Posts
- Category: Assembly Tools (continued)
- Category: Bio-chemical / Engineering
- Biochemistry Lab Suite 3.0.1 - Tools Covering different fields of Biochemistry, Biology and Chemistry
- BioSM 1.00 - Identify Biochemical Structures in Chemical Structure Space
- BISEN 1.0.6 - Biochemical Simulation Environment
- BRD 4.0 - Bioreactor Design
- DynaFit 4.06.007 - Enzyme Kinetic Data Analysis
- ECOH 0.91.4 - Enzyme COmmission numbers Handler
- EnzFitter 2 - Curve Fitting & Analysis of Enzyme Kinetics Experiments
- ENZO - Building Kinetic Models of Enzyme Catalyzed Reactions
- IBRENA 1.0 - In silico Biochemical Reaction Network Analysis
- MACiE 3.0 - Exploring the Diversity of Biochemical Reactions
- Pajek Writer - Generation of Structural Representation of Biochemical Processes in Format Pajek
- Prometheus 0.8.0 - Storage, Management, and Analysis of Fermentation data
- Scaffold Hunter 2.6.3 - Analysis of Structure-related Biochemical data
- Category: Bioinformatics Platform
- BioSeqAnalyzer 1.0 - Analyze DNA and Protein Sequences
- .NET Bio 3.0.0-alpha - .NET Library for Biological Applications
- AiO 8 - Integrate Oligo ordering/Data Base and DNA/Protein programs
- AMEN 1.5.5 - Molecular Systems Biology Data Analysis
- ARB 6.0.6 - Sequence Database Handling and data analysis
- ARCT 0.9 - Comparative Genomics of Aging
- BATMAN-TCM - Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine
- Bio C# 1.0 - C# Class Library for Bioinformatics
- Bio-jETI 1.0 - Framework for Bioinformatics Workflows
- Bio-Linux 8.0 - Bioinformatics Workstation DVD-ROM ISO Image
- Bio++ 2.4.1 - C++ Libraries for Bioinformatics
- BioAnalyzer 2100 - Analysis of BioAnalyzer data
- BioC++ 0.3 - C++ Computational Libraries for Bioinformatics
- Bioclipse 2.6.2 - Life Sciences Workbench
- Bioclojure - Functional Library for the Manipulation of Biological Sequences
- BioCocoa 2.2.2 - Cocoa Framework for Bioinformatics
- Bioconda - Software Distribution for the Life Sciences
- Bioconductor 3.13 - Open Source Software for Bioinformatics
- BioDSL 1.0.2 - Bioinformatics Domain Specific Language
- BioExcel 2.0 - Microsoft Research Biology Extension for Excel
- Biogem 1.3.6 - Bioinformatics Software Development Environment for the Ruby
- BioGridRunner 2002 - Bioinformatics Data Grid Application
- Biohazard 0.6.2 - Bioinformatics Library and Assorted tools in Haskell
- BioHPC 1Rev293 - Computational Biology Application Suite for High Performance Computing
- BioInfoServ 6.0 - Bioinformatic Platform
- BioJava 5.4.0 - Java Framework for Processing Biological Data
- BioJS 2.0 - A library of JavaScript Components to Represent Biological Data
- bioknoppix 0.2.1 - Knoppix Linux Live CD for Molecular Biologist
- BioLite 1.0.0 - Bioinformatics Framework with automated Tracking of Diagnostics and Provenance
- BioMet Toolbox 2.0 - Genome-wide analysis of Metabolism and Omics data
- Bionode 1.0.1 - Node.js JavaScript library for Client and Server Side Bioinformatics
- Biopackages 1.9 - Packages for Bioinformatics
- BioPerl 1.7.2 - Perl Code in Biology
- Biopieces 2.0 - Bioinformatic Framework of Tools
- BioPig 2.0 - Hadoop-based analytic toolkit for large-scale Sequence data
- Biopython 1.79 - Tools for Biological Computation written in Python
- BioRuby 2.0.2 - Bioinformatics Software for Ruby Language
- BioSeq-Analysis 2.0 / BioSeq-BLM 1.0 - Analyzing DNA, RNA, and Protein Sequences based on Biological Language Models
- BioSLAX 7.5 - BioInformatics LiveCD Suite
- biosmalltalk 0.5.0 - Bioinformatics Library for Smalltalk
- BioWeka 0.6.1 - Weka Framework for Bioinformatics
- BIRCH 3.80 - Provide Bioinformatics Resources to Molecular Biologists
- birgHPC 1.2.1 - Creating instant Computing Clusters for Bioinformatics
- birgHPCC 1.0 - Creating Compute Unified Device Architecture (CUDA) Computing Cluster for Bioinformatics
- BIU 2.3.7 - Bioinformatic Utility Library
- BMT - Bioinformatics Mini Toolbox
- Bpipe 0.9.10 - A Tool for Running and Managing Bioinformatics Pipelines
- canEvolve - Integrative Cancer Genomics analysis of Expression, Copy Number, miRNAs and Network
- CARGO 2.0 - Web Portal to Integrate Biological Information
- CARMO v1.0 - Comprehensive Annotation of Rice Multi-Omics
- Cell Illustrator 5.0 - Platform for Systems Biology
- CFGP 201709 - Comparative Fungal Genomics Platform
- ChemoPy 1.0 - Python package for Computational Biology and Chemoinformatics
- Chinook 1.2.2 - Peer-to-peer (P2P) Bioinformatics Service
- Chipster v4 - Analysis software for Microarray and other High-throughput data
- CLIP-Explorer - Web Server for CLIP-Seq data analysis
- CloudBioLinux - Genome Analysis for Cloud Computing platforms
- CloudDOE 2.2.0 - MapReduce-based Bioinformatics Environment
- CloVR 1.0 RC9 - Automated Sequence Analysis from Your Desktop
- Confero 0.1 - Integrated Contrast and Gene Set Platform
- Cytoscape 3.8.2 - Platform for Complex-Network Analysis & Visualization
- Darwin 2.1 - Programming Environment for Bioinformatics
- deepTools 3.5.1 - Tools for Exploring Deep Sequencing data
- DIVERGENOME - Bioinformatics Platform to Assist Population Genetics and Genetic Epidemiology Studie
- DNALinux VD - A Linux Solution for Bioinformatics
- DNAMAN 10.0 - Integrated System for Sequence Analysis
- EBiAn - Easy Bioinformatics Analysis
- EMBOSS 6.6.0 / Jemboss 1.5 - Suite of Bioinformatics Tools
- Ergatis v2r18 - A Workflow System for Bioinformatics
- G-language 1.9.1 - Genome Analysis Environment
- Galaxy 19.09 - Evolutionary and Data Processing Module Development
- GC4S v1.6.0 - Bioinformatics-oriented collection of GUI Components for (Java) Swing
- GEM library PR3 - Index/Analyze Huge Genomes
- Genamics Expression 1.1 - DNA and Protein Sequence Analysis
- Geneious 2021.1 - Bioinformatics Software Suite
- GenePattern 3.9.11 - Genomic Analysis Platform
- Genoppi 1.0.13 - Integration of Proteomic and Genetic data
- GENtle2 0.7.0 - Web-Based DNA Editor for Synthetic Biology
- geWorkbench 2.6.0.3 - Open-source Platform for Integrated Genomics
- Gitools 2.3.1 - Analysis and Visualization of Genomic Data Using Interactive Heat-Maps
- GMS 20140126 - A Turnkey system for Variant Discovery and Interpretation
- Gramene r63 - A Resource for Comparative Grass Genomics
- InteractoMIX - Exploit Interactomes in Biological and Clinical Research
- IOBIO - Realtime Genomic Data Visualization and Analysis Web Tools
- ISYS 1.35 - Platform for Integrating Heterogeneous Bioinformatic Resources
- JABAWS 2.2 - JAva Bioinformatics Analysis Web Services
- KNOB 4.1 - CD-bootable Linux for bioinformatics
- KNOWENG - Knowledge Engine for Genomics
- LabtoolsQt 1.0.3 - Program for the Molecular Biological Lab
- LiSSI 1.0 - Integrated Bioinformatics Platform for Genomic Island Analysis
- Logol - Pattern matching language and tools
- MetaR 2.0.2 - Data Analysis with the R Ecosystem
- MG-RAST 3.5.11 - Metagenomics Analysis Server
- mixOmics 6.16.1 - Omics Data Integration Project
- MOBY 1.16 / BioMoby - Interoperability between Biological Data Hosts and Analytical Services
- Mobyle 1.5.5 - Integration of Bioinformatics Software and Databanks
- MolQuest 2.4.5 - Bioinformatics Toolbox for Analysis of Biomedical Data
- MOTHUR 1.45.3 - Bioinformatics Platform of Microbial Ecology Community
- MOWServ 2 - Web platform for Bioinformatics tools Integration
- NCBI C++ Toolkit 22.0 - Collection of C++ Modules for Bioinformatics
- NG6 3.2 - Next Generation Sequencing Information System
- NYoSh Analysis Workbench 2.0 - Biological data analysis based on Meta Programming System
- O-miner - Analysis and Annotation of Complex -omics Data
- OpenAlea 1.2 - Plant Modeling Environment
- Oqtans 0.1 beta - Online Quantitative Transcriptome Analysis
- ORCA - Genomics Research Container Architecture
- OSDDlinux 201310 - Customized Operating System for Drug Discovery
- Parallel-META 3.6 - A Parallel Metagenomic Analysis Pipeline
- PeanutDB 1.0 - Integrated Bioinformatics Web Portal for Arachis Hypogaea
- PiGx v0.0.3 - Pipelines in Genomics
- PROMO 2019.5.1 - Analyzing large Multi-omic datasets
- Pse-Analysis 1.0 - Sequence analysis based on Pseudo Components and Kernel methods
- pychem 3.05g - Python and Chemometrics package
- PyCogent 1.9 - Software Library for Genomic Biology
- Pygr 0.82 - Python Graph Database Framework for Bioinformatics
- QIAGEN CLC Main Workbench 21.0.4 - Bioinformatics Workbench
- QIIME2 2021.8 - Analysis of Microbial Communities
- Quantian 0.7.9.2 - Knoppix / Debian Variant Tailored to Numerical and Quantitative Analysis
- QUT.Bio beta - Tools for Bioinformatics and Computational Biology
- RECOG 1.1.32 - Research Environment for Comparative Genomics
- RSAT 2015 - Regulatory Sequence Analysis Tools
- Rust-Bio 0.34.0 - Bioinformatics Library for the Rust language
- SB.OS 1.4.1 - Systems Biology Operational Software DVD ISO Image
- SBW 2.12.2 - Systems Biology Workbench
- scikit-bio 0.5.5 - Python 3 package providing Data Structures, Algorithms and Educational Resources for Bioinformatics
- SEQ v0.9.4 - Language for Bioinformatics
- SeqAn 2.4.0 - Open Source C++ Library of Sequences Analysis
- seqtools 8.4.071 - Program Suite for Sequence Analysis
- SeqVISTA 1.81 - Sequence Feature Visualization & Comparison
- SeqWare 1.1.1 - Tool Set to work with Next Generation Genome Sequencers
- SeWeR 3.0 - Sequence Analysis using Web Resources
- Sirius PSB 2.3.3 - Generic System for Analysis of Biological Sequences
- SMS 2 - Sequence Manipulation Suite
- SOAP 3 - Short Oligonucleotide Analysis Package
- Sockeye 1.3 - 3D Visualization for Working with Genomic Information
- Staden 2.0.0b11 - DNA Sequence Assembly , Editing and Analysis
- STINGRAY 20140221 - The System for Integrate Genomic Resources and Analyses
- Strand NGS v4.0 - Data Mining and Visualization Platform of Bioinformatics Data
- StrBio 1.3 - Java Classes for Computational Structural Biology
- TAGOPSIN 1.3 - Collating Taxa-specific Gene and Protein Functional and Structural Information
- Taiji 1.3.0 - Multi-omics Bioinformatics Pipeline
- TREVA 1 - Bioinformatics Pipelines for Targeted Resequencing and Whole-exome Sequencing
- UGENE 33.0 - Integrated Bioinformatics Tools
- VigyaanCD 1.0 - Workbench for Bioinformatics
- VLinux 2.0 alpha 2 - Linux Workbench for Bioinformatics
- WebLab 1.2 - Multifunctional Bioinformatics Analysis Platform
- WebMGA - Web Server for fast Metagenomic Sequence Analysis
- Category: Cluster Analysis
- 2D-EM - Matlab package of 2D-EM Clustering approach
- AACK 1.0 - Add Annotation
- ACES - Machine Learning Toolbox for Clustering analysis and Visualization
- AMIADA 2.0.7 - Analysis of Microarray Data
- AncestralClust - Cluster Divergent Sequences
- APCluster 1.4.8 - Affinity Propagation Clustering
- AptaCluster / AptaGUI - Efficient Clustering of HT-SELEX Aptamer Pools
- ArrayMiner 5.3 - Microarray Gene Expression Data Analysis
- AutoSOME 2.0 - Clustering method for Identifying Gene Expression Modules
- BALBOA - Extension of Bicluster Analysis to allow for the Functional Classification of ORFs
- BCCA / ACCA / DCCA - Bi-Correlation / Average Correlation / Divisive Correlation Clustering Algorithm
- BHC 1.1.0 - Bayesian Hierarchical Clustering for R
- Bi-Force v2 - Large-scale Bicluster Editing and its application to Gene Expression data Biclustering
- BicAT 2.22 - Biclustering Analysis Toolbox
- BICLIC 1.0 - BIclustering by Correlated and Large number of Individual Clustered seeds
- BiCluE - Weighted Bi-cluster Editing of Biomedical Data
- Bicluster - Seed-based Biclustering of Gene Expression Data
- BiGGEsTS 1.0.5 - Biclustering Analysis of Time Series Gene Expression Data
- Bimax - Systematic Comparison and Evaluation of Biclustering Methods for Gene Expression Data
- BiMS 1.0 - Biclustering for Mass Spectrometry data
- bio-MOSAIC 1.0 - Multiple Orthologous Sequence Analysis and Integration by Cluster optimization
- BiVisu 1.3 - Bicluster Visualization
- BnpC - Bayesian non-parametric Clustering of Single-cell Mutation Profiles
- boostKCP - Boosting k-means Clustering for the Pearson correlation distance
- CABRA - Cluster & Annotate Blast Results Algorithm
- CAFS 1.0 - Cluster of Functional Shifts
- CAGED 1.1 - Cluster Analysis of Gene Expression Dynamics
- CAGEScan-Clustering 1.2 - Create CAGEscan Clusters from CAGE paired-end reads
- Calib v0.3.6 - Clustering UMI-barcoded Sequencing data
- CAPIU 0.2 - Clustering using A Priori Information via Unsupervised decision trees
- CFinder 2.0.6 - Cluster data represented by Large Graphs
- ChAT - Unsupervised algorithm to Search Combinatorial Chromatin Signatures.
- CLAG 2.18.1 - Unsupervised Non Hierarchical Clustering algorithm
- CLCL 1.0 - CLique CLustering
- CLEAN 1.3.1 - CLustering Enrichment ANalysis
- Cleaner 1.03 - Assembly of Informative, Transcript-specific Probe-clusters
- CLENCH 2.0 - Calculate Cluster Enrichment using the Gene Ontology
- CLIC v1.0 - Clustering by Inferred Co-expression
- CLOSET r78 – CLoud Open SequencE clusTering
- CLUSPECT 1.0 - Supervised spectral clustering
- Cluster 3.0 20190830 - Enhanced Version of Cluster
- ClusterA 1004 - Calculating Silhouette scores for Assessment of SNP Genotype Clusters
- clusterGenomics 1.0 - Identifying Clusters in Genomics data by recursive Partitioning
- ClusterLustre 1.2 - Consensus Clustering
- clusterMaker2 1.3.1 - Creat and Visualize Cytoscape Clusters
- ClusterProject 1.0 - Computer Software for Clustering Analysis
- clusterScore 0.12 - Clustering of Cavbase Scores and other proximity matrices
- Clusterv 1.1 - Cluster Validation
- ClusterViz 0.2 - Cluster Visualisation
- ClustEval 1.6 - Integrative Clustering Evaluation Framework
- CLUSTOM-CLOUD 1.0.0 - CLUSTering 16S NGS Sequences by Overlap Minimization
- ClustVis - Visualizing Clustering of Multivariate data
- CLUTO 2.1.2a / gCLUTO 1.0 - Software for Clustering High-Dimensional Datasets
- ClutrFree 1.4 - Cluster Viewer Package
- COGRIM - Clustering of Genes into Regulons using Integrated Modeling
- CompClust 1.2 - Explore and Quantify Relationships between Clustering Results
- COMUSA - Combining Multiple Clusterings Using Similarity Graph
- CONCOCT 1.1.0 - Clustering cONtigs with COverage and ComposiTion
- CoSBI - Identify Combinatorial Chromatin Modification Patterns across Genomic Loci
- CRC 1.1 - Dirichlet Process Model-based Cluster
- CREAM 1.1.1 – Clustering of Genomic Regions Analysis Method
- CROP 1.33 - Clustering 16S rRNA For OTU Prediction
- CrunchClust V43 - Clustering software for 454 Sequence
- CurveSOM - Curve-based Custering of Time Course Expression data
- DBC 6.11.13 / dbOTU3 - Distribution-based Clustering
- dChip 2011.12 - Analysis & Visualization of Gene Expression & SNP Microarrays
- ddClone - Joint Clustering of Single Cell and Bulk Data
- DGEclust 20171006 - Hierarchical non-parametric Bayesian Clustering of Digital Expression data
- Diametrical Clustering - Identify Anti-correlated Gene Clusters
- DomClust - Hierarchical Clustering for Orthologous Domain Classification
- DRAGON - Matlab package of DRAGON Clustering approach
- DySC 20120601 - Software for Greedy Clustering of 16S rRNA Reads
- EDISA 1.0 - Extracting Biclusters from multiple Time-series of Gene Expression Profiles
- EFC - Evolutionary Fuzzy Clustering
- ELaSTIC 1.90 - Rapid Identification and Clustering of Similar Sequences
- EnsemblQDB - Ensembl Query-based Biclustering
- Epiclomal - Clustering of sparse DNA Methylation data
- ESPRIT-Tree 1.2 - Hierarchical Clustering Analysis of Massive Sequence data
- Excavator 2.0 - Gene Expression Data Clustering
- ExpressionView 1.00 - Explore Biclusters Identified in Gene Expression data
- FABIA 2.20.0 - Factor Analysis for Bicluster Acquisition
- FastaHerder2 - Clustering for Analysis of Protein Similarity
- FEAST - Feature selection for scRNA-seq Clustering
- FreClu - Efficient Frequency-based De novo Short Read Clustering
- FunCluster 1.07 - Functional Analysis of Gene Expression data
- Furby 3.1.3beta1 - Fuzzy Force-Directed Bicluster Visualization
- fuzzyClustering - K-partite Graph Clustering algorithm that allows for Overlapping (Fuzzy) Clusters
- GaneSh - Cluster Expression Data by Gibbs sampling procedure
- Gclust 3.5.5z3 - Genome-wide Clustering
- gCluster - General Clustering Method
- GDHC - Nonlinear Hierarchical Clustering
- GEMS 1.5 - Biclustering Analysis of Expression data
- GenClust 2.0 - Clustering Gene Expression data
- generate_oriented_clusters - Single-linkage Clustering of Chromosomal Locations
- geneRxCluster 1.22.0 - Detect Differential Clustering of Genomic Sites
- Genesis 1.8.1 / GenesisServer 1.1.0 - Cluster Analysis of Microarray data
- GenomeCluster 20140824 - Clusters of Genome Elements
- GICL 0.01 - Cluster & Assembly of a large EST/mRNA dataset
- GIMM 3.8 - Gaussian Infinite Mixture Models for Cluster Analysis of Genomics Data
- GiniClust3 1.0.1 - Detecting Rare Cell Types from Single-cell Gene Expression data with Gini Index
- GWproxy - Clustering Metagenome Short Reads using Weighted Proteins
- HAC 1.2.1 - Hierarchical Agglomerative Clustering for a large-scale Network data
- Hammock v1.2.0 - Hidden Markov Model-based Peptide Clustering algorithm
- HappieClust 1.6.1 - Fast Approximate Hierarchical Clustering using Similarity Heuristics
- hclust 1.0 - Clustering Expression data with Hopfield Networks
- Hetero-RP - Enhanced Clustering and Classification in Integrative Genomics
- HHCompare - HMM based protein Hierarchical Clustering
- HiDimViewer - Visualization tool for High-dimensional Datasets
- HiFiX 1.0.6 - High-quality Sequence Clustering
- HML - Tool to perform Hierarchical Maximum Likelihood (HML) Clustering
- HTSCluster 2.0.8 - Clustering High Throughput Sequencing (HTS) data
- iCluster 2.1.0 / iClusterPlus 0.99.4 - Integrative Clustering of Multiple Genomic Data Types
- IMHRC V1 - Inter-Module Hub Removal Clustering
- IntNMF 1.2.0 - Integrative Clustering of Multiple Genomic Dataset
- ISA 1.0.0 - Iterative Signature Algorithm
- isONclust 0.0.4 - de novo Clustering of long Transcript Reads into Genes
- J-Express 2012 - Analysis and Visualization of Microarray Data
- Java Treeview 1.1.6r4 - Gene Expression Visualization Tool
- JustClust - Analysing Biological Data with Cluster Analysis
- KAUSTNMF - Non-negative Matrix Factorization by Maximizing Correntropy for Cancer Clustering
- kClust - Fast and Sensitive Clustering of large Protein Sequence Databases
- KegArray 1.2.4 - Microarray Data Analysis & Cluster
- Kolmogorov - Compression-based Classification of Biological Sequences and Structures
- LAS - Finding Large Average Submatricies in High Dimensional Data
- LCD - Local Coherence Detection
- LCS-HIT 0.5.3 - Sequecence Clustering tool
- LEB - Localize and Extract Biclusters
- Local Clustering - Find Timeshifted and/or Inverted Relationships in Gene Expression data
- LRAcluster 1.0 - Low Rank Approximation based Multi-omics Data Clustering
- LRC - Logistic Regression Model and Clustering Approach
- LUMIWCLUSTER 1.0.2 - Implement Weighted Model based Clustering
- M-pick - Modularity-based Clustering method for OTU picking
- MACCU 0.7 - Multi-Array Correlation Computation Utility
- MACML 1.1.2 - Model Averaging Clustering by Maximum Likelihood
- MAExplorer 0.96.34.01 - MicroArray Explorer Tool
- MAGIC Tool 2.1 - MicroArray Genome Imaging & Clustering Tool
- MatrixClust 20080804 - Fuzzy Clustering of a Symmetric Matrix
- MBCluster.Seq 1.0 - Model-Based Clustering for RNA-seq Data
- MCAM v9 - Multiple Clustering Analysis Methodology
- McKmeans 0.42 - Multi-core algorithm for Clustering extremely large datasets
- MCL 14-137 / MCL-edge - Cluster Algorithm for Graphs
- MCRL v1.01 - Metagenomic Clustering by Reference Library
- MDI-GPU 1.0.1 - Accelerating integrative modelling for Genomic-scale data using GP-GPU Computing
- MetaCon - Unsupervised Clustering of Metagenomic Contigs with Probabilistic k-mers Statistics and Coverage
- Mfuzz 2.51.0 - Soft Clustering of Microarray data
- MITree - Clusterin Algorithm based on a Straightforward Geometric principle
- MMseqs2 R13 - ultra Fast and Sensitive Protein Search and Clustering suite
- MOCSVM 2 - Multiobjective Clustering with Support Vector Machine
- Modk-Prototypes - Clusters Biological Samples
- Mosclust 1.0 - Discovery of Significant Structures in Bio-molecular data
- MSBE 1.0.5 - Analysis of Gene Expression data using a new bi-clustering method
- MSClust 20130708 - Clustering 16S rRNA sequences into OTUs
- MULCCH - MULti-task spectral Consensus Clustering for Hierarchically related tasks
- NB.MClust 1.1.1 - Negative Binomial Model-Based Clustering
- NCIS - Network-Assisted Co-clustering Algorithm to Discover Cancer Subtypes based on Gene Expression
- NEMO v0.1 - Neighborhood based multi-omics Clustering
- Network Motif Clustering Toolbox 2.0 - Cluster Topological Network Motif
- NNN 1.01 - Nearest Neighbor Networks Clustering
- OC 2.1a - Cluster Analysis Program
- OCG 1.0 - Create Overlapping Class system
- OrthoClust - Orthology-based Network Framework for Clustering data across multiple Species
- OSCAR 6.1.1 - Open Source Cluster Application Resources
- PathoGiST v0.3.6 - Clustering Pathogen Isolates by combining multiple Genotyping Signals
- Pathway - Heritable Clustering Algorithms
- pcaReduce 1.0 - Hierarchical Clustering of Single Cell Transcriptional Profiles
- pClust 1.0 - Parallel Identification of Dense Protein Clusters
- PFClust - Novel Parameter Free Clustering algorithm
- piClust - Find piRNA Clusters and Transcripts from small RNA-seq data
- psi-square 1.2 - Search the Space of Gene Vectors
- pvclust 2.2-0 - Hierarchical Clustering with P-values
- QCanvas 1.2.1 - Fast Clustering and Visualization of data
- QCluster - Extending Alignment-free Measures with Quality Values for Reads Clustering
- QDB 1.1 - Query Driven Biclustering
- QuartPAC 1.16.0 - Identification of Mutational Clusters in Protein Quaternary Structures
- QUBIC2 / QUBIC-R 1.20.1 - Biclustering Tool for Microarray Data
- RAP - Association Analysis Approach to Biclustering
- RECLU 1.0 - Clustering pipeline with multiple scales for Capped Analysis of Gene Expression (CAGE) datasets
- relax_bicluster - Bicluster based the Probabilistic Relaxation Labeling Framework
- RPMM 1.25 - Recursively Partitioned Mixture Model for Beta and Gaussian Mixtures
- rsgcc 1.0.6 - Gini methodology-based correlation and Clustering analysis of Microarray and RNA-Seq Gene Expression data
- Samster 2.0 - SAM to Cluster
- SCG 20110716 - Self Consistency Grouping
- SCHype 1.0 - Spectral Clustering in Hypergraphs
- SCPS 0.9.8 - Spectral Clustering of Protein Sequences
- SCSC - Cross-species Soft Clustering
- SCUDO - Signature-based Clustering of Expression Profiles
- Secator/DPC - Sequence Clustering from a Multiple Alignment
- SEED 1.5.1 - Clustering Next Generation Sequences
- SICER 1.1 - Identification of Enriched Domains from Histone modification ChIP-Seq data
- SiLiX 1.2.11 - Ultra-fast Sequence Clustering from Similarity Networks
- SIML - Matlab package of SIML Clustering approach
- SLP - Single-Linkage Preclustering for improved OTU clustering
- SP/SS Clustering - Superparamagnetic Clustering and Sequential Superparamagnetic Clustering
- SpaCEM3 2.0 - Spatial Clustering with EM and Markov Model
- Spark 1.3.0 - Interactive Cluster Visualization Tool
- SparseDC 0.1.17 - Sparse Differential Clustering
- SPICi - Fast Biological Network Clustering Algorithm
- SS-CoSBI - Finding Combinatorial Histone Code by Semi-supervised Biclustering
- Starcode 1.4 - All Pairs Search and Sequence Clustering
- TGICL 2.1 - TGI Clustering Tools
- TiCoNE 2.0.0 - Cluster multi-patient-sample Time-series data
- TimeClust 1.3 - Clustering tool for Gene Expression Time Series
- TimesVector 1.5 - Analysis of Time Series Transcriptome data from multiple Phenotypes
- tlcluster 1.0 - Clustering on Fasta Formatted Sequences
- TransClust - A Feature-rich Clustering tool for Biomedical Data sets
- Treebic 1.11 - Hierarchical Generative Biclustering for MicroRNA Expression Analysis
- TriCluster / MicroCluster - Microarray Gene Expression Clustering
- UIcluster 3.0.5 - Parallel Clustering of EST (Gene) Sequences
- ValWorkBench 1.0 - Java library for Cluster Validation
- Venn Mapper 1.01 - Compare Heterologous Microarray Data Sets
- VISDA 1.0 - Visualization, and Discovery for Cluster Analysis of Genomic data
- VIZARD 1.2 - Affymetrix GeneChip® Data Analysis & Visualization
- WCD 0.6.3 - DNA Sequence Clustering tool
- WebGimm - Cluster Analysis Server
- Category: Cytometry / Cell
- ACME - Automated Cell Morphology Extraction
- BayesFlow 0.1 - Latent Modeling of Flow Cytometry Cell Populations
- BioLegend Flow Cytometry Application 1.6 - Information about Flow Cytometers and Fluorochromes
- C2G v1.2.2 - Visualize Clustering Results of multi-dimensional Flow/Mass Cytometry data
- CBO 1.1.2 - Describing the Intrinsic Biological Behaviors of Real and Model Cells
- CCLA - Cancer Cell Line Authentication
- Cell Culture 1.0 - Record Cell Culture Data in the lab
- cell-motility 2.0 - Analysis of Cell Motility Paths over time
- CellAtlas 1.5 – Blood Cell Morphology Guide for Mobile
- CELLector v1.2.1 - Genomics Guided Selection of Cancer in Vitro Models
- CellFinder 1.5.1 - Study Annotations, Bibliography, Gene and Protein Expression in Stem Cells and Derivatives
- cellgraphs - Datastructure to Describe Cells in Tissue
- CellMontage 2 - Gene Expression databases searching system for Cells-type Analysis
- CellNet / CellNetR - Network Biology applied to Stem Cell Engineering
- CellOrganizer 2.8.1 - Image-derived Models of Subcellular Organization and Protein Distribution
- CellTrack - Cell Tracking and Motility Analysis
- Cellular Symphony - Audio Representation of Flow Cytometric Data
- CIRCLET - Circular Trajectory Reconstruction tool
- CLOCCS 2.0.0 - Characterizing Loss of Cell Cycle Synchrony
- CoD - Inferring Immune-Cell Quantities Related to Disease States
- Cyflogic 1.2.1 - Flow Cytometry Data Analysis Tool
- Cytobank - Analytics Platform for Community Cytometry Data Analysis
- Cytospec V11.8 - Flow Cytometry Analysis Program
- DCell 1.4 - Deep Neural Network simulating Cell Structure and Function
- De-Identifier - Remove Patient Identification from FCS file
- FCS Express 7.06.0015 - Flow Cytometry Tool
- FCS File Mixer - Merge FCS Listmode Files
- FCS File Sanitizer - Changes Keywords in an FCS File
- FCSExtract 1.02 - Extracts Flow Cytometry data from binary FCS files
- FCSViewer 2.0 - Decompresses FCS data files for Display
- Ferdinand 3.10 - Read and analyze FCS 3.0 data files collected by Flow Cytometers
- FIND 0.31 - Flow Investigation using N-Dimensions
- Flow Cytometer Simulator - Simulation of a Working Flow Cytometer
- Flow Explorer 4.2 - Analysis for Flow Cytometry File
- FlowAnd 1.0 - Analyze Largescale, Multi-color Flow Cytometry data
- flowBin 1.28.0 - Combining Multitube Flow Cytometry data by Binning
- flowCL 1.30.0 - Semantic labelling of Flow Cytometric Cell Populations
- flowDensity 1.27.0 - Sequential Flow Cytometry Data Gating
- flowFit 1.24.0 - Estimate Proliferation in Cell-tracking Dye Studies
- FlowJo v10.7 - Analysis Package for Flow Cytometrists
- flowLearn - Machine-learning algorithm for Gating Flow Cytometry data
- flowPeaks 1.38.0 - Fast unsupervised Clustering for Flow Cytometry Data
- flowPhyto 2.4.1 - Analysis of Continuous Flowcytometry Data
- flowVS 1.24.0 - Variance Stabilization in Flow Cytometry
- GemStone 1.0 - Analysis of High-dimensional, Flow Cytometry Data
- GenoSIGHT - Imaging Cytometry
- Hackit - Program for Clipping & Joining FCS List Mode Data Files
- HIPPO 1.5.0 - Heterogeneity Inspired pre-processing Tool
- ImmuCellAI / ImmuCellAI-mouse - Immune Cell Abundance Identifier / for mouse
- JRIM - Joint reconstruct cis-regulatory interaction networks of multiple cell populations
- LDATAPP 2.0 - Convert FCS data to ASCII text
- ListMath 2.1 - Create Histograms & Plots from Flow Cytometry List-Files
- MFI 3.4kb8 - Analysis of Flow Cytofluorometry Data
- ModFit LT 5.0 - Flow Cytometry Modeling
- Mogrify - A Directory of defined Factors for direct Cell Reprogramming
- NetworkPainter - Pathway Animation in Cytobank
- openCyto 2.3.0 - Data Analysis pipeline for Flow Cytometry.
- ParticleStats 0.3 - Analysis of Particle Motility and Cytoskeletal Polarity
- PERT 1.0 - Expression Deconvolution under Varied Environmental Conditions
- QSpec 1.0 / QSpec-Simu 1.0 - A Raman Spectrum Acquisition and Analysis System for Single-Cell
- QUALIFIER 1.26.1 - Qualitiy Control for Gated Flow Cytometry data
- RchyOptimyx 2.32.0 - Optimyzed Cellular Hierarchies for Flow Cytometry
- RefreshRatio 4.0 - Refresh Ratios in Flow Cytometry List-Files
- SCANN 1.0 - Stem Cell Characterisation by Artificial Neural Network
- scHiCluster v0.1.1 - Single-cell Clustering algorithm for Hi-C Contact Matrices
- scHiCNorm - Eliminate Systematic Biases in Single-cell Hi-C data
- Schnitzcells - Quantitative Analysis of Fluorescent Time-lapse movies of Living Cells
- SIMBA v1.1 - SIngle-cell eMBedding Along with features
- SPADE 3.0 / CytoSPADE 2.2 - Cyto / Spanning tree Progression of Density normalized Events
- SPICE 6.1001 - Data Mining & Visualization Software for Multicolor Flow Cytometry
- T Cell Analyser 1.7.0 - Analysis of T Cell
- TestDNA - Generates FCS Histograms of Cell Cycle Data
- THANATOS 1.0 - THe Apoptosis, Necrosis, AUtophagy OrchestratorS
- TIMER - Web Server for Comprehensive Analysis of Tumor-Infiltrating Immune Cells
- TLM-Tracker - Single Cell analyses in Live-cell Imaging experiments
- Vcellid 0.4 /CellID 1.4.6 / Rcell 1.1-8 - Microscope-Based Cytometry Cell-finding, Tracking & Analysis
- VirtualCytometry - Webserver for the Study of Immune Cell Differentiation using single-cell RNA sequencing data
- ViSNE / CYT - Map High-dimensional Cytometry data onto Two Dimensions
- WEASEL 3.7.1 - Flow Cytometry Data Analysis
- WholeCellViz - Data Visualization for Whole-cell Models
- WinList 3D 9.0 - Flow Cytometry Data Analysis
- WinMDI 2.9 - Windows Multiple Document Interafce for Flow Cytometry
- WinWCP V5.5.6 - Recording and Analysing Signals from Whole Cell Voltage and Current Clamp Experiments
- X-CYT 1.3 - User-guided Automated Flow Cytometric Data Analysis
- Category: DNA / Genome Analysis
- 3PEAT - Paired-End Analysis of Transcription Start Sites in Arabidopsis Reveals Plant-Specific Promoter Signatures
- 3SEQ 1.1.0812 - Software for Detecting Recombination in Sequence data
- 3SEQ_2D 20100830 - Detecting Gene Conversion Events in Whole Genomes
- 454sim 1.04 - An efficient Simulator of 454 data using Configurable Statistical models
- 4Peaks 1.8 - View & Edit DNA Sequence Trace Files
- 6mA-Finder - Computational prediction of 6mA sites in the DNA sequences
- A program suite for Filtering False Somatic Mutations from FFPE Tumor Sequencing data
- AAT 20110305 - Analysis & Annotation of Genomic Sequences
- ABrowse - Customizable Next-generation Genome Browser Framework
- absee 1.1.1 - Reads ABIF files
- ABSOLUTE 1.0 / HAPSEG – Estimate Purity/Ploidy and absolute copy-number and mutation data
- AbundanceBin 1.0.1 - Abundance-based tool for Binning Metagenomic Sequences
- Acacia 1.53 - Error-corrector for Pyrosequenced Amplicon Reads
- AccNET V1.2 - Accessory Genome Constellation Network
- ACCUSA 20140930 / ACCUSA2 - (Multi-purpose) SNP Calling on Draft Genomes
- ACD 1.0 - Analysis of the Results of Whole Genome Scans
- ACE 1.01 - Accurate Correction of Errors using K-mer tries
- ACES v.1.2 - Analysis of Conservation with an Extensive list of Species
- ACEScan 1.0 - Prediction of Conserved Alternatively Spliced Exons from pairs of Conserved Mouse/Human Exons
- ACME v1 - Efficient Parallel Motif Extraction from Very Long Sequences
- AcrFinder - Automated Identification of Acr-Aca loci
- ACT - Aggregation and Correlation Toolbox for analyses of Genome Tracks
- ACT 13 - Display Pairwise Comparisons between DNA Sequences
- AdapterRemoval v2.3.2 - NGS Data Trimming and Collapsing
- ADHoRe - Detect Genomic Regions
- ADMIRE v1.1.0 - Analysis of DNA Methylation in Genomic Regions
- ADOPS 0.7.4 - Automatic Detection of Positively Selected Sites
- AFST 1.0 - Abnormality Filtering and Sequence Trimming for ESTs
- AGapEs - Gap filling based on Template Sequence for aDNA data
- AGB - Ancestral Genome Browser
- Agene - Automatic Generation of Species Specific Gene Predictors
- AggloIndel - Detect Structural Variations
- AGILE v1.0 - Methodologies for Genome Mining and Annotation
- AgileAnnotator 20140613 - Identifying Sequence Variants in ordered SAM files
- AgileFileViewer 20130503 - Reads Sequence Variant File and Displays Associated Information for each Variant.
Plugin by dagondesign.com