Posts
- Category: Image Analysis (continued)
- WinFluor 4.1.6 - Fluorescence Imaging & Electrophysiology Analysis Program
- Xmipp 3.1 - X-Windows-based Microscopy Image Processing Package
- YeastSpotter 2.1 - Yeast Segmentation Web Tool
- YouScope 2.1.0 - Open-source Microscope Control software
- ZebIAT 1.0 - Zebrafish Image Analysis Tool
- ZeissToSGI 1.1 - Convert Zeiss AxioVision TIFF files to files that can be read by SoftWoRx
- ZEN 2012 Lite - Free of Charge Digital Image Software
- ZFIQ 1.0 - Quantitative Zebrafish Image Analysis
- Category: Microarray Analysis
- A-MADMAN 1.4 - Annotation-based Microarray Data Meta-ANalysis tool
- AACK 1.0 - Add Annotation
- ACME 2.46.0 - Algorithms for Calculating Microarray Enrichment
- activeTF - Identify coordinately activated Transcription Factors
- ADGO 2.0 - Interpreting Microarray data and list of Genes using Composite Annotations
- AffyExtensions 0.8-2 - Analyze Affymetrix data
- AffyGCQC 1.02 - GeneChip Data Quality Control
- affylmGUI 1.66.0 - Affymetrix linear modeling Graphical User Interface
- AffyMAPSDetector 1.0 - Affymetrix MicroArray Probe SNP Detector
- Affymetrix_Error_Rate 20111004 - Identify the Error Rate in files of Affymetrix microarray SNP data
- affyParaEBI 1.0.0 - Preprocessing of Microarray Experiments
- AffyProbeMiner 1.0 - Computing or Retrieving Accurately Redefined Affymetrix probe sets
- AffyRNADegradation 1.38.0 - Analyze and Correct Probe Positional Bias in Microarray data due to RNA Degradation
- AIM 0.82 - Automatic Image Processing for Microarrays
- ALEXA 1.1 - Microarray Design platform for 'Alternative Expression Analysis'
- AltAnalyze 2.1.4.3 - Microarry and RNA-Seq Analysis
- AMIADA 2.0.7 - Analysis of Microarray Data
- AnovArray 1.1 - SAS macros for Analysing Microarray- and Macroarray-type Expressional data
- AnyExpress 1.0 - an integrated Toolkit for Cross-platform Gene Expression data
- aroma.affymetrix 3.2.0 - Open-source R framework for your Microarray Analysis
- Array Design - The efficacy of the KLab interspecies tiling program
- Array Tools 3.3 - Dictyostelium Discoideum Microarray Data Analysis
- ArrayCluster 1.0 - Mixed Factors Analysis of Microarray Gene Expression Data
- ArrayExpress 1.52.0 - Functional Genomics data
- ArrayGene 0.3 - Analysis of Genome Centered Microarray Annotation Information
- aRrayLasso - Network-based Approach to Microarray Interconversion
- ArrayMaker 2.6 - Provides Robotic Control of Microarrayer Robots
- ArrayMiner 5.3 - Microarray Gene Expression Data Analysis
- ArrayMining - Online Microarray Data Mining
- ArrayNorm 1.7.6 - Normalisation and Statistical Analysis for Microarray-experiment data
- ArrayOligoSelector 3.8.4 - Design Gene Specific Long Oligonucleotide Probes
- ArrayOme 1.0 - Estimate the sizes of Microarray-visualised Bacterial Genomes
- ArrayPipe 1.7 - Processing & Analysis of Microarray Data
- ArrayPlex 1.0.3 - Flexible Toolsets for Functional Genomics
- Arrayplot 3.01 - Visalisuation and Normalisation of Microarray data
- ArrayTrack 3.5.0 — Microarray Database, Data analysis & Interpretation tool
- ArrayXPath - Biological Pathway-based analysis of Gene Expression data
- ARSyN - Multivariate approach to Correct Batch Effects in Multifactorial Gene Expression datasets
- artefactCorrection 1.1 - Detection and Correction of Probe-level Artefacts on microarrays
- ASC 0.1.4 - Empirical Bayes method to detect Differential Expression
- Asterias - Applications for the Analysis of Gene Expression and aCGH data
- ASTRO - Analysis of Short Time-series using Rank Order preservation
- AutoIdeogram 20150224 - Displaying Autozygous Regions against an Ideogram
- AVF-filter 2.4 - Find Noisy Datasets, Measure Periodicity of Gene Expression
- Babelomics 5 - Gene Expression and Functional Profiling Analysis Suite
- BADGE 1.0 - Bayesian Analysis of Differential Gene Expression
- BAGEL 4.1.1 - Bayesian Analysis of Gene Expression Levels
- BASE 3.18.2 - Microarray Data Management & Analysis
- BATEx 0.1.2 - A Data Warehouse for Array-based Gene Expression Data of Plants
- BATS 20080710 - Bayesian Analysis of Time Series Microarray experiments
- BeadArray 2.42.0 - Analysis package for Illumina BeadArray data
- BEST 1.0 - Bayesian Expression Search Tool
- Better Bunny 3.0 - Functional Annotation for Rabbit Gene
- BGX 1.58.0 - Bayesian integrated analysis of Affymetrix GeneChips
- BicOverlapper 2.0 - Visual Analysis of Gene Expression
- BioconductorBuntu - Web-Based DNA Microarray Analysis Server
- BioProspector 2004 - Find Enriched Sequence Motifs
- BIOSAP 0.1.7 - Generate Oligos for the Inkjet Arrayer
- BMIQ 1.4 - Beta Mixture Quantile Model
- BRB-ArrayTools 4.6.2 - Visualization & Analysis of DNA Microarray Gene Expression Data
- BTW 1.0 - Web Server for Gene Expression Time series Boltzmann Time Warping
- CAFE 1.28.0 - Detection of Gross Chromosomal Abnormalities from Gene Expression Microarray data
- CAGED 1.1 - Cluster Analysis of Gene Expression Dynamics
- CalMaTe 0.12.1 - Improved Allele-Specific Copy Number of SNP Microarrays for Downstream Segmentation
- CARMAweb 1.3 - R- and Bioconductor-based web service for Microarray Data Analysis
- Caryoscope 0.4.0 - View Gene Expression Data in Genome
- CCACK 1.0 - Constant Cutoff Analysis
- ChAMP 2.16.1 - Chip Analysis Methylation Pipeline for Illumina HumanMethylation450
- chipchipnorm 1.0.1 - Normalize 2-color Microarray Data
- chipD 1.0 - Design Oligonucleotide Probes for high-density Tiling Arrays
- ChipInspector 2.1 - Microarray Data Analysis
- ChIPMonk 1.2.3 - Visualise and Analyse ChIP-on-chip Array data
- ChIPOTle 2.0 - Tool For The Analysis Of ChIP-chip Data
- ChIPpeakAnno 3.24.2 - Annotate ChIP-seq and ChIP-chip data
- ChIPper - Analysis of ChIP-chip data
- ChipSkipper 2.0 - Microarray Image analysis
- ChroMap 0.81a - A tool for Viewing and Analysis of CGH-data
- ChromoViz 1.1 - Visualization of Gene Expression data onto Chromosomes
- CHROMOWAVE 1.0 - Microarrays Data Analysis
- CIST - Analysis of Gene Expression data Generated using SAGE
- Cluster 3.0 20190830 - Enhanced Version of Cluster
- CMARRT 1.3 - Analysis of ChIP-Chip data from Tiling Arrays
- cn.FARMS 1.34.0 - Factor Analysis for Copy Number Estimation
- CNAnova 1.0 - Identify Recurrent Regions of Copy Number Changes
- CNIT 5.1 - Copy Number Inferring tool
- COCAS 2.4 - ChIP on Chip Analysis Suite
- CoCo v2.0.1 - Search, Visualise and Store different data associated with Gene Expression
- COMODO 2.0 - Identify Conserved Coexpression Modules between Organisms
- compdiagTools 1.5.3 - A Toolbox for Microarray Analysis
- CopyNumber450kCancer 1.0.4 - Baseline Correction for Copy Number Data from Cancer Samples
- Correlate 1.03 - Integrative Analysis of 2 Genomic Data Sets
- CpGassoc 2.60 - Analysis of DNA Methylation Microarray data
- CRCView 20070312 - Web-based Microarray data analysis and Visualization system
- crlmm 1.48.0 - Genotype Calling and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays
- Csbl.go 1.4.1 - Gene Ontology based Clustering using semantic Similarity
- CUDA-MI 20110425 - Speedup over Sequential Multi-threaded Implementation
- Cyber-T - Software and Server for Analysis of DNA Microarray data
- D2CMA 0.1 - Design 2 Color MicroArrays
- Dapple 0.88pre4 - DNA Microarrays Image Analysis
- dChip 2011.12 - Analysis & Visualization of Gene Expression & SNP Microarrays
- dCoxS - Biological Interpretation of Paired Gene Sets
- Decision Forest 2 - Novel Pattern Recognition method for multiclass Classification in Microarray data analysis
- decode 1.2 - Differential Co-Expression and Differential Expression Analysis
- degPrune 1.0 - Density based Pruning for Identification of Differentially Expressed Genes
- DetectiV 1.2 - Analysis of Pathogen Detection Microarray data
- DICER - Differential Correlation in Expression for meta-module Recovery
- dictyExpress 1.5 - Dictyostelium Gene Expression Analysis
- dipSFP 1.0 - SFP Detection based on Dip Statistic
- Diurnal 2.0 - Mining and Viewing Diurnal and Circadian Microarray data for Arabidopsis thaliana, poplar, and rice
- DNA-CHIP CAD - DNA Array Design
- DSection - Probabilistic Analysis of Gene Expression Measurements from Heterogeneous Tissues
- DWD - Perform Systematic Bias Adjustment in microarray data.
- E-Predict 1.0 - Microarray-based Species Identification
- EB-HMM 1.0-1 - Identification of Genes Differentially Expressed across 2 or more Conditions over Time
- EBarrays 2.56.0 - Identification of Genes Differentially Expressed across 2 or more Conditions
- EBcoexpress 1.36.0 - Differential Co-Expression Analysis
- EDGE 2.22.0 - Extraction of Differential Gene Expression
- edgeR 3.34.0 / edgeRun 1.0.9 - Empirical analysis of digital Gene Expression data
- EGPC / MVGPC 1.0 - Multi-class Classifier for Microarray data
- EMOGEE 20070704 - Estimator for MOdels of Gene Expression Evolution
- ENIGMA 1.1 - Extract Gene Expression Modules from Perturbational Microarray Data
- EPIG - Extract Microarray Gene Expression Patterns and Identifying co-expressed Genes
- ErmineJ 3.2 - Analysis of Gene sets in Expression Microarray data
- EVE v04 - Detect Differentially Expressed Genes using Microarray Data
- Event-mapper 2.53 - Find Temporal on/off Switches shared by many Genes
- ExonMiner - Web Service for GeneChip Exon Array Data Analysis
- EXPANDER 7.2 - Gene Expression Analysis & Visualization
- ExpressYourself - Microarray Data Processing Platform
- F-SCAN 1.3 - Fluorescently Probed cDNA Microarray Analysis
- FARMS 1.38.0 - Factor Analysis for Robust Microarray Summarization
- FCAnalysis 1.0.0 - Independent Component Analysis for Mining Gene Expression Data
- FIRMAGene 0.9.8 - Differential Splicing for Affymetrix Gene
- FISH Oracle 2 - Visualize Data from multiple Array CGH or SNP Array Experiments
- FLICK 1.1 - PCL File Linker
- FLUSH.LVS 1.3.2 - Compute LVS Normalization and FLUSH filtering
- FRICK 1.1 - Filter/Retrieve IDs
- fRMA 1.39.0 / frmaTools 1.39.0 - Single Microarray Preprocessing and Analysis
- GAAS 1.0.0.1 - Gene Array Analyzer Software
- GACK 3.631 - Genomotyping Analysis
- GAL File Generator 1.2 - Well Plates Files Conversion
- GEA - SAGE data analysis tool
- GECKO 20050621 - Large-scale Gene Expression Analysis Platform
- GEDAS - Gene Expression Data Analysis Suite
- GEMAT 2.0 - Genomics Experiment Management and Analysis Tool
- GemiNI - Network based integration of Gene Expression profiles with miRNA Expression Profiles
- Gemma 1.27.4 - Analyze Genomics data using Meta-analysis
- Genatomy - Visualizing Tool for Biological Data
- Gene-warp 3.2 - Generate Alignment Matrices, Explore Temporal Asynchrony in Expression of Orthologs
- GeneAnnot 2.2 - Microarray Gene Annotation
- GeneBASE - Estimate Gene-level Expression from Affymetrix Exon Arrays
- geneCBR - Perform Cancer Classification based on Microarray data
- GENECLUST 1.0.2 - Exploratory Analysis of Gene Expression Microarray data
- GeneCommittee - Testing the Discriminatory Power of Gene Sets in Microarray data Classification
- GeneCycle 1.1.4 - Identification of Periodically Expressed Genes
- GeneProgram 0.1 - Discovery of Functional Generality of Gene Expression programs
- GenePublisher 1.03 - Analysis of DNA Microarray Data
- GeneSelector 1.0 - Find Small subset of Genes for Classification of Expression data
- GeneShelf - Web-based Visual Interface for Large Gene Expression Time-series Data Repositories
- GeneTrail 3.0 - Gene Set Analysis tool / for pre-processing Microarray data
- Genetrix 3.63 - Analysis of Microarray Data
- Genevestigator 8.3.2 - Gene Expression Search Engine
- GeneXplorer 0.11 - Microarray Data Web Browser
- GENOM 2005 3.42 - Affymetrix Microarray Analysis
- GenoMap 1.0 - Graphical Representation of Microarray data
- GEOmetadb 1.52.0 - GEO Microarray Search Tool
- GEPAT - Genome Expression Pathway Analysis Tool
- Gifi Array Analyzer 1.2 beta - Analysis of DNA Microarray data and Gene Functional Classification data
- Ginkgo 1.01 - CGH & Expression Microarray Data Analysis & Normalization
- Glob-mapper 2.96 - Plot data, Find and Extract Disconcordant Genes or genes with on/off Switches
- GO-SCAN 2.2 - Gene Ontology for Significant Collection of Annotations
- GODACK 1.0 - Good Data
- GoSurfer 2.0 - Graphical Data Mining tool for Microarray data using Gene Ontology Information
- GraDe - Knowledge-based Matrix Factorization resolves the Cellular Responses to IL-6 Stimulation
- GS-LAGE - Gene-specific Analysis of Microarray Global Data
- GSCA 1.1.1 - Identification of Differentially Co-expressed Gene Sets
- GSEA 4.1.0 - Gene Set Enrichment Analysis
- gseaLda - Probabilistic Retrieval and Visualization of Biologically Relevant Microarray Experiments
- GSIM - Microarray Gene Expression Simulator
- Guide 1.2 - Application for Gene Expression analysis
- HaarSeg 1.2 - Fast and Flexible Microarray Segmentation
- HAMSTER 1.3.0 - Helpful Abstraction using Minimum Spanning Trees for Expression Relations
- hapLOH 14 - Analysis of loss of Heterozygosity in Tumor Genomes
- HCE 3.5 - Interactive Power Analysis for Microarray Hypothesis Testing and Generation
- HIMACK 1.4 - Histogram Maker
- Hot 0.3 - Computation of the Hotelling Statistic for Small Sets of Genes
- HyperPrior - Classify Gene Expression and ArrayCGH data with Prior knowledge
- IBMT - Testing for Differentially Expressed Genes in Microarrays
- iCall - Genotype-calling algorithm for rare and common Variants on the Illumina Exome Array.
- illumina 1.0.6 - Preprocessing Illumina Whole Genome Expression BeadChips
- illuminaio 0.34.0 - Parsing Illumina Microarray Output Files
- InfiniumPurify 1.3.1 - Predicting Tumor Purity from Methylation Microarray data
- ISOpure 1.0 / ISOpureR 1.1.3 - Gene Expression Deconvolution and Purification
- Istvan - Normalisation of Expression Data
- ITACA 1.0 - Integrative Tool for microArray and CESH Analysis
- ITALICS 2.52.0 - Normalize of Affymetrix GeneChip Human Mapping 100K and 500K set
- ITI 2.0 - Analysis of Gene Expression data by Superimposition of a large scale Protein-protein Interaction data
- J-Express 2012 - Analysis and Visualization of Microarray Data
- JAMIE 0.91 - Joint Analysis of Multiple ChIP-chip Experiments
- Java Treeview 1.1.6r4 - Gene Expression Visualization Tool
- JBD - Detect Binding Sites based on ChIP-chip data and Guides
- KegArray 1.2.4 - Microarray Data Analysis & Cluster
- Kerfdr 2.0.1 - A Semi-parametric Kernel-based approach to local FDR Estimations
- Knorm 1.0 – Microarray Data From Multiple Biologically Interrelated Experiments
- Koadarray 2.7.09 - Array Image Analysis software
- KTH-package 1.2.1 - Microarray Data Analysis
- L2L 1.2 - Microarray Analysis Tool
- LACK 4.3 - Lexical Analysis
- LIMMA 3.50.0 - Linear Models for Microarray Data
- limmaGUI 1.68.0 - Linear Models for Microarrays Graphical User Interface
- LombScargle - Detect Periodic Patterns in Unevenly-spaced Data
- LOX 1.8beta - Inferring Level of Expression from Diverse Methods of Census Sequencing
- LSPR - Detect Periodic Expression Profiles in DNA Microarray Time-series data
- M-align 2.8 - Align two time-series Microarray datasets using Time-warp or Gene-warp alignment matrices
- M-BISON 1.0 - Microarray-Based Integration of data SOurces using Networks
- MA2C 1.4.1 - Analyze 2-color Microarrays
- MADAM 4.1 - MicroArray DAta Manager
- MADIBA - MicroArray Data Interface for Biological Annotation
- MAExplorer 0.96.34.01 - MicroArray Explorer Tool
- MAGE-ML Visualize 1.0 - Generate MAGE-ML Graph
- MAGIC Tool 2.1 - MicroArray Genome Imaging & Clustering Tool
- MAGNOLIA 1.2 - Microarray Data Management & Export System for PFGRC Microarrays
- MAIA 2.75 - Microarray Image Analysis
- MALA - MicroArray Logic Analyzer
- MAmodel 20060511 - Microarray Simulator
- MANOR 1.64.0 - Micro-Array NORmalization of array-CGH data
- maPredictDSC 1.30.0 - Ouctome Prediction using Microarray data
- MaRe - Searching and large scale Retrieval of public Microarray data
- MARQ - Mine GEO for Experiments with Similar or opposite Gene Expression Signatures
- MARS 1.2.0 - Microarray Analysis and Retrieval System
- maSigPro 1.62.0 - R package for the analysis of Microarray and RNA-seq Time Series data
- Mask / maskBAD 1.36.0 - Mask bad Probes in Affymetrix Expression data
- MASQOT-GUI 1.0.1 - Two-channel Microarray Spot Quality Control
- massiR 1.28.0 - MicroArray Sample Sex Identifier
- matrix2png 1.2.2 - Visualization tool for Display of Matrix data
- maxd 2.0 - Storage & Analysis of Microarray Data
- Mayday 2.14 - Microarray Data Analysis
- MBCB 1.40.0 - Illumina Bead-array Data
- MBR 20070206 - Microarray Blob Remover
- MCGH 20090717 - Analyse Microarray-based CGH Experiments
- MDCS - Microarray Data Classification Server
- MDScan 2004 - Find Motif from ChIP-on-chip Targets
- MEAP 2.0.2 - Multiple Exon Array Preprocessing
- MEED - Model Expansion Experimental Design
- MERAV - Metabolic gEne RApid Visualizer
- metaArray 1.66.0 - Integration of Microarray Data for Meta-analysis
- MetaDE 1.0.5 - Meta-analysis for Differential Expression Analysis
- MetaOmics - a suite of packages for Microarray and Genomic Meta-analysis
- MetaQC 0.1.13 - Quality Control and Diagnosis for Microarray Meta-analysis
- MethLAB 2.1 - Analysis of DNA Methylation Microarray data
- METRADISC / METRADISC-XL - METa-analysis of Microarrays Datasets / Heterogeneity Testing
- MeV 4.9.0 - Multiple Experiment Viewer
- MIAMExpress 7.5 - Submission Tool for Microarray Experiments
- MicroarrayRUS 1.0 - Analysis of Microarray data
- MicroGen - Web Server for Microarray Experiments
- MIDClass 2 - Gene Expression Classification
- MIMAS 3.0 - Microarray Information Management and Annotation System
- Minfi 1.38.0 - Analyze Illumina's 450k Methylation Arrays
- MIRACLE 1.0.2 / Rmiracle - Microarray R-based Analysis of Complex Lysate Experiments
- Mixer 1.03 - ChIP-chip Analysis by Mixture Model approach
- MMBGX 0.99.26 - Multi-Mapping Bayesian Gene eXpression for Affymetrix whole-transcript arrays
- MMC 0.2 - Statistical Model for calculating Gene Coexpression
- MOSAICS 1.0.0 - Analysis of ChIP-seq data
- MPDA 20081110 - Microarray Pooled DNA Analyzer
- MPP 2.0 - Microarray-to-Phylogeny Pipeline
- Mprobe 2.0 - Computer-aided Probe Design for Oligonucleotide Microarrays
- MSCLtoolbox 200902 - Statistical Analysis of Microarray data
- mvama 1.0 - Multivariate Analysis of Microarray data
- MWT 0.2.7 - Moderated Welch Test
- NACEP 20140602 - Network-based Comparison of Temporal Gene Expression Patterns
- NACK 1.2 - Name Averaging
- NIA Array Analysis Tool 2.0 - Statistical Significance Analysis of Microarray Data
- NMF - Metagenes and Molecular Pattern discovery using Matrix Factorization
- nnNorm 2.56.0 - Spatial and Intensity based Normalization of cDNA Microarray data
- nucloc 1.06 - Analyzing Gene Positions in the Yeast Nucleus
- OliCheck - Test Validity of Potential Microarray Probes
- OligoWiz 2.3.1 - Design oligonucleotides for DNA microarrays
- OLIN 1.68.0 - Optimized Normalization, Visualization and Quality Testing of two-channel Microarray data
- OOMPA 3.1.0 - Object-Oriented Microarray and Proteomic Analysis
- opm 1.1.0 - Analysing Phenotype Microarray and Growth Curve Data
- oposSOM 2.10.0 - Comprehensive Analysis of Transcriptome Data
- OpWise - Operons Aid the Identification of differentially Expressed Genes in Bacterial Microarray Experiments
- Orange-Bioinformatics 3.28.0 - Orange Bioinformatics add-on for Orange data mining software package
- ORIOGEN 4.01 - Analyzes Gene Expression data obtained from Time-course/Dose-response studies
- OsCAS - Annotation platform for Rice Microarray data
- P-SCAN 1.2 - Peak quantification using Statistical Comparative ANalysis
- PAA 1.26.0 - Biomarker Discovery with Protein Microarrays
- PADOG 1.34.0 - Gene Set Analysis using Gene Expression data
- PAGE - Phase-shifted Analysis of Gene Expression
- PaGE 5.1.6 - Patterns from Gene Expression
- PageMan 0.12 - Annotates, Investigates, and Condenses Microarray data in the Context of Functional Ontologies
- PAM 2.1 - Prediction and Survival Analysis for Genomic Expression Data Mining
- ParaSAM - Parallel Version of the SAM Algorithm
- Pathprint 2.0 - Pathway Fingerprinting for Analysis of Gene Expression Arrays
- PathVar - Microarray Analysis of Pathway Expression Variance
- PBM - Universal Protein Binding Microarray Analysis Suite
- Peak-mapper 2.7 - Find Disconcordances in Gene Expression, shared by many gene pair orthologs
- PhylochipAnalyzer 1.0 - Analyse Hierarchical Probe sets
- Piano 2.8.0 - An R/Bioconductor package for Gene Set Analysis
- Picky 2.2 - Optimal Oligonucleotide Design & Analysis
- PIIKA 2 - Analyzing data originating from Kinome Microarrays
- Prf-browser 2.6 - Browse and Display Gene Expression Profiles
- Probe Select - Select Oligos for DNA Microarray
- ProbeLynx 1.2.2 - Update the Association of Microarray Probes to Genes
- Probemapper 2.1.0 - Connect to QBRC's ProbeMapper platform
- ProbePlus 1.0 - Analytic Tool for Analyzing Affymetrix GeneChip Gene Expression Array Data
- Prodesign 1.0 - Generate Oligonucleotide Probes for Genes and Gene Families
- PubArray 1.0.0 - Turn Analyzed Results of Microarray Experiment into Web Application
- PUMA 3.34.0 - Propagating Uncertainty in Microarray Analysis
- PWKmeans 1.0 - Penalize & weight K-means Extends the Target Function of K-means
- QCC 1.1 - Measure Reproducibility of ChIP-chip data
- QuSAGE 2.20.0 - Quantitative Set Analysis for Gene Expression
- R functions for cDNA array analysis - cDNA Microarray Analysis
- R-Cloud Workbench 1.2.0 - Remote Access to R/Bioconductor on EBI's 64-bit Linux Cluster
- R-SVM 2.0 - Recursive Sample Classification and Gene Selection with SVM
- R/maanova 1.60.0 - Environment for Microarray Analysis
- Rankgene 1.1 - Rank Genes from Expression data
- rapier 0.1 - T test on pairs of Array Experiments
- rapmad - Robust Analysis of Peptide MicroArray Data
- rCGH 1.22.0 - Analyzing and Visualizing Agilent and Affymetrix Array-Based CGH Data
- Re-Annotator 1.0.0 - Re-annotates Microarray Probes
- REA 1.1 - RIP-chip Enrichment Analysis
- REDUCK 1.0 - Remove Duplicates
- rGN - Ratio-adjusted Gene-wise Normalization
- Ringo 1.57.0 - Analysis of ChIP-chip data
- RMAExpress 1.2.0 - Generate RMA Expression Measures for Affy data
- RobiNA 1.2.4 - Open Source Microarray and RNA-Seq Processing
- RPA 1.48.0 - Robust Probabilistic Averaging for probe-level analysis
- RPS 1.0 - Reproducibility Probability Score for Microarray Data
- RSEG 0.4.9 - Identify Epigenomic Domains from ChIP-Seq data
- RZ-smooth 3.5 - Resample, Smooth and Normalize Microarray time-series data
- SAFEGUI 1.0 - Resampling-based Tests of Categorical Significance in Gene Expression data made easy
- SAGAT 1.0 - Svd Augmented Gene expression Analysis Tool
- SAM 4.01 - Significance Analysis of Microarrays
- SCAN-UPC 2.32.0 - Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
- ScoreGene 1.0 - A Gene Expression Data Analysis toolkit
- SEL.TS.AREA v2 - Significance Analysis of Microarray Transcript Levels in Time Series Experiments
- SeqExpress 1.3.2 - Analysis and Desktop Visualisation program for Gene Expression Experiments
- SignalViewer - Image Analysis of cDNA Microarrays
- SIGNATURE 20111025 - Gene Expression Signature Analysis
- SiGPAT 0.1 - Finding significant Expression Patterns of Gene Set
- Simcluster 0.9.2 - Clustering Enumeration Gene Expression data on the Simplex Space
- SKNN 1.0.1 - Sequential K-Nearest Neighbor method for Microarray data Imputation
- SlideMap 1.2.1 - Create a Row/Column to Plate/Well Map of a Microarray Slide
- SLIM 1.1 - Sliding Linear Model for Estimating the Proportion of true null Hypotheses in Datasets
- SLIMarray 0.3.5 - Lightweight software for Microarray Facility Management
- SMA 0.5.13 - Statistics for Microarray Analysis
- SMD 2.12 - The Stanford Microarray Database
- smoothseg 0.0.4 - Robust smooth segmentation approach for array CGH data analysis
- snapCGH 1.62.0- Segmentation, Normalisation And Processing of Array CGH data
- snm 1.38.0 - Supervised Normalization of Microarrays
- SNOMAD - Standardization & Normalization of Microarray Data
- SNPchip 2.14.0 - R Classes and methods for SNP Array data
- SPACC 2.0 - Spectral Analysis for Class Discovery and Classification
- sparse.inv.cov 1.0.4 - Fitting very large Sparse Gaussian Graphical Models
- Spatter 0.5.3 - Image Analysis on cDNA Microarrays
- SPD V2 - Sample Progression Discovery underlying Microarray Gene Expression data
- SpeCond 1.46.0 - Detect Condition-specific Gene Expression
- SPELL 2.0.3 - Serial Pattern of Expression Levels Locator
- spkTools 1.43.0 - Collection of Functions to Analyze Microarray Spike-in data
- Spotfinder v3.2.1 - Microarray Images Analysis & Gene Expression Quantification
- SPP 1.13 - Analysis of Sequencing data from Chromatin Immunoprecipitation Experiments
- SQN 1.0 - Normalizes based a Subset of Negative Control Probes
- SRMA 1.0.0-2 - Analyze Array-based Sequencing data for Identifying Rare DNA Variants
- SSHscreen 2.0.1 - High-throughput screening of SSH cDNA libraries using DNA microarray data
- SSPA 2.32.1 - Power and Sample Size analysis for Microarray Experiments on the basis of Pilot data
- StabPerf 0.5.4 - Reliable Gene Signatures for Microarray Classification
- STAC 1.2 - Significance Testing for Aberrant Copy-Number
- Starr 1.38.0 - Simple Tiling ARRay analysis of Affymetrix ChIP-chip data
- STEM 1.3.8 - Short Time-series Expression Miner
- Stepgram 2.12 - Application for Aberration Calling in aCGH data
- SUMO 1.60i - A Statistical Utility for Microarray and Omics data
- SuperPC 1.05 - Survival and Regression Analysis for Microarrays
- survGenesInterim 1.0 - Simulation of Survival Studies with Microarray Data
- SVA 3.40.0 - Surrogate Variable Analysis
- SVDMAN 0.9b - Singular Value Decomposition Microarray ANalysis
- SVN - Remove Systematic Variation in Microarray Gene Expression data
- T2 1.3 - Tiling Microarray Analysis Tools
- TableButler - Data table Pre-processing and Handling
- TACITuS 0.2.0 - Transcriptomic Data Collector, Integrator, and Selector
- targetedRetrieval 120705 - Targeted Retrieval of Gene Expression Measurements Using Regulatory Models
- TFInfer 1.0 - Inference of Transcription Factor Activities from Microarray data
- TightClust 1.0 - Resampling Based Clustering Method for Microarray data
- TileHMM 1.0-7 - Hidden Markov Models for ChIP-on-Chip Analysis
- TileMap v2 - Tiling Array Peak Detection
- Tilescope 2.0 - Online Analysis Pipeline for High-density Tiling Microarray data
- TileShuffle 0.2.0 - Statistical Analysis of Tiling Array Expression Data
- tilingArray 1.71.0 - Transcript mapping with high-density oligonucleotide tiling arrays
- TilingScan - Analyze Tiling Array results online
- TiMAT 3.4.4 - Process Chip-chip Tiling Array Experiments
- TIPMaP - Transcript Isoform Profiles from Microarray Probes
- tpWY - t-statistics, p-values, and Westfall and Young step-down method
- TRANS-MNET 20070315 - Time Series Analysis of Gene Expression Profiles
- TreeBuilder3D 1.0 - Interactive Viewer for Gene Expression Data
- tRMA 1.0 - Modification of RMA to Normalize Microarray Experiments
- tspair 1.50.0 - Top Scoring Pairs for Microarray Classification
- TurboNorm 1.40.0 - A fast Scatterplot Smoother Suitable for Microarray Normalization
- TWILIGHT 1.68.0 - Estimating the Local False Discovery Rate
- UCSF Spot 2.1 - Microarray Image Quantification
- UNDO 1.34.0 - Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions
- VAMPIRE - Interpret Microarray Gene Expression Data
- VarMixt 0.2-4 - Differential Analysis of Microarray data whose Variances are Modelled by a Mixture model
- Venn Mapper 1.01 - Compare Heterologous Microarray Data Sets
- VennMaster 0.38.2 - Venn Diagram Drawing tool for MicroArray Analysis
- VERA & SAM 1.0 - Find Significant Expression Differences in DNA Microarray Data
- ViDaExpert 1.2 - Multidimensional Vectorial data Visualization
- VIPR 2.0 / VIPR HMM - Viral Identification with a PRobabilistic Algorithm / Hidden Markov Model
- VIZARD 1.2 - Affymetrix GeneChip® Data Analysis & Visualization
- vsn 3.61.0 - Normalization and Variance Stabilizing Transformation of Microarray data
- W-ChIPeaks - Process ChIP-chip and ChIP-seq data
- waviCGH - Server Application for the Analysis and Visualization of Array-CGH data
- WebArray 1.4 - Web platform for analysis of Microarray data
- WeGet - Weighted Gene CoExpression Tool
- WIFA 20110617 - Wavelet-based Identification of DNA Focal Genomic Aberrations
- WKL - Pathogen Detection Algorithm
- XMAS - eXperiential Microarray Analysis System
- XPN - Merging Two Gene-expression studies via cross-platform normalization
- ZODET 1.0.9 - Identification, Analysis and Visualisation of Outlier Genes in Microarray Expression Data
- Category: Microbiology
- AXIOME 1.5 / AXIOMATIC - Exploration of Microbial Diversity
- BacSim - Simulator of Bacterial Growth
- BioAtlas - Location-specific analysis of Microbial profiles
- BURRITO - Visualization Tool for Exploratory Data Analysis of Metagenomic data
- CoMiDA v1.0.0 - Designing Minimal Microbial Communities with specified Metabolic Functions
- Community-Analyzer - Microbiome Community Network Analysis
- COP 0.3 - Competition Plotter
- E-vident - Elucidating Sampling Effort for Microbial Analysis Studies
- EMPeror 1.0.0-beta.20 - Analysis of High Throughput Microbial Ecology datasets
- FishTaco 1.1.3 - Linking Taxonomic and Functional Shifts in the Microbiome
- GrowthRates 4.0 - Calculates Bacterial Growth Rates
- InforBIO 5.28 - E-Workbench for Databasing, Classification & Identification of Microbes
- mcaGUI 1.37.0 - Microbial Community Analysis Graphical User Interface
- microbiome beta - R tools for Microbiome Analysis
- micropower - Power Estimation for Microbiome Studies
- MiRKAT 1.2.1 - Microbiome Regression-Based Analysis Tests
- MycPermCheck 1.1 - Mycobacterium Tuberculosis Permeability Prediction tool for small Molecules
- NetCooperate - Determining Host-microbe and Microbe-microbe Cooperation
- PhysioFit 1.0.2 - Estimation of Extracellular Fluxes and Growth Rate
- RevEcoR 0.99.3 / shiny-RevEcoR 0.1.1 - Reverse Ecology Analysis of Microbiomes
- Seed - Exploring and Visualizing Microbial Community Data
- SGAtools 20131030 - Web-based Analysis System for Designer Genetic Screens
- ZIBR v0.1 - Zero-Inflated Beta Random Effect model
- Category: Miscellaneous
- @Note2 2.5.0 - Biomedical Text Mining platform
- 2020plus v1.2.3 - Ratiometric Prediction of Cancer driver Genes
- 3TierMA - Three-Tiered Meta Analysis of Gene Expression Profiles of Co-morbid Diseases
- A-DaGO-Fun / DaGO-Fun - Gene Ontology Semantic Similarity based Functional Analysis
- ABC 1.3 - Allele-specific Binding from ChIP-Seq
- ABC-GWAS - Analysis of Breast Cancer GWAS variants
- ABCreg 0.1.0 - Automating Approximate Bayesian Computation by Local Linear Regression
- ABCRF 1.8 - Approximate Bayesian Computation via Random Forests
- ABE - Extract Bioinformatics from NCBI
- ABE 1.0 - Bioassay Analysis program
- ABNER 1.5 - Molecular Biology Text Analysis
- ACD/Column Selector - Search & Choose Columns
- ACD/NMR Processor Academic Edition 12 - Free NMR processing software
- ADAPT 1.00 - Alignment of DNA Associated Profiles Tool
- ade4 1.7-13 / ade4TkGUI 0.2-9 - Ecological Data Analysis
- AEGIS - Augmented Exploration of the GO with Interactive Simulations
- Aequatus - Open-source Homology Browser
- AFDP v2.4a - Automated Fluorescence Data Processing
- affy2sv 1.0.14 - Tools for newest Affymetrix Arrays.
- agplus 1.0 - Rapid and Flexible tool for Aggregation Plots
- AHTPDB - Anti Hypertensive Inhibiting peptide database
- AHTpin - Predicting, Designing and Screening of AHT Peptides
- AIBench 2.10.2 - Artificial Intelligence WorkBench
- AIMS 2.10 - Assay Information Management System
- Aldy 2.2.5 - Allelic Decomposition and exact Genotyping of highly polymorphic and structurally Variant Genes
- Alexa Fluor® Selection Guide - Find the Perfect Alexa Fluor® Dye
- Alkemio 20150517 - Ranking thousands of Chemicals for any topics using Document Categorization
- AlleleHMM - Find Allele-specific Signal in distributed Functional Genomic data
- ALoFT 1.0 - Annotation of Loss-of-Function Transcripts
- ALPHA-DEMO - Study in Differential Evolution
- Amordad 1.0 - Database Engine for comparing Metagenomic data
- An Array of Genetic Tools from Gene Link Inc. 1.2.1 - iPhone / iPad APP
- Anduril 1.2.23 - ANalysis of Data Using Rapid Integration of aLgorithms
- ANDY 0.2 - Large Biological Database Searching on Computer Clusters
- ANM 2.1 / aANM 1.1 - Adaptive / Anisotropic Network Model (Web Server)
- Anni 2.1 - Text-mining tool for the Life Sciences
- Annokey - Gene-based Search for Key-terms in NCBI Gene Database and Associated PubMed Abstracts
- Annotare 1.3 - Tool for Annotating High-throughput Biomedical Investigations and Resulting data
- AnnotCompute - Annotation-based Exploration and Meta-analysis of Genomics Experiments
- antibacTR - Identifying potential Antimicrobial Drug Targets on Gram-negative Bacteria
- Antigen Explorer - Antigen Combinations for Precision Cancer Recognition
- AntigenMap 1.0 / AntigenMap 3D - 3D / Antigenic Cartography Construction
- AntiTbPdb - Anti-Tubercular Peptide Database
- AOD - Antioxidant Protein database
- AOP-helpFinder - comprehensive analysis of the Literature to Support Adverse Outcome Pathways Development
- APACE – Automated Protein Annotation by Coordinate Evolution
- APECS - Intensity-based Peptide Selection
- apLCMS 6.6.6 - adaptive processing of high resolution LC/MS data
- ApoCanD - Database of Human Apoptotic Proteins in the Context of Cancer
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