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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 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 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 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 1 year ago

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)

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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

batch download GEO data (samples/series) by Sisi Ma

This file batch download files from NCBI GEO according to a list of urls. (bioinformatics, geo, data download)

batch_download_geo_data(url_list,savepath)

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updated 1 year ago

GEO Platform Annotation Table Reader by Sisi Ma

reads and parses platform annotation table (*.annot) from GEO. (bioinformatics, geo, data import)

[annotation, platform_table]=read_annot_file(filename)

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updated 1 year ago

read and write CAD Data files using matlab (DX format) by Evan

read and write CAD data in a DX format (bioinformatics, biotech, pdb)

dx2mat(readFile)

mat2dx(DXdata)

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updated 1 year ago

read and write PDB files using matlab by Evan

These two programs accept and output a variety of PDB file-formatted data (bioinformatics, biotech, pdb)

mat2pdb(input)

pdb2mat(readFile)

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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 2 years 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 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

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)

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updated 2 years ago

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)

determineLocationsOfMaximaMinimaPlateauFromProclivityFeat...

determineProclivity( currentInput, previousInput )

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updated almost 3 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 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 almost 3 years ago

GSEA2 by Wei Keat Lim

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

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

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updated 3 years ago

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...

b=normalize_norm(a)

b=normalize_norm_mean(a)

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updated 3 years ago

dnaTranslate by Alexander Wallar

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

dnaTranslate(dnaVec)

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updated 3 years ago

Generate Exhaustive Permutations by Michael Chan

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

computePermutationSeqForSpecificIndex (bases, lengthOfPer...

convertIndexRepresentedPermutationsToSymbolPermutations (...

generateExhaustivePermutation(bases, lengthOfPermutation)

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updated almost 4 years ago

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)

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updated almost 4 years ago

Motif Finding by Michael Chan

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

PWM( alignmentSetMatrix )

computeNewPWM_GivenSeqBasedOnPWM (alignmentSetMatrix, mot...

computeProbabilityOfSubsequence(sequenceToBeChecked, prob...

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updated almost 4 years ago

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, prob...

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updated almost 4 years ago

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 )

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updated 4 years ago

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

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updated 4 years ago

seqlogo generator by Malcolm McLean

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

imseqlogo(pwm, width, height)

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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 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

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)

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updated 5 years ago

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.m

calculateFrecuencies(sequence, word)

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updated 5 years ago

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

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updated 5 years ago

MGWT by Jesús P. Mena-Chalco

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

MGWT(varargin)

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updated 5 years ago

ORMA (Oligonucleotide Retrieving for Molecular Applications) by Marco Severgnini

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

MeTeBaSS.m

ORMA()

[cons_seq,score]=consensus_revised(seqs_in,type,thres,thr...

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updated 5 years ago

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...)

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updated 7 years ago

Taxonomic Annotation of BLAST Reports by Paola Favaretto

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

Annotating BLAST Reports with Taxonomy Information

mapNodeFile(nodeFilenameIn, nodeFilenameOut1, nodeFilenam...

mapTaxoFile(taxonomyFilenameIn, taxonomyFilenameOut, bloc...

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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 8 years ago

gethgvbase by Colin Clarke

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

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updated 8 years ago

General Viterbi Algorithm by Jacob Shin

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

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updated almost 10 years ago

Gene Expression Colormap by Michael Driscoll

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

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