo as a true colour array. (seqlogo, sequence logo, dna)

imseqlogo(pwm, width, height)

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)

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)

Application Of Method ODE45 Matlab For Model Pacemaker VI1 Of Cardiac Cells by Dit Papa Lamine ndao

It is application of solving ODe modele pacemaker VI1 of cardiac cells with function ODE45 mat lab (bioinformatics, simbiology, simcardiology)

Genomic signature using FCGR by Jesús P. Mena-Chalco

Genomic signature using Chaos game representation of frequencies. (chaos game representa..., genomic signature, dna)

buildComplementarDNA(sequenceA)

buildDNAStrand(DNAMatrix)

calculateFrecuencies(sequence, word)

plotDNA by Jesús P. Mena-Chalco

A simple Matlab function to visualize DNA sequences using four binary sequences. (dna, plot, binary sequences)

plotDNA(sequence)

test.m

MGWT by Jesús P. Mena-Chalco

Identification of protein coding regions using the Modified Gabor-wavelet transform. (protein coding region, gene, identification)

MGWT(varargin)

ORMA (Oligonucleotide Retrieving for Molecular Applications) by Marco Severgnini

ORMA searches positions within multi-aligned sequences and designs oligonucleotide probes (bioinformatics, biotech)

Designing serial method computing of cardiac partial differential equations VI1,on 1D,2D and 3D by Dit Papa Lamine ndao

To solve cardiac PDe equations i propose *-serie,or x-serie solution V(x,t)=no(t)+n1(t)x+n2(t)*x*x (pde, non linear system pde, cardiac modele of pro...)

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

Taxonomic Annotation of BLAST Reports by Paola Favaretto

Annotate BLAST reports with taxonomic information (blast, biotech, taxonomy)

Annotating BLAST Reports with Taxonomy Information

mapNodeFile(nodeFilenameIn, nodeFilenameOut1, nodeFilenameO...

mapTaxoFile(taxonomyFilenameIn, taxonomyFilenameOut, blockS...

Quantitative High-Throughput Gene Expression Imaging by Sam Roberts

Image Processing for Quantitative Gene Expression Analysis of Drosophila Embryo Images (image processing, bioinformatics, gene expression)

Quantitative High-Throughput Gene Expression Imaging

flyproc(im)

dctflyexdemo.m

dbSNP tool by Colin Clarke

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

dbSNP(varargin)

dbsnpTool()

gethgvbase by Colin Clarke

Extraction of single nucleotide polymorphism data from HGVBASE (biotech, pharmaceutical, bioinformatics)

gethgvbase(SNPID)

MATLAB for Bioinformatics by Kristen Zannella

PowerPoint presentation from the MATLAB for Bioinformatics webinar. (biotech, pharmaceutical, bioinformatics)

General Viterbi Algorithm by Jacob Shin

This function runs Viterbi algorithm given valid parameters and returns optimal path into a file (ou (viterbi, bioinformatics, computational biology)

getViterbi(Ptransition, Pemission, Pinitial, S, SeqTxt)

Gene Expression Colormap by Michael Driscoll

Returns a colormap for visualizing gene expression. (biotech, pharmaceutical, bioinformatics)

C=exp_colormap(colors, N)

PDBRead by Sachin Nikumbh

Read a PDB file into a MATLAB structure. (biotech, pharmaceutical, protein data bank)

PDBRead(filename)