Posts
- Category: Genetics & Pedigree (continued)
- SNiPA v3.4 - a tool for Annotating and Browsing Genetic Variants
- Sniper 1.6.4 - SNP Discovery Utilizing Multi-mapping Reads
- SNiPlay v3 - SNP and Polymorphism Analysis
- SNIPPEEP r1 - Visualise Results from whole Genome Genotyping
- SNIPPER 1.2 - Investigate Genes near Associated Loci
- SnIPRE - Identifying Genes under Natural Selection
- SnipViz - A SNP Visualizer
- sNMF 2.0 - Inference of Population Structure using Sparse Non-negative Matrix Factorization algorithms
- SnoopCGH Beta - Visualise and Explore Comparative Genomic Hybridization (CGH) data
- SNP HiTLink 1.5.1 - SNP High-Throughput Linkage Analysis System
- SNP ratio test v3 - Pathway Analysis of Genome-wide Association Datasets
- SNP tools 1.80 - Analysis and Conversion of Genotype data
- SNP-HWE - Routines for exact SNP tests of Hardy-Weinberg Equilibrium
- snp.plotter 0.5.1 - SNP/haplotype Association and Linkage Disequilibrium plotting package
- SNP2CAPS - SNP and INDEL Analysis Tool for CAPS Marker Development
- SNP2GO 1.0.5 - Functional Analysis of Genome-Wide Association (GWA) studies
- SNP2HLA 1.0.3 - Imputation of Amino Acid Polymorphisms in Human Leukocyte Antigens
- SNPAAMapper 2.0 - A SNP Amino Acid Mapping tool
- SNPAAMapperT2K - Genome-wide SNP Downstream Analysis and Annotation Pipeline
- SNPALYZE 8.0 - SNP and Disease Association Analysis Software
- SNPannotator 20090828 - Adding Physical and Genetic Position data to Affymetrix Genotype files
- SNPAssoc 1.9-2 - SNPs-based Whole Genome Association Studies
- SNPAssociation - Detecting Two-locus Associations allowing for Interactions in GWAS
- SNPCaller - Smarter Clustering Methods for SNP Genotype Calling
- SNPduo 1.02a - Pairwise Comparisons of SNP data sets
- snpEff 4.3T - Variant Annotation and Effect Prediction Tool
- SNPEVG 3.2 - SNP Effect Viewing and Graphing
- SNPExpress - Visualization of Gene Expression, DNA copy number and Genotype data
- SNPflow 1.3.5 - SNP Workflow Manager
- SNPHAP 1.3.1 - Estimate Frequencies of Haplotypes of SNPs
- SNPHarvester - Detect Epistatic Interactions in Genome-wide Association studies
- SNPHunter 1.75 - dbSNP Search & Management
- SNPHunter 2.22 - Search Alignment File for SNPs
- SNPidentifier 1.10 - Discover SNPs based on CAP3 Alignments
- SNPLINK - Multipoint Linkage analysis of Densely Distributed SNP data
- SNPMStat 4.0 - Statistical Analysis of SNP-Disease Association with Missing Genotype Data
- SNPnexus v4 - Functional Annotation of novel and publicly known Genetic Variants
- SNPPicker 2 - tag SNP Selection Across Multiple Populations
- SNPPIT 1.0 - Perform Fast and Accurate, Likelihood-based, Parentage Inference with SNPs
- snpQC - Quality Control of Illumina SNP Genotyping Array data
- SNPrank 0.1.0 - Network Analysis tool for GWAS
- SNPRuler - Predictive Rule Inference for Epistatic Interaction Detection in Genome-wide Association studies
- SNPscan - Affymetrix SNP (10K, 50K, 100K, 500K) Visualization
- SNPsea 1.0.3 - Identify Cell Types and Pathways Affected by Risk Loci
- SNPsetter 20101215 - Standardization of SNP data
- SNPsim 0.8 - Coalescent Simulation of Hotspot Recombination
- SNPsnap - Identification and Annotation of matched SNPs
- SNPSpD / SNPSpDlite - Single Nucleotide Polymorphism Spectral Decomposition
- SNPSplicer 1.0.0 - Analyse SNP-dependent Splicing in Genotyped cDNAs
- SNPsyn 1.2b - Gene Interaction Analytics Application
- SNPTEST v2.5.6 - Analysis of Single SNP Association in Genome-wide Study
- SNPTools 1.0 - SNP analysis in Next Generation Sequencing data
- SnpTracker 0.1 - Extract the latest version rsID and Genomic Coordinates of SNPs given any version of rs ID(s)
- SNPtrio - SNP Trio Visualization tool
- SNPWEIGHTS 2.1 - Inferring Genome-wide Genetic Ancestry using SNP Weights
- SNPYGoat 1.0 - Identify Several Goat Y-chromosomal Haplotypes
- SNV-PPILP 1.3 - Refined SNV calling for Tumor data using perfect Phylogenies and ILP
- Socrates 0.95 - SOft Clip re-alignment To IdEntify Structural Variants
- SOLAR-Eclipse 8.1.1 - An Imaging Genetics Analyses Software
- SOLOMON 1.0-1 - Parentage Analysis using Bayes' Theorem
- Somatic mutation FDR - FDR Calculation for Somatic Mutations
- SomVarIUS 1.1 - Somatic Variant Identification from unpaired Samples
- SOOP 2.16 - System for Optimized Overgo Picking
- SPA 1.13 - Spatial Ancestry Analysis in Genetic data
- SPA3G 1.0 - Gene-centric Gene-Gene Interaction
- spaa 0.2.2 - Species Association Analysis
- SpaceMix - Understanding Population Structure and Admixture
- SPADS 1.0 - Spatial and Population Analysis of DNA Sequences
- SPAGeDi 1.5d - Spatial Pattern Analysis of Genetic Diversity
- SPAM 3.7b - Genetic Stock Identification Software
- SPANR - Splicing-based Analysis of Variants
- Sparse PCA - Sparse principal component analysis
- SparSNP - Fit Lasso-penalized linear models to SNP data
- SPASIBA 0.0.2 - Spatial Continuous Assignment from Genetic Data
- SPEA2 - The Strength Pareto Evolutionary Algorithm 2
- SPEC - Cell Subset Prediction for Blood Genomic Studies
- SpectralTDF - Spectral Representation of Transition Density Functions
- SPERMSEG - Analysis of Segregation Distortion in Single Sperm Data
- SpideR 1.5.0 - SPecies IDentity and Evolution in R
- SPIP 1.0 - Simulate Pedigrees and Genetic data in Age-structured Population
- SPLATCHE 3.0 - Simulate Genetic Diversity taking into Account Environmental Heterogeneity
- SPLINK 1.09 - Sib Pair Linkage analysis
- Spotter 0.5 - Identify Region of Interest near Associated Variant
- SPREG 2.0 - Regression Analysis of Secondary Phenotype Data in Case-Control Association Studies
- SPrime - Detect Introgressed Genetic Variants
- SPSSQTL 1.0 - Statistical Power and Sample Size for QTL Detection
- SQTDT/SPDT - Semiparametric Family-based Tests of Association
- SQTL - Semiparametric QTL Mapping in General Pedigrees
- SSEA 1.0 - SNP Set Enrichment Analysis for Genome-wide Association Studies
- ssSNPer 20070329 - Identify statistically similar SNPs (ssSNPs) in the HapMap
- ssw2pop - Programs for Simulation and Composite Likelihood Snalysis of Selective Sweep
- Stacks 2.59 - Analyse RAD Sequencing data
- staRank 1.28.0 - Ranking Variables based on their Stability
- STARRInIGHTS - Strain-based Tree Analysis and Recombinant Region Inference In Genomes from High-Throughput Sequencing projects
- START - Find Starting Points for MCMC analysis
- Statistical Genetics Utility 201807 - Set of Small Executable Statistical Genetics Programs
- StepBrothers 1.0.1 - Inferring partially shared Ancestries among Recombinant Viral Sequences
- STEPC - Statistical Explanation for Positional Cloning
- Strainer 0.9.7 - Multi-platform Visualization tool for Metagenomics Data
- STRAT 1.1 - Companion program to Structure
- StreamTree 20090303 - Map Genetic Differences between Populations
- Strelka 2.9.10 - Small Variant Caller
- StructHDP 1.1 - Inference of number of Clusters and Population Structure from Admixed Genotype data.
- Structurama - Infer Population Structure from Genetic Data
- Structure 2.3.4 - Use Multi-locus Genotype Data to Investigate Population Structure
- STRUCTURE HARVESTER 0.6.93 - Collating Results Generated by the program STRUCTURE
- Strudel 1.15.08.25 - Genetic and Physical Map Viewer
- Sub-GSE - Testing Gene Set Enrichment for Subset of Genes
- SubPatCNV - Mine CNV Subspace Patterns
- SUGEN v8.1 - Genetic Association Analysis Under Complex Survey Sampling
- SUMSTAT / SumstatQ - Sum Statistics for multi-locus Genetic Association Mapping
- SUP 20110711 - SLINK/FastLINK Utility Program
- SuperLink 1.3 - Genetic Linkage Analysis
- SV-M 0.1 - Structural Variant Machine
- SVAMP 2.10 - Sequence Variation Analysis,Maps and Phylogeny
- SVDetect 0.8b - Detect Genomic Structural Variations from Paired-end and Mate-pair Sequencing data
- svm-agp - Detection of Atypical Genes
- SVMiner 1.0 - Structure Variation Detection tool
- SVS 8 - Analytic Tools for Genomic and Phenotypic data
- SWAP 0.9 - Analyse Genetic Parameters in Half Sib Families
- SWAPSC 1.0 - Sliding Windows Analysis Procedure to detect Selective Constraints in Protein-coding Genes
- SweeD 3.2.1 - a faster version of SweepFinder
- Sweep 1.1 - Large-scale Analysis of Haplotype Structure
- SweepFinder 20060814 - Detect the Location of a selective Sweep based on SNP data
- sweepsims 0.1.2 - Coalescent Simulation Software
- SwiftLink 2.0 - Parallel MCMC Linkage Analysis
- SXTestPlate 1.0.0 - Analyses Genotypes of a SNPlexâ„¢ Control Plate
- Syntenator 2 - Multiple Gene Order Alignments with a Gene-specific Scoring Function
- Synthesis-View - Visualization and Interpretation of SNP Association Results
- Syzygy 1.2.7 - SNP and Indel Calling for pooled and individual Targeted Resequencing Studies
- TADA - Transmission And De novo Association test
- Tagger - Selection and Evaluation of tag SNPs
- tagIMPUTE 1.0 - Tag-based imputation
- TagMix - Genome-wide Tag SNPs Selection
- tagSNPfinder - Mutilocus LD Measure and Tag SNP Selection
- TAGster - Single or Multi-Population Tag SNPs Selection, Evaluation and Visualization
- Tandem2 - Automated Microsatellite Allele Binning for Population Genetics Workflows
- Tangram 0.3.1 - Structural Variation(SV) Detection based on MOSAIK Alignments
- TARV v1 - Tree-based Analysis of Rare Variants
- TASSEL 5.0 / rTASSEL 0.9.23 - Association And Diversity Analyses In Plants And Animals
- TATES - multivariate GWAS based on P-values from GWAS
- TDT Power Calculator 1.2.1 - Power Calculation for the TDT
- TDTP 2.0 / TDT2G 2.0 - Software Implementing Multimarker TDTP / TDT2G
- TEAM 0.0.4 - Two-locus Epistasis tests in human Genome-wide Association Study
- TEAM 1.2.0 - Design and Management of Panels of Genes for Targeted Enrichment and Massive Sequencing
- TEMP v1.04 - Analyzing Transposable Element Polymorphism in Populations
- TESD 1.0 - Transposable Element Simulator Dynamics
- TESS 2.3.1 - Bayesian Clustering using Tessellations and Markov models for Spatial Population Genetics
- TetraploidMap 1.0.6 - Calculate Linkage Maps for Autotetraploid Populations
- TFCoEvolve - Transcription Factor CoEvolution Analysis
- TFPGA 1.3 - Analysis of Allozyme and Molecular Population Genetic data
- THESIAS 3.1.1 - Testing Haplotype Effects In Association Studies
- thunder 0.10 - LD-based Genotype Caller and Haplotyper on Massively Parallel Sequencing data
- TIGRA-SV v0.1.3.3 - Conduct Targeted local Assembly of Structural Variation
- TIPS 1.0beta - Tree-guided Bayesian inference of Population Structures
- TLINKAGE 20 - Two-locus Linkage Analysis
- TM 20110802 - Multiple Trait Estimation of Variance Components
- tmax - Single Locus Tests for Association
- tmle.npvi 0.10.0 - Targeted Learning of a NP Importance of a Continuous Exposure
- TO-DAG - Timed Oncogenetic Directed Acyclic Graphs
- topGO 0.97 - Calculat Significance of Biological Terms from Gene Expression Data
- TOROCOR 1.0 - Assess the Association between Spatially Autocorrelated Variables using Torus-translation tests
- Tractatus 0.0.1 - Exact and Subquadratic Algorithm for IBD Inference.
- traitRate 201612 - Detection of Trait-dependent Shifts in the Rate of Sequence Evolution
- TranscriptSimulator 0.7 - Simulate Transcriptome Next-gen Reads, including 454 and Illumina
- TransFIC - Transformed Functional Impact score for Cancer
- TRANSMIT 2.5.4 - Transmission Disequilibrium Testing
- TRAP 1.1 - Tiled Regression Analysis Package
- traseR 1.14.0 - GWAS Trait-associated SNP Enrichment Analyses in Genomic Intervals
- TREAT 0.0.5 - Detecting Complex Joint Effects in Case-control Studies
- TreeFit 20120420 - Evaluate How well a UPGMA or Neighbor-joining Tree fits a Genetic Distance Matrix
- TreeLD 1.0.1 - Map Complex Trait Loci
- treemix 1.13 - Inference of Population Trees with Admixture
- TreeQTL 2.0 - Hierarchical error control for eQTL studies
- TREESELECT 1.1 - Infer Natural Selection from unusual Population Differentiation
- Trimhap 1.2 - Linkage Disequilibrium
- TRIMM - TRIad Multi-Marker
- Trinculo 0.96 - Flexible tools for Multinomial Association
- TrioCaller 20120626 / FamLDCaller 20160215 - LD-aware Genotype Calling and Phasing program for Sequence data
- TrioCNV 0.1.2 - Joint Detection of Copy Number Variations in Parent-offspring Trios
- Triodenovo 0.06 - A Bayesian framework for de novo Mutation Calling in Parents-offspring Trios
- trioPhaser - Using Mendelian inheritance logic to improve Genomic Phasing of Trios
- tripleM 1.0 - Use Partition-Ligation strategy and EM Algorithm to Reconstruct Hplotypes in trios
- TroX 1.0 - Analyzing Trisomic data
- trueFS - Find Ascertainment Corrected Frequency Spectrum based on Ascertained SNP data
- TSSV 1.1.0 - Characterization of Complex Allelic Variants in pure and mixed Genomes
- Tumorscape 1.6 - Copy Number Alterations Across Multiple Cancer Types
- TWIN - Twin Zygosity Determination
- Twin Analysis - Twin Analysis Using SAS
- TWINSIM - Simulate Twin-nuclear Families in which QTLs and Linked Markers are Segregating
- TWOLOC - Analyze Two-locus Susceptibility Gene Models in affected Sib-pair data
- TwoPhaseInd 1.0.0 - Two-Phase Independence
- UMVCUE - Unbiased Estimator of Odds Ratios
- UNCcombo 0.1 - Likelihood based Association Testing for NGS data without intermediate Genotype Galling
- UNPHASED 3.1.7 - Association Analysis in Nuclear Families and Unrelated Subjects
- UVPAR - Fast Detection of Functional Shifts in Duplicate Genes
- VarB 1.4 - Population Genomic Variation Browser
- VarEff 1.2 - Detecting the Evolution of the Coalescent Effective Population Size
- Variant Tool Chest 0.9.3 alpha - Analyzing Variants
- VariantAnnotation 1.36.0 - Annotation of Genetic Variants
- variants2plink - var File SNPs to PLINK converter
- VariationHunter 0.04 - Structural Variation Detection
- VARiD 1.0.7f - Variation Detection
- VarioBox 1.4.6 - Exploring Human Genetic Variations
- VarioWatch 20171116 - Providing large-scale and comprehensive Annotations on human Genomic Variants in the Next Generation Sequencing era
- varLD 1.0 - Comparison of Variation in Linkage Disequilibrium between Population
- VarSifter 1.9 - Analyse Sift Variation Data
- VASP - Variant Analysis of Sequenced Pedigrees
- vBsr 0.0.1 - Fitting an Ultra-sparse Variational Bayes Spike Regression model
- VCGE - Gene-environment Interaction with Varying Coefficient Model
- VEGAS 0.8.27 - Versatile Gene-based Association Study
- verifyBamID 1.1.3 - Identify Contamination of Sample Swap in Sequence data
- VIP 1.0 - SNP Variant Detection tool from Pooled DNAs
- VIPER 1.01 - Exploring and Cleaning Inheritance Inconsistencies within Pedigree/Genotype Data
- vipR 0.0.16 - Variant Identification in pooled DNA using R
- VIRAPOPS 2.1 - Simulates Viral Population from Seed Sequences Family
- Virmid 1.2.0 - Virtual Microdissection for SNP Calling
- visPIG 1.1 - Visual Plotting Interface for Genetics
- ViTraM 2.0 - Visualization of Transcriptional Modules
- Volume Measures - Volume Measures for Linkage Disequilibrium
- VSEAMS 0.1 - Variant Set Enrichment Analysis using Multivariate Sampling
- vt 0.57721 - A tool set for Short Variant Discovery in Genetic Sequence Data
- WAFFECT 1.2 - A package to Simulate Constrained Phenotypes under Disease model H1
- wANNOVAR 20190509 - Annotating Genetic Variants with respect to Disease Phenotypes
- wclique 0.1 - Genetic Marker Selection program
- WebGestalt 2019 - WEB-based GEne SeT AnaLysis Toolkit
- weighted_FDR 1.2 - Apply Weighted False Discovery Rate for Multiple Testing
- WeiSum - Finding Genetic Overlaps among Diseases Based on Ranked Gene Lists
- Weka-CG 0.1.1 - Data Mining software package for Human Genetics
- WGPA - Web-based Gene Pathogenicity Analysis
- WH - Fit Speciation Model to DNA Sequence data sets
- WHaIT - Weighted Haplotype and Imputation dosage Tests
- Wham 1.8.0 - Identifying Structural Variants of Biological Consequence
- WHAMM 0.14c - Whole-Genome Homozygosity Analysis and Mapping Machina
- WHATIF - Management of Incidental Findings from Next-generation Sequencing Variant data
- WhichGenes 1.5 - Gene Set building tool
- WHICHLOCI 1.0 - Use Genotype data to Identify the loci most useful for Population Assignment
- WHICHPARENTS 1.0 - Use Mutlilocus Genotype data to Determine the Most likely Parents of Offspring
- WhichRun 4.1 - software for Assigning Individuals to Populations
- Willows 1.1 - Tree and Forest Construction package
- WinHAP 2.0 - Fast Haplotype Phasing program for long Genotype Sequences
- WinXPCNVer - Calculating Vst values between two Populations Probe
- WOMBSOFT - R package for Wombling Analyses
- Wright_Fisher_MP / Moran_MP - Multi-locus Match Probability
- ws2m 3.2 - Software for the Measurement and Analysis of Species Diversity
- X-LRT 1.0 - Estimate Genetic Risks and Test Association with X-linked Markers
- XHMM 20140711 - eXome-Hidden Markov Model
- XP-BLUP - Trans-ethnic Trait Prediction
- XP-CLR 1.0 - Cross-population Composite Likelihood Ratio Test
- XPEB 0.1.1 - Cross-population Empirical Bayes
- XQTL 1.0 - Gamily-based Allelic / Haplotype Association Test
- XWXW - Linkage Analysis of Quantitative Traits
- YAMAS 2014 - Meta-analysis of Genome Wide Association Studies
- YCDMA 3.1.1 - Manage Microsatellite Data
- Yleaf v2 - Human Y-chromosomal Haplogroup Inference from Next Generation Sequencing data
- Zinfandel v0.9 - Detecting CNVs from Low-pass WGS data
- ZygProb - Zygosity Probability Calculation
- Category: Image Analysis
- ACC 1.1 - Advanced Cell Classifier
- ACE 2.4 / ACE2 1.0 - Automated CTF Estimation
- AdipoCount - Automatic Adipocyte Counting
- AFINITI 1.0 - Volumetrics Measurement of Human Brain Tumor
- AISO 0.3 - Image Segmentation tool
- AMASS - MSI Analysis by Semi-supervised Segmentation
- AnnoFly - Annotation of Drosophila Embryonic Images Based on an Attention-Enhanced RNN Model
- AutoSPOTs - Batch Analysis of JPEG images for Fluorescent Spots
- AxonTracker 1.0 - Track and Label Axon Structures
- bcfind 1.0 - Brain cell finder
- BDB 0.91 - Deformable Curve in n-dim
- BEADS 1.1.13 - Spot Detection on 2-D Gel Images
- bfDICOM 1.03j - A tool for analysis of Ultra Sound Contrast images
- Bio-Formats 6.6.1 - Java Library for Reading & Writing Biology Image File Formats
- BioImage Convert 1.55 - Image Conversion Utility
- BioImageXD 1.0 r1799 - Analysis & Visualization of Multidimensional Biomedical Images
- bioView 1.1.18 - Visualize EM, Confocal, etc. Biology Imagery
- bioView3D 0.1.18 - Visualize 3D Stack Image
- Bisque 0.5.8 - Platform for Bioimage Analysis & Management
- BlurLab 0.9 - 3D Simulated Microscopy Software Package
- BMIPT 1.1 - Biomedical Image Processing Tool
- BmpFrame 0.01 - Draw a Frame with Tick Marks around an 8-bit Bitmap
- BQBisqueJ 0.1 - ImageJ plugin for Bisque DataBase System
- BQJavaLib 0.1 - Java Library for Matlab to Direct Access to the Bisque DataBase System.
- BQMatlabToolbox 0.1 - Direct Access to the Bisque DataBase System
- Braincells 1.1 - Follow Cell and Axon Movements in Image Sequences
- Bsoft 2.1.0 - Image & Molecular Processing in Structural Biology
- CalMorph 1.3 - Process Microscopic Images and Generate Quantitative Data about Yeast Cell
- CASP 1.2.3beta2 - Image Analysis of Comet Assay
- CecogAnalyzer 1.6.1 - Time-resolved Analysis of Single Cells
- Cell Counting Aid 1.0 - Keep Records of Cell Counting
- CellAging - Study Segregation and Partitioning in Division in Cell Lineages of Escherichia coli
- CellC 1.2 - Quantification of Labeled Bacteria by Automated Image Analysis
- CellClassifier - Supervised Learning of Cellular Phenotypes
- CellCognition Explorer 1.0.2 - Analysis of Cellular Phenotypes Images in Microscopy
- CellExplorer 1.0 - 3D C. elegans atlas Building & Application Tools
- CellH5 / CellH5Browser 1.1 - Format for Data Exchange in High-content screening / Image Browser
- CellProfiler 4.2.1 - Cell Image Analysis Software
- CellSegmenter 1.0 - Set Cell Image Boundaries
- CellTracer 1.0.3 - Automated Dynamic Image Analysis in Single Cell Fluorescent Microscopy studies
- CellTracker 1.1 - Cell Migration Detection
- CellX 2.12 - MATLAB Image Segmentation Package
- cellxpress pro 1.4.2 - Cellular Phenotype Profiling Software Platform
- CFNet - Conic Convolution and DFT Network for classifying Microscopy Images
- CI Micro v2.1 - Analyzing Time-lapse Experiments of Cell Migration, Invasion and Wound Healing assays
- CLSM Tools 20080903 - MATLAB Library for Nuclear Segmentation & Lineage Analysis
- CMEIAS Color Segmentation 1.0 - Segment & Analyze Foreground Objects within Complex Images
- ColorDecontmas 1.00 - ImageJ macros for Color Deconvolution for TMA images
- COMSTAT 2 - Quantification of Biofilm Structures
- Confocal Assistant 4.02 - 3D Analysis of Confocal Images
- CoPlot 6.45 - Software for Great Scientific Graphs, Maps, and Technical Drawings
- Costanza 1.0 - ImageJ Plugin for Image Segmentation & Analyzing Stacks
- CP ATLAS 2.0 - Thin Layer and Gel Analysis Software
- CRImage 1.34.0 - Tumour Image analysis
- Cross Checker 2.91 - Genetic Fingerprint Gel Image Analysis
- Cytomine 3.0.1 - Collaborative Analysis of Multi-gigapixel Images
- Dapple 0.88pre4 - DNA Microarrays Image Analysis
- DCellIQ 1.0 - Quantitative Time-lapse Nuclei Image Analysis
- DeadEasy Caspase - Counting of Apoptotic Cells in Drosophila
- DeadEasy Mito-Glia - Counting of Mitotic Cells and Glial Cells in Drosophila
- DeadEasy Neurons - Count Neuronal Nuclei Stained with HB9 in whole Drosophila Embryos
- Deconvolve 2.1 - Remote Batch Restorations of 3D/2D Fluorescence Images
- DeStripe 2 - Removing stripe noise in AFM images
- Dicoogle v3.0.2 - Information Retrieval System for Medical images
- Digital Notebook 1.2.28 - Image Management & Annotation
- DigitizeIt 2.0 - Extract Data Values from Graphs
- DoGpicker 0.2.1 - Particle Picker
- DP2 - Distributed 3D Image Segmentation using Micro-labor workforce
- EBImage 4.35.0 - Image Processing and Analysis Toolkit for R
- ECC - Classification of Cells or other Biological Objects
- eDens - Electrophoretic Densitometry
- ELLIPSE 2.08 - Image Analysis program
- EM-SURFER - Navigating 3D Electron Microscopy Maps
- EM3D 2.0 - Software for Electron Microscope Tomography
- EMAN 2.91 - a suite of Scientific Image Processing tools
- Endrov 2.23.3 - Multi-purpose Image Analysis program
- Engauge Digitizer 12.2.2 - Convert an Image File into Numbers
- Farsight 0.4.4 - Quantitative Tools for Studying Complex and Dynamic Biological Microenvironments from 4D/5D Microscopy Data
- FIATAS 1.0 - Fast Image AnnoTAtion Software
- Fiji 20141125 - Image Processing Package based on ImageJ
- FiloDetect - Detect & Quantify Filopodia in Single-cell Fluorescence Confocal Microscopy Images
- FindEM 2.0 - Fast Local Correlation Function Particle Picker
- FISH Finder 0.27 - A High-Throughput Tool for Analyzing FISH Images
- Flicker 0.87.2 - Compare 2D Gel Images
- FLINO - ImmunoFLuorescence Image NOrmalization
- Flower Shape Analysis System 1.52 - Program for the Area Measurement on Digital Image
- FluoRender 2.26.3 - Rendering Tool for Confocal Microscopy data Visualization
- Fluorescence Spectraviewer 3.1.1 - Plot & Compare Spectra for iPhone/iPad
- FOCAL - Cluster Analysis for Super-Resolved Microscopy
- FocalPoint 0.6 - Image Browser designed to work with more Complex Image Type
- Fragmentation - Fragmentation of the Gel Image into Sections
- FreeSFP - FREE Volume Rendering with one push on a button
- FRETSaw 1.0 - Image Browser for Examining Pairs of images generated by a FRET experiment
- Frida 1.1.0 - FRamework for Image Dataset Analysis
- G3data 1.5.4 - Extract Data from Graphs
- GCellIQ 1.0 - Genomic Cell Image Quantitator
- Gel Analyzer 2010a - 1D Gel Electrophoresis Image Analysis
- Gelapp 1.2.7 - DNA & Prot Gel Analyzer
- GelQuest 3.1.7 - Analysis of DNA Fingerprints
- GelScape 20030728 - Web-based Gel Viewing and Annotation System
- GelyMac - Calculate DNA Fragment sizes from Gel Electrophoresis Migration data
- GemIdent 2.1 - Statistical Image Segmentation System
- GetData 2.26 - Digitize Graphs and Plots
- Giotto 1.0.3 - Single-cell Spatial Analysis pipeline
- GoFigure 2.0.9.0 - Software package for the Analysis of in toto Image Sets
- GoIFISH 1.2 - Semi-automated Analysis of IFISH Images
- Graph Digitizer 2.16 - Digitization of Orthogonal Graphs
- GridMos 1.0 - Mosaicing tool (in MATLAB) to Improve Cell Counting
- GroupTracker 1.0.1 - Video Tracking system for multiple Animals under Severe Occlusion
- GSA Image Analyser 4.0.3 - 2D Images Analysis
- GSA Image Analyser Batch Edition 1.1.2 - Analyse Images in Batch Mode
- HCA-Vision 2.1.6 - Analysis of Cell Images
- HiTRACE 2.3.0 / HiTRACE-Web - High-Throughput Robust Analysis for Capillary Electrophoresis
- HTML5 PivotViewer 1.0 - A HTML5 Data Exploration Tool for Image based data sets
- HTPheno - Image Analysis Pipeline for High-Throughput Phenotyping
- Huygens 4.4 - 3D Huygens Deconvolution & Analysis Software
- Hybsweeper 02 - Detect High-density Plate Gridding Coordinates
- HypoTrace - Image Analysis Software for Measuring Hypocotyl Growth and Shape
- iCluster 1.05 - SubCellular Localisation Image Visualiser
- Icy 2.2.0.0 - Open Community Platform for Bioimage Informatics
- ilastik 1.3.3 - the Interactive Learning and Segmentation Toolkit
- Image 3.10 - The Fingerprint Image Analysis system
- Image SXM 2.05 - Scanning Microscope Images Analysis
- imageHTS 1.43.0 - Analysis of high-throughput Microscopy-based Screens
- ImageJ 2.2.0 - Image Processing & Analysis in Java
- ImagePlane - Analysis of Images of the Animal S. Mediterranea
- ImageSurfer 2.6.1 - 3D Imaging software to Visualize and Analyze Multi-channel Volumes
- ImageTracker 3.00 - Analysis and Measurement of Motion in Video
- imago 1.0.104 - Store, Organize, Search, and Analyze Scientific Images
- Imaris 9.3.1 - Analysis, Segmentation and Interpretation of 3D and 4D Microscopy datasets
- img2net - Automated Network-based Analysis of Imaged Phenotypes
- ImgLib2 2-5.12.0 - Image Processing JAVA Library
- IMOD 4.9.12 - Tomographic 3D Reconstruction & Modeling
- ITCN 1.6 - ImageJ Plugin for Image-based Tool for Counting Nuclei
- JavaScope 1.01 - Operate Philips CM200 Microscope & View Digital Images Remotely
- JVirGel 2.2.3b - Create Virtual 2D Pretein Gel
- KymoRod v0.12.0 - Matlab Graphical Interface for the Study of Hypocotyl Growth
- LaneRuler 1.1 - Identify Lanes in Gel Image
- LAS X 3.7.4 - Lite version of the confocal software Leica Application Suite
- LeafNet 0.0.1 - A CNN for Plant Identification
- LEVER - Stem Cell Segmentation, Tracking and Lineaging
- LSJuicer 0.2rc2 - Program for Squeezing Results from Linescan images
- MAGIC Tool 2.1 - MicroArray Genome Imaging & Clustering Tool
- Make2D-DB II 3.10.2 - Gel Electrophoresis 2D-PAGE Databases
- MAMLE 1.0 - Image Analysis of E. coli and other Bacteria
- MCF - Image Segmentation Algorithms for automated Single Cell Analysis
- Melanie 8.0 - 2D Gel Analysis Platform
- MELANIE VIEWER 7.0.7 - Visualize Gels and Related Data obtained from Melanie
- MENT - Microarray comprEssiOn Tools
- MicroCounter 1.00 - automatic Counting of Objects such as Bacterial Colonies from an JPEG Image
- microManager 2.0.0 - ImageJ Plugin of Imaging & Control of Automated Microscopes
- Micropilot v094 - Automation of Fluorescence Microscopy–based imaging
- MIPAV 10.0.0 - Medical Image Processing, Analysis, and Visualization
- MorphoGraphX 1.1.1280 - Visualization and Processing of 3D Biological Datasets
- MorphoLibJ 1.4.3 - Collection of Mathematical Morphology Methods and Plugins for ImageJ
- MOSAIC 2016 - ImageJ plugin for Biological Fluorescence Microscopy
- Mr T - Tomography software written in Python.
- MSight 3.0.2 - Image Analysis for LCMS
- Mytoe - Image analysis of Mitochondria
- NEMO 1.5.2 - Analyzing Gene and Chromosome Territory Distributions from 3D-FISH Experiments
- NeuriteIQ 1.0 - Quantitative Neurite Image Analysis
- NeuronIQ 1.5 - Quantitative Neuron Image Analysis
- NeuronStudio 0.9.92 - Reconstruction of Neuronal Structures from Confocal and Multi-photon Images
- NucleusJ 1.0.3 - Quantifying 3D Images of Interphase Nuclei
- NucType 1.5 - Measure Distances/Size of Chromosomes and analysis Karyotype
- OBCOL 1.45 - Organelle-based Colocalisation Analysis
- OMERO 5.6.3 - Management & Analysis of Biological Microscope Images
- OMERO.searcher 1.3 - Content-based Image search for Microscope Images
- OpenCFU 3.9.0 - Software tool to Count Cell Colonies Growing on Plates
- OpenSPIM 20150427 - Open-access Light-sheet Microscopy Platform
- OsiriX 12 - DICOM Viewer
- Packing Analyzer 8.5 - Detects the Geometry of Epithelial Tissues
- PALMsiever 1.0.1 - Visualization and Analysis Platform for Single-molecule Localization Microscopy
- PatternUnmixer 2.0 - Calculate the Fraction of Probe in each Subcellular Compartment for images containing mixed pattern
- PCaAnalyser - 2D-Image Analysis Based Module for Effective Determination of Prostate Cancer Progression in 3D Culture
- Peak Explorer 2.11 - Automatic Processing of Spectra
- PeakHeights 20180328 - Efficient Analysis of Fluorescent Peak Intensities in Electropherograms
- PFT3DR 20100707 - Compute 3D Reconstruction from 2D Projections of 3D Objects
- PhenoCapture 8.1 - Scientific Image Capture and Analysis software
- Phoretix 1D / Phoretix 1D Pro - 1D Gel Analysis
- Plasmodium Autocount 0.1 - Count Red Blood Cells infected with Plasmodium
- pyHIVE 1.0.8 - Health-related image visualization and engineering system using Python
- Q-IHC 2 - Cancer Imaging Analysis tools
- QuantiFly v2.0.35 - Automated Drosophila Egg Counting
- QuantiScan 3.0 - Densitometry using Ordinary Office Scanners
- RegStatGel 1211 - Identifying differentially Expressed Proteins based on 2D Gel Images
- RHScorer 2.1 - Score Gels
- RootArray - Microfluidic Device for Automated High Throughput Live Imaging of Gene Expression
- SAFA 1.1 - Semi Automated Footprinting Analysis
- Sassign 2 - C++ & MatLab Library for Image Target Tracking
- ScientiFig v2.99 - Build Publication-ready Scientific Figures
- SCIP 1.0 - Single-Cell Image Processor
- Scipion 3.0 - An Image Processing Framework for 3D Electron Microscopy
- SDA 1.0 beta - Statistical DIGE Analyzer
- Seg2Dgel 0.5.12 - 2D Electrophoresis Gel Spot Segmenter
- Segtrack - C++ & MatLab Library for Image Tracking & Segmentation
- sephaCe v3 - Segmentation of Adherent Biological Cell Boundaries
- SerialEM 3.7.11 - Electron Tomography Data & Image Acquisition
- SIA 0.9.0.23 - Shotgun Imaging software
- SIMToolbox 2.12- MATLAB toolbox for Structured Illumination Fluorescence Microscopy
- SLIF 2-2 - Subcellular Location Image Finder
- Software tools for analysis of Immunogold Labeling 1.3.4
- SparkSpotter 1.1 - ImageJ plugin to identify 'Spark' events
- SPIDER 26.06 - Image processing system for Electron Microscopy
- Spot 3.2 - Analysis of Microarray Images
- SpotCaliper - Fast Wavelet-based Spot Detection with Accurate Size Estimation
- Spotfinder v3.2.1 - Microarray Images Analysis & Gene Expression Quantification
- StackMeasure 1.0 - ImageJ Plugin to identify features of interest and measure the distance
- starrynite II 20150713 - Accurate, Probabilistic Tracking for Single Cell analysis and understanding
- Suprim 5.3.1 - Process Electron Microscopy Image
- SyncX CT Aligner 1.0 - Image Alignment for Tomography Reconstruction from Synchrotron X-ray Microscopic Images
- TACTICS 2.21 - MATLAB Platform For Customized Time-Lapse Microscopy Analysis
- TANGO 0.94 - Tools for Analysis of Nuclear Genome Organization
- TeraStitcher v1.10.18 - 3D Stitching tool designed for Teravoxel-sized microscopy images
- ThunderSTORM 1.3 - ImageJ plugin for PALM and STORM data analysis and super-resolution imaging
- TIKAL - 4-D Image Processing Platform
- TiltPicker 2.0b13 - Particle Picker for Image Tilt Pairs
- TimeLapseAnalyzer 1.34 - High Throughput data processing for Live Cell Imaging
- TinyQuant v1.55 - Gel Image Analysis
- TiQuant 2 - Biological Tissues Image Analysis and Quantification
- tkImgDip 1.00b0 - Data Image Portal
- TMAJ 3.7.1 - Tissue MicroArrays Information & Image Analysis Software
- TMARKER v2.158 - Cell Nuclei Counting and Staining Estimation
- TOMOJ 2.6 - Tools for Electron Tomography
- Tool for Biomedical Image Processing & Detection of Cancer using ANN
- top2maya - View 2D Atomic Force microscope Images as 3D Objects
- topaln 0.1 - Topological Alignments for Cell Tracking
- TopSpot 3.0 - Analysis of the Gel Image
- TrichEratops 1.0.6 - Analysis of Trichome Patterning
- TROPICAL 1.0 - Simulation and Parameter Estimation of Reaction-diffusion Models
- UnGraph 5 - Digitizer Program Which Gives X,Y Coordinates of Lines or Points on Scanned Images
- Vaa3D 4.001 - Bioimage Visualization & Analysis
- VANO 1.741 - 3D Image Annotator
- VIAS 2.4 - Multiple Stacks of Tiled optical sections obtained from Laser Scanning Microscopy
- Video Spot Tracker 8.11 - Track Motion of one or more Spots in Video
- ViewIt 4.23 - Multidimensional Image Processing Software
- VisBio 3.40rc1 - Biological Visualization Tool
- VisIt 3.2.1 - Visualization and Analysis tool for Viewing Scientific Data
- Visual3D 1.2 - Generate 3D Visualization of Fluorescence Microscopy Images
- Volume Browser 2.0.393 - View Three Dimensional Images over the internet
- Well Layout 1.2.1 - Describe 96-Well Experiment
- WinDig 2.5 - Image Data Digitizer
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