Microarray Analysis
- BRB-ArrayTools 4.3.0 Beta3 – Visualization & Analysis of DNA Microarray Gene Expression Data
- FreeView & FreeOView – Gene Expression Dendrogram Viewer & Optimizer
- BADGE 1.0 – Bayesian Analysis of Differential Gene Expression
- GSCA 1.1.1 – Identification of Differentially Co-expressed Gene Sets
- EB-HMM 1.0-1 – Identification of Genes Differentially Expressed across 2 or more Conditions over Time
- hapLOH 1.2 – Analysis of loss of Heterozygosity in Tumor Genomes
- BRAT – Identify Differentially Expressed Probesets in Normalized Microarray datasets
- GEMAT 2.0 – Genomics Experiment Management and Analysis Tool
- GEDAS – Gene Expression Data Analysis Suite
- BASE 3.2.2 – Microarray Data Management & Analysis
- Mprobe 2.0 – Computer-aided Probe Design for Oligonucleotide Microarrays
- SLIMarray 0.3.5 – Lightweight software for Microarray Facility Management
- Echidna 2.0 – Repository for Microarray data
- nucloc 1.06 – Analyzing Gene Positions in the Yeast Nucleus
- Eu.Gene Analyzer 1.5 – Microarray data analysis in the context of Biological Pathways
- Simcluster 0.9.2 – Clustering Enumeration Gene Expression data on the Simplex Space
- Orange-Bioinformatics 2.5a – Orange Bioinformatics add-on for Orange data mining software package
- GeneCycle 1.1.2 – Identification of Periodically Expressed Genes
- GProcesser 3.0 – Statistical Analysis of GenePix data
- GPmerge 5.0 – Pool Replicated Microarray Datasets exported from GenePix Pro
- QAnalyzer 1.0b – Statistical Analysis of QuantArray data
- GeneShelf – Web-based Visual Interface for Large Gene Expression Time-series Data Repositories
- Probemapper 1.0 – Connect to QBRC’s ProbeMapper platform
- MAP – Mining Co-regulated Gene Profiles
- Peanut v1 – Protein Expression ANalysis Unified Tool
- engene – Gene-Expression Data Processing and Exploratory Data Analysis
- Qnorm – Quantile Normalization algorithm for large Microarray datasets
- ASTRO – Analysis of Short Time-series using Rank Order preservation
- CrazyQuant – Spot-finding tool
- VERA & SAM 1.0 – Find Significant Expression Differences in DNA Microarray Data
- RobiNA 1.2.4 – Open Source Microarray and RNA-Seq Processing
- Genetrix 3.62 – Analysis of Microarray Data
- MetaQC 0.1.13 – Quality Control and Diagnosis for Microarray Meta-analysis
- AltAnalyze 2.0.8 – Microarry and RNA-Seq Analysis
- HCE 3.5 – Interactive Power Analysis for Microarray Hypothesis Testing and Generation
- ViDaExpert 1.2 – Multidimensional Vectorial data Visualization
- SiGPAT 0.1 – Finding significant Expression Patterns of Gene Set
- SAFEGUI 1.0 – Resampling-based Tests of Categorical Significance in Gene Expression data made easy
- MethLAB 1.5 – Analysis of DNA Methylation Microarray data
- MeV 4.8.1 – Multiple Experiment Viewer
- MCGH 20090717 – Analyse Microarray-based CGH Experiments
- TMA Foresight 3.01 – Tissue Microarray Software for Data Analysis
- Array-A-Lizer 1.03 – DNA Microarray Quality Analyzer
- MAIA 2.75 – Microarray Image Analysis
- UCSF Spot 2.1 – Microarray Image Quantification
- MEAP 2.0.1 – Multiple Exon Array Preprocessing
- Csbl.go 1.4.0 – Gene Ontology based Clustering using semantic Similarity
- GSEA 2.0.10 – Gene Set Enrichment Analysis
- OSCAR – Clustering Analysis, and Cross-species Analysis of Microarray data
- EXPANDER 6.06 – Gene Expression Analysis & Visualization
- POE 0.2-7 – analysis of Gene Expression Microarrays using Three-component Mixtures
- SNOMAD – Standardization & Normalization of Microarray Data
- EDGE 1.1.291 – Extraction of Differential Gene Expression
- HAMSTER 1.3.0 – Helpful Abstraction using Minimum Spanning Trees for Expression Relations
- Microbiology 1.05 – Access the latest Microbiology News with Mobile Phone
- MicroarrayDesigner – Search Tool and Repository for Near-Optimal Microarray Experimental Designs
- chipchipnorm 1.0.1 – Normalize 2-color Microarray Data
- W-ChIPeaks – Process ChIP-chip and ChIP-seq data
- MicroPreP – Microarray data Preprocessing framework
- SurvBART – R Package for Bayesian Ensemble Methods for Survival Prediction in gene expression data
- NMF – Metagenes and Molecular Pattern discovery using Matrix Factorization
- GeneCruiser 3.2.2 – Annotation of Microarray data
- SIGNATURE 20111025 – Gene Expression Signature Analysis
- GoSurfer 2.0 – Graphical Data Mining tool for Microarray data using Gene Ontology Information
- RPS 1.0 – Reproducibility Probability Score for Microarray Data
- NACEP 20111205 – Network-based Comparison of Temporal Gene Expression Patterns
- Caryoscope 0.4.0 – View Gene Expression Data in Genome
- Istvan – Normalisation of Expression Data
- Diurnal 2.0 – Mining and Viewing Diurnal and Circadian Microarray data for Arabidopsis thaliana, poplar, and rice
- SSHscreen 2.0.1 – High-throughput screening of SSH cDNA libraries using DNA microarray data
- MADIBA – MicroArray Data Interface for Biological Annotation
- MicroarrayRUS 1.0 – Analysis of Microarray data
- HyperPrior – Classify Gene Expression and ArrayCGH data with Prior knowledge
- FISH Oracle – Visualize Data from multiple Array CGH or SNP Array Experiments
- D2CMA 0.1 – Design 2 Color MicroArrays
- GeneCAT – Gene Co-expression Analysis Tool-box
- PageMan 0.12 – Annotates, Investigates, and Condenses Microarray data in the Context of Functional Ontologies
- dChip 2011.12 – Analysis & Visualization of Gene Expression & SNP Microarrays
- LOX 1.8beta – Inferring Level of Expression from Diverse Methods of Census Sequencing
- MARQ – Mine GEO for Experiments with Similar or opposite Gene Expression Signatures
- PreP +07 – Gene-Expression Data Pre-Processing Tool
- Babelomics 4.3 – Gene Expression and Functional Profiling Analysis Suite
- waviCGH – Server Application for the Analysis and Visualization of Array-CGH data
- Asterias – Applications for the Analysis of Gene Expression and aCGH data
- AnovArray 1.1 – SAS macros for Analysing Microarray- and Macroarray-type Expressional data
- dictyExpress 1.5 – Dictyostelium Gene Expression Analysis
- CAPweb 2.4 – Web based platform for CGH-array Management and Analysis
- SLIM 1.1 – Sliding Linear Model for Estimating the Proportion of true null Hypotheses in Datasets
- OOMPA 2.15.1 – Object-Oriented Microarray and Proteomic Analysis
- IBMT – Testing for Differentially Expressed Genes in Microarrays
- MBR 20070206 – Microarray Blob Remover
- MA2C 1.4.1 – Analyze 2-color Microarrays
- BGX 1.22.0 – Bayesian integrated analysis of Affymetrix GeneChips
- MMBGX 0.99.22 – Multi-Mapping Bayesian Gene eXpression for Affymetrix whole-transcript arrays
- R-Cloud Workbench 1.2.0 – Remote Access to R/Bioconductor on EBI’s 64-bit Linux Cluster
- TBrowser 3.1 – Transcriptome Browser
- ORIOGEN 4.01 – Analyzes Gene Expression data obtained from Time-course/Dose-response studies
- CpGassoc 1.3 – Analysis of DNA Methylation Microarray data
- FIRMAGene – Differential Splicing for Affymetrix Gene
- TileShuffle 0.2.0 – Statistical Analysis of Tiling Array Expression Data
- PhylochipAnalyzer 1.0 – Analyse Hierarchical Probe sets
- SMD 2.14 – The Stanford Microarray Database
- ChipInspector 2.1 – Microarray Data Analysis
- CNAnova 1.0 – Identify Recurrent Regions of Copy Number Changes
- WebArray 1.4 – Web platform for analysis of Microarray data
- VennMaster 0.37.5 – Venn Diagram Drawing tool for MicroArray Analysis
- VAMPIRE – Interpret Microarray Gene Expression Data
- M@IA 1.2 – Microarray Integrated Applications
- GeneXPress 1.0 – Visualization and Analysis tool for Gene Expression data
- Rankgene 1.1 – Rank Genes from Expression data
- DetectiV 1.1 – Analysis of Pathogen Detection Microarray data
- DEEP 1.0.3 – Differential Expression Effector Prediction
- SPP 1.11 – Analysis of Sequencing data from Chromatin Immunoprecipitation Experiments
- MARS 1.2.0 – Microarray Analysis and Retrieval System
- ITACA 1.0 – Integrative Tool for microArray and CESH Analysis
- MetaDE 1.0.5 – Meta-analysis for Differential Expression Analysis
- SAM 4.0 – Significance Analysis of Microarrays
- ArrayNorm 1.7.6 – Normalisation and Statistical Analysis for Microarray-experiment data
- CARMAweb 1.3 – R- and Bioconductor-based web service for Microarray Data Analysis
- BTW 1.0 – Web Server for Gene Expression Time series Boltzmann Time Warping
- ArrayPlex 1.0.3 – Flexible Toolsets for Functional Genomics
- AffyMAPSDetector 1.0 – Affymetrix MicroArray Probe SNP Detector
- AffyGCQC 1.02 – GeneChip Data Quality Control
- LeFEMiner Build8 – The Learner of Functional Enrichment
- AffyProbeMiner 1.0 – Computing or Retrieving Accurately Redefined Affymetrix probe sets
- MatchMiner Build137 – Batch-translation among many types of Gene and Protein Identifiers
- E-Predict 1.0 – Microarray-based Species Identification
- ExpressionNet 1.0 – Explore Relationships among Random Variables to Generate Network models
- J-Express 2012 – Analysis and Visualization of Microarray Data
- CUDA-MI 20110425 – Speedup over Sequential Multi-threaded Implementation
- dCoxS – Biological Interpretation of Paired Gene Sets
- SeqExpress 1.3.2 – Analysis and Desktop Visualisation program for Gene Expression Experiments
- L2L 1.2 – Microarray Analysis Tool
- PROSECUTOR 1.0.0 – Infer Gene Function based on available Gene Expression data
- STEM 1.3.8 – Short Time-series Expression Miner
- Decision Forest 2 – Novel Pattern Recognition method for multiclass Classification in Microarray data analysis
- ArrayTrack 3.4.5 — Microarray Database, Data analysis & Interpretation tool
- MDCS – Microarray Data Classification Server
- geneCBR – Perform Cancer Classification based on Microarray data
- Prf-browser 2.6 – Browse and Display Gene Expression Profiles
- Glob-mapper 2.96 – Plot data, Find and Extract Disconcordant Genes or genes with on/off Switches
- Peak-mapper 2.7 – Find Disconcordances in Gene Expression, shared by many gene pair orthologs
- M-align 2.8 – Align two time-series Microarray datasets using Time-warp or Gene-warp alignment matrices
- Gene-warp 3.2 – Generate Alignment Matrices, Explore Temporal Asynchrony in Expression of Orthologs
- Event-mapper 2.53 – Find Temporal on/off Switches shared by many Genes
- RZ-smooth 3.5 – Resample, Smooth and Normalize Microarray time-series data
- AVF-filter 2.4 – Find Noisy Datasets, Measure Periodicity of Gene Expression
- TFInfer 1.0 – Inference of Transcription Factor Activities from Microarray data
- Knorm 1.0 – Microarray Data From Multiple Biologically Interrelated Experiments
- GMEP 1.0.1 – Compute Genome-mean Expression Profiles from Expression and Sequence data
- Cyber-T – Software and Server for Analysis of DNA Microarray data
- GO-SCAN 2.2 – Gene Ontology for Significant Collection of Annotations
- MSCLtoolbox 200902 – Statistical Analysis of Microarray data
- P-SCAN 1.2 – Peak quantification using Statistical Comparative ANalysis
- F-SCAN 1.3 – Fluorescently Probed cDNA Microarray Analysis
- PAM 2.1 – Prediction and Survival Analysis for Genomic Expression Data Mining
- STAC 1.2 – Significance Testing for Aberrant Copy-Number
- GSIM – Microarray Gene Expression Simulator
- PaGE 5.1.6 – Patterns from Gene Expression
- tpWY – t-statistics, p-values, and Westfall and Young step-down method
- AffyExtensions 0.8-2 – Analyze Affymetrix data
- RMAExpress 1.0.5 – Generate RMA Expression Measures for Affy data
- SMA 0.5.13 – Statistics for Microarray Analysis
- SlideMap 1.2.1 – Create a Row/Column to Plate/Well Map of a Microarray Slide
- ArrayOme 1.0 – Estimate the sizes of Microarray-visualised Bacterial Genomes
- DSection – Probabilistic Analysis of Gene Expression Measurements from Heterogeneous Tissues
- TiMAT 3.4.4 – Process Chip-chip Tiling Array Experiments
- FARMS 1.4.1 – Factor Analysis for Robust Microarray Summarization
- BATEx 0.1.2 – A Data Warehouse for Array-based Gene Expression Data of Plants
- Mayday 2.13 – Microarray Data Analysis
- rapier 0.1 – T test on pairs of Array Experiments
- TreeView 1.66 – Cluster Results Visualization Software
- EMOGEE 20070704 – Estimator for MOdels of Gene Expression Evolution
- CALIB 1.2.0 – Estimate absolute Expression levels from two color Microarray data
- COMODO 1.0 – Identify Conserved Coexpression Modules between Organisms
- CIST – Analysis of Gene Expression data Generated using SAGE
- ErmineJ 2.1.21 – Analysis of Gene sets in Expression Microarray data
- Gemma 1.5 – Analyze Genomics data using Meta-analysis
- matrix2png 1.2.2 – Visualization tool for Display of Matrix data
- KNNimpute – Estimation of Missing Values in Microarray data
- ChARMview 1.8 – Visualization-based Discovery and Analysis of Genomic Abberations in Microarray data
- MEFIT – Microarray Experiment Functional Integration Technology
- HIDRA 1.1.1 – Multi-dataset Microarray Visualization System
- geneVAnD 1.0 – Visualization of Statistical Snalysis of Microarray Clusters
- PubArray 1.0.0 – Turn Analyzed Results of Microarray Experiment into Web Application
- J/maanova 1.1.1 – Java GUI for R/maanova
- R/maanova 1.16.0 – Environment for Microarray Analysis
- CHROMOWAVE 1.0 – Microarrays Data Analysis
- Mask – Mask bad Probes in Affymetrix Expression data
- GeneProgram 0.1 – Discovery of Functional Generality of Gene Expression programs
- JBD – Detect Binding Sites based on ChIP-chip data and Guides
- GSE – Database System for the Representation, Retrieval, and Analysis of Microarray data
- NTAP 0.2 – Analysis of NimbleGen Tiling Array data
- MAF – LIMS with Extended support for Nylon based Microarrays
- BZScan 2 – Quantification of DNA Microarrays with Radioactive Labeling
- AgiND 2.12 – Quality Control and Normalisation Tools for Agilent arrays
- VIMIDA – Java-applet for VIsualization of MIcroarray DAta
- ExpressYourself – Microarray Data Processing Platform
- A-MADMAN 1.4 – Annotation-based Microarray Data Meta-ANalysis tool
- iMISS 1.0 – Integrative Missing Value Estimation for Microarray Data
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