Posts
- Category: Miscellaneous (continued)
- GiA Roots - Analysis of Plant Root system Architecture
- GIC - Gene Importance Calculator
- GIFT 1.0.0 - Global Optimization-based Inference of Chemogenomic Features from Drug-Target Interactions
- Gigwa 2.4.1 - Genotype Investigator for Genome Wide Analyse
- Gimli 1.0.2 - Annotation of Biomedical Entity Names
- GIPSy 1.1.3 - Genomic Island Prediction Software
- GIVE v0.2.0 - Genomic Interaction Visualization Engine
- GLAD4U 2018 - Gene List Automatically Derived For You
- GLFD - Guided Latent Factor Discovery
- glmgraph 1.0.3 - Graph-Constrained Regularization for Sparse Generalized Linear Models
- GLnexus v1.4.1 - Scalable Joint Variant Calling
- Glo-DB - Genomic Locus Operations Database
- GMQL 1.0.1 - GenoMetric Query Language
- GMS-MP 1.0 - Gibbs Motif Sampler for Pare Correlation Model
- GNomEx - Genomic Experimental Data Repository and Core LIMS
- gNOMO - Host and Microbiome analysis of non-model Organisms
- gnuplot 5.4 - Simple Data Plotting Program
- GO2MSIG 20131106 - GO based GSEA Gene Set Generator
- Gobe - interactive Comparative Genomics Viewer
- GOGO - Measure Semantic Similarity between Gene Ontology terms
- GOMEP - Gene Ontology-based Missing Enzyme Predictor
- GOplot 1.0.2 - Visualization Of Functional Analysis Data
- GOssTo 1.01 – the Gene Ontology Semantic Similarity Tool
- GPKB - Genomic and Proteomic Knowledge Base
- GPSmatch - Genomic-Binding Profile Similarity Match
- GQL 1.0 - GHMM-based tool for Querying and Clustering Gene-Expression time-course data
- GQT 1.0 - Genotype Query Tools
- Gracob - Graph-based Constant-Column Biclustering Algorithm
- GRAM - Predict Molecular Effect of Non-coding Variant in Cell Type-specific Manner
- GrandForest 0.1 - Discovering Disease-associated modules from Genomic Profiling data
- GRAPES 2.9 - SMP Querying system for Efficient Parallel Subgraph Isomorphism in databases of Graphs
- GRAPHITE - Graph-based Variant Adjudication
- Graphviz 2.46.0 - Easy Drawing of promoter->gene->terminator Diagrams
- Grid Cell Counter 0.9.9 - Count the Cells Shown on Computer Screen
- GSCA / cGSCA - Gene Set Control Analysis
- GSCA / GSCALite - Gene Set Cancer Analysis
- GSCANDB 1.0 - Portable System for Managing and Viewing Genome Scan Data
- GSKernel 1.1 - Generic String Kernel
- GsmPlot - Web Server to visualize Epigenome data in NCBI
- GUARDD 2017 – Graphical User-friendly Analysis of Relaxation Dispersion Data
- GUcal 1.2 - Capillary Electrophoresis based Glycan Analysis
- GUIDEseq 1.20.0 - Identifying Off-targets with GUIDE-seq data
- guiLiner 0.4 - Graphical User Interface for Biological Analysis Software
- GWAB - Web Server for Network-based Boosting of Human Genome-wide Association data
- HacDivSel 1.5 - Detection of Divergent Selection
- HAIviz v.0.3 - Healthcare-associated infections Visualization tool
- Halvade 1.3.0 - Implementation of the best Practice DNA-seq Pipeline
- HaMMLET - Fast Bayesian Hidden Markov Model with Wavelet Compression
- Handlebar 2.2.2 - Web Based Sample Inventory Manager
- HapTree-X v1.0 - Haplotype Reconstruction tool Tailored towards RNA-seq Reads
- Harmonizome 1.5 - Integrated Knowledge About Genes & Proteins
- HATSEQ / HAT - Hypergeometric Analysis of Tiling-arrays and SEQuence data
- Haystack 0.5.5 - Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline
- HCCDB - Integrative Molecular database of Hepatocellular Carcinoma
- Heat*seq - High-throughput Sequencing Experiment Comparison with Public data
- HeatmapGenerator 5 - Create Customized Gene Expression Heatmaps
- Heatmapper - Visualizing Various Types of data as Heat Maps
- HelixMC - Python-based Monte Carlo simulator for DNA/RNA duplexes
- HemI 1.0.1 - Heatmap Illustrator
- Hemolytik - Database of Hemolytic and Non-hemolytic Peptides
- HerceptinR - Database of Herceptin Resistance
- HGNChelper 0.8.1 - Handy functions for working with HGNC Gene Symbols and Affymetrix probeset identifiers
- hiBRCApCR 1.0 - Predicting pCR for Breast Cancer Subtypes
- HiCat - Hi-C data analysis tool
- HiChIP - A high-throughput pipeline for Integrative Analysis of ChIP-Seq data
- HiCNN 2 - Enhance the Resolution of Hi-C data
- HiCNorm - Removing Biases in Hi-C data via Poisson Regression
- HiCPlotter 0.6.6 - Integrating HiC data with Genomic datasets
- HiCseg 1.1 - Detection of Domains in HiC data
- HiCUP 0.8.2 - Hi-C User Pipeline
- hiddenDomains 3.1 - A modern HMM to Identify ChIP-seq Enrichment
- hiHMM - Bayesian non-parametric joint inference of Chromatin State Maps
- HINT 0.1.1 - Hmm-based IdeNtification of Tf footprints
- HiNT v2.2.7 - Hi-C for Copy Number Variation and Translocation Detection
- HiSIF 1.0 - HiC Significant Interacting Fragments
- histoneHMM 1.8 - Differential Analysis of Histone Modifications with broad Genomic Footprints
- HitSeekR - High-Throughput Screening Kit for R
- HIVE - High-performance Integrated Virtual Environment
- HIVE Pubcast Beta - Pubmed Buzzfeed for Android Mobile Devices
- HLA Assignment 2 - Determine which HLA Genes are responsible for Patient’s Reaction
- HLA Completion 2.0.0.3 - Input HLA typing data (loci A,B,C) and Resolves the Typing Ambiguities
- HLA-IMPUTER - HLA Imputation and Association analysis using Population-specific Reference Panels
- HOODS - Finding Context-specific Neighborhoods of Proteins, Chemicals and Diseases
- HPV-EM 1.0.2 - HPV Detection and Genotyping tool
- HTRgene - Integrating Heterogenous Multiple Time-series Data to Investigate Stress Response Gene and Signaling
- hts-nim v0.2.22 - Scripting high-performance Genomic Analyses
- htsint 0.5.2 - High Throughput data Integration tool
- HubPredictor v1.0 beta - Predicting Chromatin Interaction Hubs using Histone Marks information
- HumCFS - A Database Of Human Chromosomal Fragile Sites
- HumMeth27QCReport 1.2.14 - Quality Control of Illumina’s Infinium BeadChip Methylation Assays
- HyDe v0.4.3 - Hybridization Detection
- i-cisTarget - Prediction of Regulatory Features and Cis-regulatory modules in Drosophila
- I, Librarian 5.9.2 - PDF manager for Scientific Articles
- iARG - Imperfect Ancestral Recombination Graph Reconstruction
- Ibidas 0.1.26 - Integrated Database System for Biological Data
- ICeE 2.10 - Interface for C. Elegans Experiments
- iCut DNA 2.5.0 - Search the Restriction Enzyme Database (REBASE) for Enzymes
- iDES 1.1 - Integrated Digital Error Suppression
- iDNA-ABT - Detecting DNA Methylation with Adaptive Features and Transductive Information Maximization
- iDTP - integrated structure- and system-based approach of Drug-target Prediction
- Igloo-Plot / Web-igloo - Interactively Visualizing multivariate data without Feature Decomposition
- IgPred - Prediction of Antibody-specific B-cell Epitopes
- iHOP - Information Hyperlinked over Proteins
- IL-10Pred - Prediction of Interleukin-10 inducing peptides
- IL4pred - Designing and Disovering of Interleukin-4 inducing peptides
- iLAP 1.3.3 - Laboratory Data Management, Analysis and Protocol Development
- iLocator - An Image-based Multi-label Human Protein Subcellular Localization Predictor
- IM-PET - Integrated Methods for Predicting Enhancer Targets
- imCellPhen Alpha - Interactive Mining of Cellular Phenotypes
- iMCMC - Illustrate Markov chain Monte Carlo (MCMC) for a Simple Landscape
- imDEV 1.4.2 - omics data exploration and visualization in Excel
- Impact Factor Calculator - Calculate dozens of personal Impact Factors from Citation data
- IMPACT_S 1.0.0 - Integrated Multiprogram Platform to Analyze and Combine Tests of Selection
- ImpG-Summary 1.0.1 - Imputation from Summary Statistics
- Indicspecies 1.7.9 - Studying the Statistical Relationship between Species and groups of sites
- Infomap Bioregions - Interactive mapping of Biogeographical Regions from Species Distributions
- InfoMating 0.4 - Non-random mating and Information Theory
- InParanoid 8 - Eukaryotic Ortholog Groups
- INSIGHT 1.1 - Inference of Natural Selection from Interspersed Genomically coHerent elemenTs
- Insyght - Conserved Synteny Homolog Browser
- inTB - Platform for Molecular and Clinical Epidemiological Analysis of Tuberculosis
- Intensification - A Resource for Amplifying Population-genetic Signals with Protein Repeats
- InteractiVenn - Analysis of Sets through Venn Diagrams
- InterMine 5.0.3 - Open Source Biological Data Warehouse System
- InterSIM 2.2.0 - Simulation of Inter-Related Genomic Datasets
- IntervalStats - Statistical Evaluation of ChIPseq Dataset Similarity
- iONMF 1.1 - Integrative Orthogonal Non-negative Matrix Factorization
- IPBT 2.0 - Informative Prior Bayesian Test
- iRefWeb 13.0 - Consolidated Protein Interactions from many source DBs
- IRMa 1.31.1 - Validation of MS Peptides Identification
- iRNA-m7G - Identifying N7-methylguanosine Sites by Fusing Multiple Features.
- irootlab 0.17.8.22 - MATLAB toolbox for Vibrational Spectroscopy
- iRSpot-Pse6NC 2.0 - Identifying Recombination Hotspots in Saccharomyces Cerevisiae
- ISIF 1.1.3 - Performs in silico AFLP
- ISMAGS 1.1.3 - Cytoscape app for Motif Enumeration
- ISOGO - Functional Annotation of Protein-coding Splice Variants
- IsotopeCalculator 2 - Compute Isotopic Distributions for Large Proteins
- iTagPlot 1.0 - Computation and Interactive Visualization of Tag Density
- iTAK 1.7 - Plant Transcription Factor & Protein Kinase Identifier and Classifier
- iVikodak - A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets
- jackstraw 1.3 - Non-parametric Jackstraw for Principal Component Analysis
- Jane - Journal / Author Name Estimator
- JASSA v4 - prediction of SUMOylation sites and SIMs
- JColorGrid 1.860 - Transform Numerical or Text Data into Color-grids
- JEnsemb 1.78 - Java API to Ensembl data systems
- Jflow 1.2 - A Workflow Management System for Web Applications
- jHeatmap 1.1.0 - Create interactive Heatmaps on the Web
- Judi 1.0 - Data and Model Integration for Biology
- jvenn 1.7 - An Interactive Venn Diagram Viewer
- KAGIANA 200906 - Retrieve Information of the Arabidopsis Genes
- Kaks_Calculator 2.0 - Calculate Ka and Ks through Model Selection and Model Averaging
- KaPPA-Average 1.0 - Convert Probe ID-based Gene Expression data to Gene ID-based Data
- KdPrediction - Predict protein-DNA Binding Affinity
- KEA2 - Kinase Enrichment Analysis
- KeBABS 1.20.0 - R Package for Kernel-Based Analysis of Biological Sequences
- kernel-compute 1.0 - Profile-based Kernel Compute Package
- KEX 1.21 - A simple Knowledge EXtraction tool
- KGGSEE 1.0 - Biological Knowledge-based Mining Platform for Genomic and Genetic association Summary statistics using gEne Expression
- Kinship 20091112 - Estimate Kinship Coefficients for Case-control analyses in the presence of Cryptic Relatedness
- KL-Rare - Kullback-Leibler Distance Methods for Detecting Disease Association With Rare Variants
- KmerStream 1.1 - Computing kmer statistics for massive Genomics Datasets
- KMgene 1.3 - Gene-based Association analysis for complex Traits
- KOSMOS 3.0 - Morph server for Nucleic Acids, Proteins and their Complexes
- Krona 2.8 - Hierarchical Data Browser
- kronos 2.3.0 - Workflow Assembler for Cancer Genome Analytics and Informatics
- kSolutionVis 1.4 - Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances
- KSP-PUEL - Predicting novel Substrates of Kinases of Interest
- L-Measure 5.3 - Extract quantitative Morphological Measurements from Neuronal Reconstructions
- L1000FWD - Large-scale Visualization of Drug-induced Transcriptomic Signatures
- Lab7 Public Beta - Sequencing Workflow Management Platform
- LabKey Server 21.7 - Organize, Analyze, and Share Biomedical Research data
- Labmatica 2.2.3 RC1 - Laboratory Information Management System
- LabTargets - Keep Track & Report the Status of Targets & Complexes
- Labux 0.1 - Open Source software for Laboratory Automation Control
- LACS - Validate Protein NMR Chemical Shifts
- LAILAPS - Search Engine for Life Science data
- Landmark 3.6 - 3D Morphological Models on Trees
- LARVA - Large-scale Analysis of Variants in noncoding Annotations
- LAVA - NGS-based computational SNP Array
- lcmix 0.3 - R package using Hierarchical Mixture Models for Genomic data Integration
- LD50 Calculators
- LDA 1.6.2 - Lipid Data Analyzer
- LDDist 1.3.2 - Calculating LogDet Pair-wise Distances for Protein and Nucleotide Sequences
- LEAF GUI 2 - Analyze Macroscopic Structure of Veins in Leaves
- LFA 1.20.0 - Logistic Factor Analysis for Categorical Data
- LFC 1.0 - Count Ratio Model Fold Changes
- LGT3State 20081223 - Detect LGT (swapping) of two non-homologous Enzymes
- librfn - Rectified Factor Networks
- lightCUD 1.0 - Discriminating ulcerative colitis and Crohn's disease
- LILY - Detection of Super-enhancers in Cancer Samples
- LIMS Tools - includes AssayManager, OrderTool and ProjectManager
- linACC 0.1.4 - Detection of Lineage Specific Accelerated Substitution Rates
- LinkedOmics - Analyzing Multi-omics data within and across 32 Cancer Types
- LINNAEUS 2.0 - Species Name Recognition and Normalization software
- Lipidsig 1.1 - Web-based tool for Lipidomic data Analysis
- LIQA - Long-read Isoform Quantification and Analysis
- LKM 2.0 / LFKM 2.0 / MFKM 1.1 - Quantitative Traits in Longitudinal ( Multivariate) (Family) Data
- LocExpress - real-time Expression Estimation of novel Transcripts
- locsmoc 0.1.1 - Piecewise Polynomial Curves for Genomic Signals
- LocusFocus 1.4.9 alpha - Web-based colocalization for the Annotation and Functional follow-up of GWAS
- LogMiNeR 0.1.0 - Logistic Multiple Network-constrained Regression
- LogOddsLogo 1.0.3 - Generation of Sequence Logos from Biological Sequence
- Logopaint 1.0 - Exploring Visualisation of Bias in Regulatory DNA or RNA Element
- LOHCRP / CRP_LOH v.1 - LOH Inference based on the Conditional Random Pattern (CRP) model
- LongISLND 0.9.5 - In silico Sequencing of Lengthy and Noisy Datatypes
- Longshot v0.43 - Diploid SNV Caller for Error-prone Reads
- LONI Pipeline 7.0.3 - Free Workflow Application
- LONUT - Improve the Detection of the Enriched Regions for ChIP-seq
- MACE 1.2 - Model-based Analysis of ChiP-exo
- Magallanes - Multi-Architecture Resources Discovering
- MAGeCK 0.5.9.4 / MAGeCK-VISPR 0.5.6 - Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout + Visualization of CRISPR Screens
- MAGeCKFlute 1.6.0 - Analysis of pooled CRISPR Functional Genetic Screens
- MAìSTAS - Modeling and Assessment of ISoforms Through Automated Server
- Maltcms 1.3.2 / Maui 1.2.1 - Modular Application Toolkit for Chromatography Mass-Spectrometry
- Mango 1.0.3 - ChIA-PET Analysis Software
- ManhattanPlotter 1.4 - Create Manhattan Plots and qq plots from P-values obtained in Genomic Studies
- MAnorm - Robust Model for Quantitative Comparison of ChIP-seq datasets
- Manta 1.6.0 - Structural Variant and Indel Caller for Mapped Sequencing data
- Manteia v.7.0 - Data Mining system for Vertebrate Genes
- MANTIS 3.0 - Multilocus ANTIgenic Simulator
- maplet 1.1.1 - Metabolomics Analysis PipeLinE Toolbox
- MAPMUTS 1.1 - Analyzing Deep Mutational Scanning data
- mapscape v02 - Visualization tool for spatial Clonal Evolution
- MAPSD - Markov Affinity-based Proteogenomic Signal Diffusion
- MaRIboES 2.1.0 - Metabolite and Reaction Inference based on Enzyme Specificities
- Marky 2.3.0 - Annotate Biomedical Texts using different Annotation Classes
- MARRVEL v2 - Model organism Aggregated Resources for Rare Variant ExpLoration
- MarVis Suite 2.0 - Clustering & Visualization of Metabolomic Markers
- MASAL - Multivariate Adaptive Splines for Analysis of Longitudinal Data
- MascotDatfile 3.6.1 - java API for MS/MS search results by Mascot
- Mash v2.3 - Fast Similarity Estimates via MinHash
- Mashup - Compact Integration of Multi-Network Topology for Functional Analysis of Genes
- Mason - JavaScript Widget for Viewing Sequence Features and Annotations
- MassiveSAR - Small molecule structural similarity analysis and clustering
- MassXpert 3.4.0 - Polymer Chemistry Modelling & Simulation/Analysis of Mass Spectrometric Data
- MatCompare 1.3 - Compare Transcription Factor Binding Site (TFBS) position Frequency Matrices (PFMs)
- MateSim 1.0 - Monte Carlo Simulation of Mating
- MathDAMP 1.0.0 - Mathematica package for Differential Analysis of Metabolite Profiles
- MausDB 1.5 r126 - Laboratory Mouse Information and Management System
- MAW - Suite on the Computation and Application of Minimal Absent Words
- maxLRc - Rare Variant Prioritization
- MBA - Inferential Assignment of Protein Backbone Nuclear Magnetic Resonances
- mBISON - Find Enrichment of miRNA Targets on lists of Genes
- MBRole 2.0 - Enrichment Analysis of Metabolomic data
- MCPD 2.02 - Markov Chain Pooling Decoder
- MCRobot 2.1 - Illustrates the basic principles of Markov chain Monte Carlo Simulation
- mCross - Modeling RBP Binding Specificity by registering protein-RNA Crosslink Sites
- MDM 1.0 - Analysis of Chromatin Interactions using MC_DIST model
- Meander 1.0 - Visualization of Genomics based on Read Depth (RD) and Pair-End (PE) information
- Mechismo - Mechanistic Interpretations of Structural Modifications
- MEDEA - Motif Enrichment of Differential Elements of Accessibility
- medMatch 1.2 - Generating a Gene Index of Medline
- MEIGO / MEIGO-M 20140703 / MEIGO-R 0.99.6 / pymeigo 1.0.0 - MEtaheuristics for bIoinformatics Global Optimization
- Melting 5.2.0 - Compute Nucleic Acid Duplex Melting Temperature
- MeltingCurves 20100712 - Analyse the Melt Curve data, from an Idaho Technology Lightscanner
- MEMHDX - Mixed Effects Models for HDX-MS analysis
- MendeLIMS 3.2 - Laboratory Information Management System for Clinical Genome Sequencing
- Meredys 20100209 - Multi-compartment Reaction-diffusion Simulator
- MERLIN - Predict Regulators for individual Genes and Modules
- MeRP 1.0 - Mendelian Randomization analysis
- MESMER - Minimum Ensemble Solutions to Multiple Experimental Restraints
- MET-IDEA 2.08 - Data Extraction Tool for Mass Spectrometry-based Metabolomics
- Meta-Storms 2.2.1 - A Metagenomic Database system toolkit
- MetaboAnalyst 5.0 - Metabolomic Data Analysis
- MetaboliteDetector 3.3 - Deconvolution and Analysis of GC/MS Data
- MetaboMiner - Identification of Metabolites from 2D NMR spectra of Complex Biofluids
- MetaboQC 1.0 - Evaluation of peak picking quality in LC-MS Metabolomics data
- metabosearch - Mass-based Metabolite Identification using multiple databases
- metaCCA 1.20.0 - Multivariate meta-analysis of GWAS using Canonical Correlation Analysis
- MetaClean 1.0.0 - Detection of Low-Quality Peaks in Untargeted Metabolomics Data
- MetaFIND 0.8 - Java-based Metabolomics Analysis software
- MetaGeneAlyse - Analysis of Gene Expression and Metabolite data
- MetaMap 2020 - Mapping of Biomedical Text to the UMLS Metathesaurusext
- metaMix 0.3 - Bayesian Mixture Analysis for Metagenomic Community Profiling
- MetaOmGraph 1.8.1 - Plotting and Analyzing large sets of Biological data
- metaP 2 - web-based Metabolomics data analysis tool
- MetaQuant 1.3.5 - Quantification of GC/MS based Metabolome data
- MetATT - Metabolomics tool for Analyzing Two-factor and Time-series data
- MetExpert - Metabolite Expert System
- MethFlow 1.1 - Integral Analysis of WGBS Methylation data
- MetPA - Pathway Analysis and Visualization of Quantitative Metabolomic data
- MetPP 20140812 - Analysis of Metabolomics data acquired on a GC×GC-TOF MS system
- MetProc 1.0 - Separate Metabolites into Likely Measurement Artifacts and True Metabolites
- MetQy - Query Metabolic Functions of Genes and Genomes
- Metrans 1.2.1 - Taxonomical and Functional Analysis of Metatranscriptomes
- MetTailor 2.0 - Dynamic Block Summary and Data Normalization for Robust Analysis
- mf2q - Calculating Scaled Q matrices from Mutation Counts using the DCFreq method
- MFPaQ 4.0.0 - Parse, Validate, and Quantify MS Proteomics Data
- MGKit 0.4.2 - Metagenomic Framewotk for the Study of Microbial Communities
- mGPfusion - Predicting Stability Changes upon Single and Multiple Mutations
- MHCBN 4.0 - Database of MHC/TAP Binding Peptides and T-cell Epitopes
- MHScalculator 1.1 - Minimal Hitting Sets Calculator
- MICC 1.0 - Model based Interaction Calling from ChIA-PET data
- MICE 1.4 - Mouse Information & Classification Entity
- MicroPattern - Microbe Set Enrichment Analysis and Disease Similarity Calculation
- Microscope Simulator 2.3.0 - Simulating a Fluorescent Torus
- MIDAS 1.1 - A Database-Searching Algorithm for Metabolite Identification in Metabolomics
- MIKADO 2.0rc4 - Determine and Select the best RNA-Seq Prediction
- MIL - Multiple Instance Learning for Protein-DNA Interaction Modeling
- MIMA v1.0 - Automation of the MS to IMS Peak Assignment
- MIMOSA 2.0.0 - Model-based Integration of Metabolite Observations and Species Abundances
- MiningABs 1.0.0 - Mining Associated Biomarkers across multi-connected Gene Expression datasets
- MIPgen 1.1 - Analysis and Design of Molecular Inversion Probes for Targeted Resequencing
- miRTex - Text Mining System for miRNA-Gene Relation Extraction
- MISO 0.2.195 - Managing Information for Sequencing Operations
- MixChIP - Cell Type Specific Protein-DNA Binding analysis
- MixDTrees - Mixture of Developmental Trees
- MLbias 1.0 - Correct Machine Learning Bias
- MLPERCEP 2.0 - Multiple Layer Perceptron Implementation for the Biological Problems
- MM2S 1.0.6 - Personalized Diagnosis of Medulloblastoma Subtypes Across Patients and Model Systems
- mmCSM-NA - Predicting Effects of Single and Multiple Mutations on Protein-nucleic Acid Binding affinity
- MMR - Tool for Read Multi-Mapper Resolution
- Moara 1.0.6 - Extract & Normalize Gene and Protein Mentions
- MOAT v1.0 - Mutations Overburdening Annotations Tool
- Mockrobiota - Public Resource for Microbiome Bioinformatics Benchmarking
- MOIRAI 20140528 - Compact Workflow System for CAGE Analysis
- Molgenis 9.1.0 - Generate Databases for Life Science Experiments
- MolScat 0.8 - Evaluation of Solution Scattering of Biological Macromolecules from Atomic Coordinates
- MoMaVis 1.31 - Molecular Marker Visualization tool
- MONA - Multilevel ONtology Analysis
- MonoClad - Find meaningful partitions using Semi-supervised Class Discovery
- Monocle 3 0.2.0 - Differential Expression and Time-series analysis for Single-cell RNA-Seq and qPCR Experiments
- Morgan2McClintock 3.0 - Predicting Chromosomal Locations of Genetically Mapped Loci in Maize
- MOSAICS 4.0 / PymoSAICS 0.2.0 - Methodologies for Optimization and SAmpling In Computational Studies
- Motevo 1.03 - Integrated Bayesian Probabilistic Methods
- MotiveValidator 1.1.15.8.8e - Validate Ligand and Residue Structure in Biomolecular Complexes
- mOTUs 2.5.1 - Tool for Marker Gene-based OTU (mOTU) Profiling
- Mouse Atlas Data Analysis CD-ROMs 0403
- MPA 1.0 - Multiple Peak Alignment
- MPFit - Moonlighting protein Prediction with Missing Feature Imputation
- MPSA - Multi-path Simulated Annealing
- MPSS 1.2 - Multi-platform Segmentation
- MPTM 1.0 - Mining Protein post-Translational Modifications from literature
- MR-JTI v1 - Joint-tissue Transcriptome-wide Association and Mendelian Randomization analysis
- MRC - Metagenomic and Metatranscriptomic data and analysis Management Workflow
- MRFSeq 0.1 - Gene Expression Analysis using Coexpression and RNA-Seq data
- MRHMMs 2 - Multivariate Regression Hidden Markov Models and the variantS
- mRMRe 2.1.0 - Parallelized mRMR Ensemble Feature Selection
- MSA v1.1 - Mutational Signature Attribution pipeline
- MsatAllele 1.05 - Visualize the Binning of Microsatellite Alleles
- MSEA - Metabolite Set Enrichment Analysis
- msgl 2.3.9 - High Dimensional Multiclass Classification using Sparse Group Lasso
- MSI 20100526 - Multiscale Systems Immunology
- MSPC 5.4.0 - Using Combined Evidence from Replicates to Evaluate ChIP-seq Peaks
- mSpecs Editor 1.01 - Tool for Managing Mass Spectral Libraries
- MSPrep 1.1 - Post Processing of Metabolomic data
- MSProGene 02 - Integrative Proteogenomics beyond Six-frames and SNPs
- MSstats v3.18.1 - Protein Quantification in label-free and label-based LC-MS experiment
- MSTD - Identify multi-scale Topological Domains
- MtbVeb - Designing Vaccine for Mycobacterium Tuberculosis
- MTR - Metagenomics software for Clustering at multiple ranks
- MUFFINN - Cancer Gene Discovery via Network Analysis of Somatic Mutation data
- MUGBAS 20150313 - Species free Gene-based Programme Suite for Post-GWAS Analysis
- MULSEA - Mutual enrichment in aggregated ranked lists
- MulteeSum - Visualize Comparison of Cellular Gene Expression Profiles
- MultiGlycan 1.0 - Annotation of Glycomic Profiles in the LC-MS data
- MultiMotif - Finding Statistically Significant labeled Motifs in multi-relational networks
- MultiQC 1.11 - Aggregate Results from Bioinformatics Analyses across many samples into a single Report
- multiSwitch - Combinatorial Regulation
- MuSERA v.2.3 - Multiple Sample Enriched Region Assessment
- MUSIC - MUltiScale enrIchment Calling for ChIP-Seq Datasets
- MutaGeneSys 20071020 - Use Genome-wide Genotype Data to Estimate Individual Disease
- Mutanalyst - Assessing the Mutational Spectrum of epPCR Libraries
- Mutant Design - Restriction Enzyme / Codon Optimization for Mutant Protein Design
- Mutation Reporter Tool - Interrogate Loci of Interest
- mutation3D 201512 - Find Clusters of Cancer-causing Mutations in the human Proteome
- MUTPATH - Map Mutational Paths through Protein Sequence Space
- mvngGrAd 0.1.5 - Software for Moving Grid Adjustment in Plant Breeding Field Trials
- MVQueries - Classify Short Gene Expression Time-courses
- MyMiner - Text Mining tools for Biology
- MyMRM 1.2 - Designing Targeted Proteomics Methods
- myPhyloDB v.1.2.0 - A Local Web Server for the Storage and Analysis of Metagenomic Data
- Myriads v1.2 - p-value-based Dependence Detection, Simulation, and multiple testing correction
- Mystic - Inferred Biomass Biogeochemical Model of Mystic Lake
- mySyntenyPortal / SYNTENY PORTAL- Websites for Synteny Block Analysis
- MyWEST - My Web Extraction Software Tool
- mz2m 2.17 - Interpretation of Peptide Mass Spectra
- MZmine 2.53 - Mass-Spectrometry Data Process
- NADfinder 1.14.0 - Bioinformatic analysis of the NAD-seq data
- Nature ENCODE 1.1 - Bring together the Results of the ENCODE project for iPad
- Nature Human Genome Special Edition 1.0
- NaviGO - An analytic tool for Gene Ontology Visualization and Similarity
- NCG 6.0 - Web Resource to Analyze Duplicability, Orthology and Network Properties of Cancer Genes
- nCOP - Network-based Coverage of Mutational Profiles
- ncPred - ncRNA-Disease Association Prediction
- NEJI 2.0.2 - Framework for Faster Biomedical Concept Recognition
- NestedCluster 0.0.1 - Biclustering Method for AP-MS Data
- Net-RSTQ - Network-based method for RNA-Seq-based Transcript Quantification
- NetSets - Compositional Assessment of Biological Networks through Venn and Network Diagrams
- NetShift - Identification of Driver Nodes between Case-control Association networks
- NetVenn - Network Analysis Web platform for Gene Lists
- neuroants - Simulation of Ant Colony
- Neuron 1.1.20 - Simulation of Neuron
- nextflu 1.0 - Real-time Tracking of Influenza Evolution
- nextNEOpi v1.2 - NeoEpitope predictions Nextflow Pipeline
- NGLess 0.6.1 / NG-meta-profiler 0.9.1 - NGS Processing with Less Work
- NGSEA - Network-augmented Gene Set Enrichment analysis tool
- NLDMseq - Expression Calculation at both Gene and Isoform levels from RNA-seq data given a Reference Transcriptom
- NLProt 2.0 - Mining Natural Language text for PROTein names and their UniProt-IDs
- NMF-mGPU 1.0 - Non-negative Matrix Factorization on multi-GPU Systems
- nMLSA / MLSA - Network-based / Modular Latent Structure Analysis
- NOISeq 2.30.0 - Differential Expression in RNA-seq
- NoLogo - Statistical Model for NESs
- Normalyzer 1.1.1 - Normalization methods for Omics data sets
- NOVA 0.8.0 - Visualization and Analysis of Complexome Profiling data
- novoSpaRc 0.4.3 - de novo Spatial Reconstruction of Single-Cell Gene Expression
- Nozzle 1.1-1 - Generation of Reports in High-throughput data analysis pipelines
- ntEGFR - Predicting and Designing of EGFR Inhibitors
- NucHunter - Inferring Nucleosome Positions from ChIP-seq Experiments
- NVT 1.0 - R package for the Assessment of RNA-Seq Normalization methods
- ODIN 0.4.1 - Detecting Differential Peaks in ChIP-seq Signals
- OFF-TARGET PIPELINE 1.5.4.2 -Identify Off-targets of Pharmaceuticals
- OLYMPUS - Hybrid Clustering method in Time Series Gene Expression
- Omics Integrator 0.3.1 - Python Scripts for Analyzing Diverse Forms of 'omic' data
- Onco-STS - Web-based Laboratory Information Management System
- OncodriveROLE - Classifying cancer driver genes into Loss of Function and Activating roles.
- OncomiRDB - Database for the Experimentally Verified Oncogenic and Tumor-suppressive microRNAs
- OncoPaD - Rational Design of Cancer NGS Panels
- OncoRep - Oncogenomics Report
- OneStopRNAseq - Comprehensive and Efficient analyses of RNA-seq data
- OnTheFly 2.0 Beta - Automated Annotation of Biochemical Terms in PDF, Text and Microsoft Office documents
- OOMMPPAA 1.2-0 - Directed Synthesis and Data Analysis tool
- openBIS 19.06.0/ openBIS ELN-LIMS - Managing Biological Information
- OpenFreezer 201402 - Laboratory Reagent Tracking and Workflow Management System
- OpenLabFramework v1.4.0 / OpenLabNotes - An open-source framework for Sample Management
- OptiCount 201303 - Enumeration of Plankton and Particles
- OrthoGNC 3.0 - Accurate Identification of Orthologs based on Gene Neighborhood Conservation
- OrthoVenn2 - Comparison and Annotation of Orthologous Gene Clusters among multiple Species
- OSIRIS 2.51.1 - Analysis of Multiplex DNA Profiles
- OSS - Optimal Seed Solver
- Outbreak 2.11.0 - Predict Survival of Reintroduced Populations
- OVA - Ontology Variant Analysis Tool
- PACSY / PACSY Maker b032814 / PACSY Analyzer - Database Management system for Protein Structure and Chemical Shift analysis
- PAEA - Dimensionally Reduced Multivariate Gene Set Enrichment Analysis Tool
- pairheatmap 1.0.1 - A tool for Comparing Heatmaps
- PAnDA - Protein And DNA Associations
- ParaCountStudio 3.1.0 - Count Cell Numbers within Image
- ParaPep - Database of Anti-parasitic peptides
- parredHMMlib 1.0 - Library for Hardware Accelerated HMM Parallelizing Analysis
- PASS 2 - Control the FDR level in ChIP data analysis
- PASSIM - The Patient and Sample System for Information Management
- PAST 1.4 - Store & Archive Multiple Datestamped Snapshots of PDB
- PAST 2.17c - PAlaeontological STatistics
- Path2Models - Collection of Models automatically generated from Pathway Resources
- PATHMATRIX 1.1 - GIS tool to Compute Effective Distances among Samples
- pathrecon - Temporal Reconstruction Algorithm
- PathScore - A Web tool for Identifying Altered Pathways in Cancer data
- Pathway Processor 2.0 - Pathway-based analysis of High-throughput data
- PCMdb - Pancreatic Cancer Methylation Database
- pdCSM-PPI - Using Graph-Based Signatures to Identify Protein-Protein Interaction Inhibitors
- PDEGEM 20140325 - Modeling non-uniform Read Distribution in RNA-seq data
- PEA v1.1 - Plant Epitranscriptome Analysis
- PEA-m5C 0.1.3 - An R package for Plant m5C analysis
- Peakhood v0.3 - Individual Site Context Extraction for CLIP-Seq Peak Regions
- PeakLink 1.0 - Peptide Peak Linking method in LC-MS/MS using Wavelet and SVM
- Peakr - Simulating 2D Solid-state NMR Spectra
- PeakRanger 1.18 - Multi-purpose, ultrafast ChIP Seq Peak Caller
- peakrots 1.01 - Optimized procedure for ChIP-seq Peak Detection
- PeakSeq 1.31 - Identify and Rank Peak Regions in ChIP-Seq Experiments
- PEDI - Scalable Parameter Estimation of Gene Circuit models
- PEGS 0.6.4 - Peak-set Enrichment of Gene-Sets
- PentaPlot 20040723 - Illustration of Genome Mosaicism
- PEP - Predict Enhancer Promoter interactions
- PEPlife - Database of Half-life of Peptides
- PepPSy - A Web Server to prioritize Gene Products in Experimental and Biocuration Workflows
- PepQuery 1.6.2 - Peptide-centric Search Engine for novel Peptide searching
- PePr 1.1.18 - Peak Prioritization Pipeline
- PepSurf 3.0 / Mapitope 20070210 - Epitope Mapping using Affinity-selected Peptides
- Percolator 2.04 - Confident Peptide Identifications from a collection of Tandem Mass Spectra
- PESCADOR - Extract and Analyse a Network of Gene and Protein Interactions from a set of Medline abstracts
- PESS 1.0.0 - Full-scale Protein Fold Recognition using 1NN
- PETModule - Motif Module based approach for Enhancer Target Prediction
- PFFF 1.0 - Probabilistic Fast File Fingerprinting
- Pftools 3.2.1 - suite of tools to build and search generalized profiles
- PGA v2.0.4 - Post-GWAS Analysis
- pGenN - Gene Normalization Tool for Plant Genes and Proteins in Scientific Literature
- pgltools 2.2.0 - Paired Genomic Loci Tool Suite
- PGM 1.1 - Proteogenomic Mapping Tool
- pGQL - Analyzing Gene Expression Time Courses
- PharmacoGx 2.2.4 - Analysis of large Pharmacogenomic Datasets
- Phen2Gene 1.2.3 - Real-time Phenotype-based Gene Prioritization tool from HPO IDs or clinical notes on patients
- PhenoFam - Gene Set Enrichment Analysis in the Protein Domain Context
- phenomeImpute 1.0 - R package to Impute Missing values in large-scale High-dimensional Phenome data
- PhenoMeter 1.0 - Metabolome Database Search Tool
- Phenomizer - Identify Correct Differential Diagnosis in Field of Human Genetics
- PhenoTips 1.4.7 - Patient Phenotyping software
- PhosCalc 1.2 - Evaluating the sites of Peptide Phosphorylation
- PhpLabWare 0.63 - Web-driven Life Sciences Lab Database Management System
- phylogeo - Geographic Analysis and Visualization of Microbiome data
- PhyloGrapher 20030403 - Graph Drawing of Biological Data
- PhySca - SCJ small parsimony problem for weighted Gene Adjacencies
- Phyto-PhyloPars - Phylogenetic approach to the Estimation of Phytoplankton Traits
- PICA Browser 0.9 - Integrating and Exploring Multiple Connected Datasets
- piMGM 1.0 - Mixed Graphical Model with Prior Information
- PIMS 4.4.0 - Protein Information Management System
- PINCAGE - Probabilistic INTegration of CAncer GEnomics data
- PINES - Phenotype-Informed Noncoding Element Scoring
- PinSnps - Structural and Functional analysis of SNPs in the Context of Protein Interaction Networks
- PINT - Probabilistic Data Integration for Functional Genomics
- PiPa - Setup and Maintain a Database for Information on PPI and Biological Pathways
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