Posts
- Category: Miscellaneous (continued)
- APPEX 1.0 - Analysis Platform for Identification of Prognostic Gene EXpression Signature in Cancer
- APTANI2 - Select Aptamers through Sequence-structure Motif analysis of HT-SELEX data
- AptaSim - Virtual SELEX
- ARCADE 0.1 beta - Query and Visualize Data from Multiple Databases
- ARCHS4 - All RNA-seq and CHIP-seq Signature Search Space
- ARco 1.0 - Association Rules collaborative tool
- AREM 1.0.1 - Aligning Short Reads from ChIP-sequencing by Expectation Maximization
- ARGweaver - Sampling and Manipulating Genome-wide Ancestral Recombination Graphs
- ARN - Studying the Mechanism and Regulation of Autophagy
- ArtiFuse v1.0.0 - Computational Validation of Fusion Gene Detection tools without relying on simulated reads
- ARTO - Analysis of Replication Timing and Organization
- ASCA-genes 1.2.1 - R package for the analysis of Multifactorial Gene Expression data
- ASD - Genome-wide predictions of Autism-associated genes
- ASMF - Approximate String Matching via Filtering
- AssayZap 3.0 - System for Analyzing RIAs, ELISAs, IRMAs and other Assays
- asymptoticMK - Tool for Asymptotic McDonald-Kreitman Test
- ATACseqQC 1.14.4 - Quality Assessment of ATAC-seq data
- AuthorReward 0.5 - Increasing Community Curation in Biological Knowledge Wikis through automated Authorship Quantification
- AutoClickChem 1.0.0 - Performing Click-chemistry Reactions in silico
- AutoFACT 3.4 - An Automatic Functional Annotation and Classification Tool
- AutoRT v1.0 - Peptide Retention Time Prediction using Deep Learning
- AVAtar 0.4.11 - Analysis and Visualization of Alteration data
- AVeMap - Cell Migration in Wound-healing Assays
- B-LORE - Bayesian multiple logistic Regression for GWAS Meta-analysis
- B3 3.31 - Bibliography Base for Biologists
- BACH / BACH-MIX - Bayesian 3D constructor for Hi-C data / Characterize Structural Variations of Chromatin Folding
- BackCLIP 2.1 - Tool to Identify common RNA Background in PAR-CLIP Datasets
- Baescs 2.0 - Estimate Calibration Curves and unknown Concentrations in Immunoassays
- BALD - Bayesian Analysis of Linkage Disequilibrium Differences
- BANFF 2.0 - Gene Network Feature Selection
- BANNER 0.2 - Named Entity Recognition System
- Barcode generator 2.8 - Generator of Sequence Barcodes suitable for Illumina Sequencing
- Base Pad 1.0 - Base Sequence Editor
- BATMAN 1.2.1.11 - Bayesian AuTomated Metabolite Analyser for NMR spectra
- BATMat - Bioinformatics Autodiscovery of Training Materials
- BATVI 1.03 - Determine Viral Integrations
- Bayesian Joint Analysis
- bbcontacts - Prediction of β-strand Pairing from Direct Coupling Patterns
- BCseq - Accurate Single Cell RNA-seq Quantification with Bias Correction
- BDML4DViewer 0.20 - Plugin of ImageJ software for Visalizing BDML files
- BDVAL 1.2 - Biomarker Discovery in High-throughput datasets
- BECAS - Biomedical Concept Annotation Tool, API and Widget
- BEESEM - Binding Energy Estimation on SELEX with Expectation Maximization
- bellmansgap 20150520 - Dynamic Programming for Bioinformatics
- BEnDS – Binding Energy Distribution Simulator
- BEReX 1.0 - Biomedical Entity-Relation eXplorer
- BETA 1.0.7 - Binding and Expression Target Analysis
- BetaCavityWeb - Computing Molecular Voids and Channels with their Mass Properties
- BEW 2.1.0 - Biofilms Experiment Workbench
- BGFit - Fitting of Biological Growth Curves
- bgmm 1.8.3 - Belief-based Gaussian Mixture Modeling
- BGT 1.0 - Genotype Query across many Samples
- BiblioSpec 2.0 - Creat and Search MS/MS Peptide Spectrum Libraries
- BIDCHIPS - Bias-Decomposition of ChIP-seq Signals
- BIDDSAT 0.3 - BIoDiversity DataSet Assessment Tool
- biMM 1.0.0 - Bivariate Linear Mixed model
- binda 1.0.3 - Multi-Class Discriminant Analysis using Binary Predictors
- Bio-SeCo - Bioinformatics Search Computing Application
- BioAnnote 2.0.0 - Annotate Biomedical Texts by using different high-quality online Resources
- Biobar 2.0.9 - Firefox Toolbar for Browsing Biological Data and Databases
- BioBlend 0.16.0 - Python library for interacting with CloudMan and Galaxy‘s API
- BioC 1.1 - A Minimalist Approach to Interoperability for Biomedical Text Processing
- BioCircos.js v1.1.1 - Circos JavaScript Library for Biological Data Visualization on Web Applications
- BioClass - tool for Biomedical Text Classification
- BioContext 1.0 - System for Extraction and Contextualization of Biomedical Events
- BioCRF 0.9 - Grammatical-Restrained HCRF tool for Bioinformatics applications
- BioCyc Pathway 3.0.6 - Mobile Interaction for EcoCyc
- BioDB-Loader - Lisp tools for bioinformatics
- BIODICA - Independent Component Analysis for Big Omics Data
- BioDoser 1.1 - Dose-estimation software for Biological Radiation Dosimetry
- BioDownloader 2.2.1.0- Download and/or Update Files from Servers
- BioDWH 0.2 - Bioinformatics Data Warehouse
- bioECS 1.0 - Biology Easy Cluster Search
- BioFVM 1.1.6 - 3-D Diffusion Solver for Biological Problems
- BioGPS - Gene Annotation Portal
- Biogrep 1.0 - Optimised Version of Grep for matching Patterns against Sequences
- BioGUI 0.2 - GUI for highly used Bioinformatics Tools
- BioIDMapper 3.0 - Mapping Biological IDs
- Bioinformatics Analysis Scripts
- BioJupies - Automatically Generates RNA-seq Data Analysis Notebooks
- BiolAD-DB 3.0.1 - Informatics System for Clinical and Genetic Data
- BioLegend CD Posters 1.4 / BioLegend Tools for iPad 1.4 - Information about Mouse and Human CD Molecules
- BioLegend ELISA 1.1 - ELISA Active Protocol
- BioLemmatizer 1.2 - Lemmatization tool for Morphological Processing of Biomedical Text
- BioMAJ 3.0.20 - Workflow Engine Dedicated to Data Synchronization and Processing
- BioMuta 4.0 - Single-nucleotide Variations (SNVs) in Cancer
- BioMyn - Mining Gene and Protein Knowledge
- bioNMF 2.0 - Non-negative Matrix Factorization in biology
- BioPartsBuilder - Synthetic Biology tool for Combinatorial Assembly of Biological Parts
- BioPartsDB - DNA Synthesis Workflow System for Synthetic Biology
- BioPlat 2 - Human Cancer Biomarker Discovery
- BioProfiling.de - Analytical Web portal for High-throughput Cell Biology
- BioRAT 2.0 - Information Extraction for Biological Research
- BioSAVE 0.11 - Biological Sequence Annotation Viewer
- bioservices 1.7.12 - Access to Biological Web Services from Python
- BioShaDock - A Curated BioInformatics Container Registry
- BioStat 5.3.0 - Biology Statistical Software
- BioSVG 0.02 - Generate Scalable Vector Graphics (SVG) data for Biological objects
- BioSynther - Biosynthetic Potential Explorer
- Biota 3.00 - Biodiversity Database Manager
- BioTextQuest+ - Literature Mining and Concept Discovery
- BioVenn 1.1.3 / DeepVenn - Comparison and Visualization of Biological lists using Area-proportional Venn diagrams
- BioWarehouse 4.6 – Database Integration for Bioinformatics
- Biowep - Workflow Enactment Portal for Bioinformatics
- Biowine - Knowledge base for Vitis vinifera Functional analysis
- BioXpress 3.0 - Gene Expression in Cancer
- Bis-class v2 - Bisulfite-sequencing data Classification
- BLOSpectrum 20091230 - Split BLOSUM Score into numbers of Biological Significance
- BMix - Probabilistic Modeling of Occurring Substitutions in PAR-CLIP data
- BNFinder 2.1.1 - Bayesian Network Topology Inference
- BNW - Bayesian Network Web Server
- BOXIT 2007 - Database for Molecular Biology Laboratories
- BQuant 1.0 - Bayesian Quantification
- Brain 1.5.1 - Library for Biomedical Knowledge Manipulation
- Brass 3.0 - Biological Rhythms Analysis Software System
- BRepertoire - Analysing Antibody Repertoire Data
- BRISK - Biology-Related Information Storage Kit
- BRM 2.3 - Bioinformatics Resource Manager
- Browndye 2.0 - Brownian Dynamics Simulations on Large Biological Molecules.
- Brownian Motion Simulator - Estimating Minimum Passage Time and Docking Ratio of Nanoparticles to Specified Target
- Brownmove 1.4 - Many-particle Brownian-Dynamics Simulation package
- BTL 3.4 - The Bioinformatics Template Library
- Bubble GUM 1.3.19 - Extraction of Phenotype Molecular Signatures and Comprehensive Visualization
- BVS - Matlab toolbox for Bayesian logistic and Probit Regression
- bwt 0.2 - Interactive computation of the Burrows-Wheeler Transform
- bz-rates - Calculate Mutation Rates from Fluctuation Assays
- C-State 0.2.3 - Query and Plot Chromatin Landscapes across multiple loci and Cell Types
- C3 - Correlation Clustering method for Cancer Mutation analysis
- C3P/CCCPart - Merging Two or More Graphs Representing Biological Data
- C3Part/Isofun - Local Alignement of two or more Graphs Representing Biological Data
- CAA - Chromosome Aberration Analyzer
- CAFA 0.41 - Capillary Automated Footprinting Analysis
- CAFU - A Galaxy framework for exploring unmapped RNA-Seq data
- CAGEd-oPOSSUM 1.0 - Motif Enrichment analysis from CAGE-derived TSSs
- CAGEr 1.34.0 - Analysis of CAGE (Cap Analysis of Gene Expression) Sequencing Data
- CalcuSyn 2 - Dose-effect analysis
- CalFitter 1.3 - Analysis of Protein Thermal Denaturation data
- CalSpec 1.3 - Calculate Spectra
- CAMP 3.3 - Conditional Allele Mouse Planner
- Cancer3D 2.0 - Patterns of Mutations in Cancer
- cancerCSP - Clear Cell Renal Cancer Stage Prediction
- CancerDP - Prioritization of Anticancer Drugs
- CancerDR - Cancer Drug Resistance Database
- CancerIN - Classification and Designing of Anticancer Compounds
- CancerLSP - Liver Heptacellular Carcinoma Stage Prediction
- CancerPDF - Cancer Peptidome Database of BioFluids
- CancerPPD - Database of Anticancer Peptides and Proteins
- CancerSPP - Webserver to Predict the Progression of Skin Cancer
- Cancertope - Designing genome-based Personalized Immunotherapy or Vaccine against Cancer
- CancerVar - Cancer Variants interpretation
- CanProVar 2.0 - Human Cancer Proteome Variation Database
- Canto v1651 - Community Literature Curation
- CARE - Computational Analysis of REsistance
- care 1.1.10 - High-Dimensional Regression and CAR Score Variable Selection
- CaRpools 1.025 - Analysis CRISPR/Cas9 Pooled Screens
- CAS 1.8 - Chromosome Aberration Simulator
- CASSys - Interactive Analysis of ChIP-seq data
- CATCH 3 v513 - Unsupervised Clustering of ChIP profiles
- Categorizer 1.0 - Classifing Genes into user-defined Categories
- CateGOrizer 3.218 - Gene Ontology (GO) Terms Classifications Tool
- Catfish v0.2.1 - Minimum Path Flow Decomposition Problem
- CATNAP - Compile, Analyze and Tally NAb Panels
- CATT 1.9 - CharActerzing TCR Repertoires
- cb2bib 2.0.1 - Manage Bibliographic data in BibTeX Format
- CBrowse 1.11 - SAM/BAM-based Contig Browser for Transcriptome Assembly
- CBT++ - Collection of C++ Classes to Computational Biology Applications
- CCLasso - Correlation Inference for Compositional Data through Lasso
- ccRemover 1.0.4 - Removes the Cell-Cycle Effect from Single-Cell RNA-Sequencing Data
- CDK 1.4.19 - Java Library for Structural Chemo- & Bioinformatics
- CDK-Taverna 2.0.5.4 - Workflow Management System for Cheminformatics
- CDpal 2.18 - Analysis of Protein Thermal and Chemical Stability
- CEDER - Detection of Differentially Expressed Genes by combining significance of exons using RNA-Seq
- Cell BLAST 0.5 - scRNA-Seq Querying Algorithm.
- Cell Counter 4.0 - Count Cells
- cellassign v0.99.2 - Automated, Probabilistic Assignment of Cell Types in scRNA-seq data
- CellMix 1.6.2 - Gene Expression Deconvolution
- CellR 0.1.0 - Single-cell RNA-Seq guided Deconvolution of Cellular Composition from Bulk-tissue RNA-Seq
- CellVGAE - Unsupervised scRNA-seq analysis Workflow with Graph Attention Networks
- CENTDIST - Discovery of Co-associated Factors by Motif Distribution
- CEpBrowser 20150219 - Comparison of Epigenomic Modifications across Species
- CFAssay 1.26.0 - Statistical analysis for the Colony Formation Assay
- CGD - Comprehensive Guide Designer for CRISPR-Cas systems
- CGDSR 1.3.0 / CGDS Toolbox 1.07 - Accessing the MSKCC Cancer Genomics Data Server (CGDS)
- CHANCE 2.0 b / CHANCE-HT 20140522 - ChIP-seq Data Pre-processing software
- ChEA3 - Gene-list Enrichment Analysis against the manual database
- Check My Metal - Metal Binding Site Validation Server
- ChemmineR 3.44.0 - Cheminformatics Toolkit for R
- ChemSpot 2.0 - A Hybrid System for Chemical named Entity Recognition
- ChemSpotlight 2.0 - Plugin of MacOsX Spotlight for Reading Chemical Files
- ChemT 1.1.0 - Build Template-based 3D Chemical Libraries
- Chemulator - Converter for Chemical Concentrations
- chemViz2 1.1.0 - Cheminformatics Plugin for Cytoscape
- CheNER - Chemical Named Entity Recognizer
- ChiLin 2.1 - ChIP-seq Data quality and Analysis Pipeline
- ChimeraUGEM 1.01 - Unsupervised Gene Expression Modeling in any given Organism
- Chimericognizer - Optical Map based Chimeric Contigs Correction tool
- ChIP-Enrich 2.14.0 - Gene Set Enrichment Testing for ChIP-seq data
- ChIP-PED 0.99.2 - Predict Biological Contexts in which a TF is Functionally Active
- ChIPComp 1.23.0 - Quantatitive Comparison of multiple ChIP-seq dataset
- ChIPmeta 091009 - HHMM Analysis of ChIP-seq and ChIP-chip Data
- ChIPseeker 1.22.0 - ChIP peak Annotation, Comparison & Visualization
- ChIPXpress 1.36.0 - Improve ChIP-seq and ChIP-chip Target Gene Ranking using publicly available Gene Expresison data
- CHOCO 13.03 - Java Library for Constraint Satisfaction Problems
- Chromaligner - Chromatogram Alignment
- ChromaSig - Find Common Chromatin Signatures
- Chromatin Cutter 1.00 - Simulates the distribution of DNA in a Gel Electrophoresis Study of Yeast Chromatin cut by Enzymes
- ChromHMM 1.20 - Chromatin State Discovery and Characterization
- ChromSDE 2.2 - Inference of Spatial Organizations of Chromosomes Using Semi-definite Embedding Approach and Hi-C Data
- ChromSDE 2.2 - Inference of Spatial Organizations of Chromosomes Using Semi-definite Embedding Approach and Hi-C Data
- CIBERSORTx / CIBERSORT - Determining Cell Type Abundance and Expression from Bulk Tissues
- CINDEL - CRISPR AsCpf1 INDEL Score
- Cis-regPred - Cis-regulatory Element Predictor
- cisTopic v3 - Probabilistic Modelling of cis-regulatory topics from Single Cell Epigenomics data
- Cistrome - Platform for Transcriptional Regulation Studies
- CITE-sort - Artificial-cell-type Aware Surface Marker Clustering method for CITE-seq data
- ClassifyMM 1.1 - Classify Hyperdiploidy Status of Multiple Myeloma Patients using Gene Expression Profiles
- ClassifyR 2.12.0 - Performance Assessment of Classification with Applications to Transcriptomics
- cleanUpdTSeq 1.28.0 - Classifiying Putative Polyadenylation sites as True or False/internally oligodT Primed
- CLIMS 2.1.4 - Laboratory Information Management System for protein Crystallography
- clinker v0.0.23 - Gene Cluster Comparison Figure Generator
- CLIPSeqTools 0.1.10 - Suite to analyse CLIP-Seq datasets
- Clone Manager 0.1 - Cloning and Protein Expression LIMS
- clonealign 2.0 - Bayesian Inference of clone-specific Gene Expression Estimates
- CLONET v2 - CLONality Estimate in Tumors
- Clotho 4 - Creating, Deploying, and Sharing BioCAD tools
- Cluster Flow 0.5 - A Simple and Flexible Bioinformatics Pipeline tool
- ClusterControl 2.0 - Monitor Bioinformatics Applications on Linux Cluster Systems
- Clustergrammer 1.19.5 - Web-based Heatmap Visualization and Analysis Tool for High-Dimensional Biological Data
- CLUSTERnGO v0.31 - Gene Expression Analysis Tool
- CNet - Discovery of Clinically Associated, Combinatory Genomic Signatures
- CoDiDi - Correlation between Diversity and Diferentiation
- CoevDB - Database of Pair-wise Nucleotide Coevolution
- COEXPEDIA - Exploring Biomedical Hypotheses via co-expressions Associated with Medical Subject Headings (MeSH)
- Coloc-stats 1.0b1 - Web Interface to perform co-localization analysis of Genomic Features
- ColonyCount BETA - Assist Counting Bacterial Colonies on Agar Plates
- Comb-p 0.50.2 - Combining, Analyzing, Grouping and Correcting Spatially Correlated P-values
- Companion - Easy and reliable Parasite Genome Annotation
- COMPASS 1.0.1 - Generating Serial Samples under an Infinite Sites Model
- COMPASS 2.01 - Protein Backbone Resonance Assignment
- compmerge 1.3 - Tool that tries to solve the same problem as Cuffmerge
- COMSPARI 20031215 - Comparison of Spectral and Retention Information
- consensusOV 1.12.0 – Gene Expression-based Subtype Classification for High-grade Serous Ovarian Cancer
- Context-MMIA - miRNA-mRNA Target Prediction system combining Expression data and Literature data.
- CoNVaQ 0.1.3 - Copy Number Variation-based Association tudies
- CoNVEM - CNV Allele Frequency Estimation by Expectation Maximisation
- CoordinateCleaner v2.0-13 - Automated Cleaning of Occurrence Records from Biological Collections
- COPS Benchmark 2009/6 - Interactive Analysis of Database Search Methods
- Cordova 1.0.0 - Web-based management of Genetic Variation Data
- Core Hunter 3.2.0 - A Program for Sampling Genetic Resources
- CoRe v1.0.2 - Identifying Core-fitness Genes in Genome-wide Pooled CRISPR-Cas9 Screens
- CoreArray 1.0 - Developed Portable and Scalable Storage Technologies for Bioinformatic data
- CorSig - Statistical Inference of Correlation Significance
- COSMID - CRISPR Search with Mismatches, Insertions and/or Deletions
- COSMOS 2.6.24 - Powerful Workflow Management System
- CoStat 6.45 - Statistics Software
- CPPsite 2.0 - Database of Cell Penetrating Peptides
- CRAPome v.0 - Contaminant Repository for Affinity Purification - Mass Spectrometry data
- CRCRpred - Webserver for Risk Prediction in Colo-rectal Cancer Patients
- creDB 0.1.9 - Cis–REgulatory elements DataBase
- CREEDS - Crowd Extracted Expression of Differential Signatures
- CRISPR-SKIP 1.0.1 - Programmable Gene Splicing with Single Base Editors
- CRISPR-SURF 1.0 - Screening of Uncharacterized Region Function
- CRISPRCloud2 - Deconvolution of your CRISPR pooled screening data
- CRISPRitz - Perform in-silico CRISPR analysis and Assessment
- CRISPRO v1.0.2 - Analysis and Visualization of Saturating Mutagenesis CRISPR Screens
- CRISPRone - Annotation of CRISPR-Cas systems
- CRISPRtrack 1.0.1 - Using CRISPR Spacer Content for Bacterial Species Tracking
- CrossClassify - Mapping between different Taxonomic Classifications
- Crossfinder 20150212 - Search for Protein Crosslinks formed by Site-specifically Incorporated Crosslinkers
- CRP_CNV - Conditional Random Pattern Model for Copy Number Aberration (CNA) Detection
- CS-Cal 1.30h - A tool for Evaluation of Clonogenic Survival Experiments
- CSEM v2.4 - ChIP-Seq multi-read allocation using Expectation-Maximization
- CSI-ANN - Discover functional DNA Elements based on their Epigenetic Profiles
- CSNAP 1.0 - Chemical Similarity Network Analysis Pull-down
- CSO validator 20120216 - Curation Workflow for Biological Pathways
- CT-CBN 0.1.04b - Continuous Time Conjunctive Bayesian Networks
- CTCF-MP - Predicting CTCF-mediated Chromatin Loops
- CTCM - Classifying Transcripts from Coral Metatranscriptome
- CTMBR - Classfication Trees for Multiple Binary Responses
- CummeRbund 2.28.0 - Exploration, Analysis and Visualization of Cufflinks high-throughput RNA-Seq data
- CurlyWhirly 1.19.09.04 - Multi-Dimensional Data Visualization
- curveFDP 2.0 - Estimation of Confidence Levels for Peptide Identifications
- Customprodbj v1.2.0 - Customized Protein Database Construction
- CUT&RUNTools - A pipeline for analyzing CUT&RUN data
- Cutoff Finder v1 - Determination of Cutoff Points in Molecular data
- CyanoEXpress 2.3 - Exploration of curated Genome-wide Expression data for the Cyanobacterium Synechocystis sp. PCC 6803
- Cytoscape.js 3.18.2 - Graph Theory Library for Visualisation and Analysis
- CytoTRACE beta - Cellular (Cyto) Trajectory Reconstruction Analysis using gene Counts and Expression
- cyvcf2 v0.11.5 - Fast, Flexible Variant Analysis with Python
- DACO 1.03 - Transcription Factor Complex Prediction Algorithm
- DailyCalcs 4.1 - Science Calculator for iPhone / iPad
- DAIRRy-BLUP 0.1 - High Performance Computing approach to Genomic Prediction
- DamMet 1.0.2 - a full probabilistic model for Mapping Ancient Methylomes
- DANCE 0.99.0 - Deregulation of Copy-number and Expression
- DanteR 0.2 - Quantitative Analysis of -omics Data
- DASS - Discovery and P-value Calculation of Substructures in Unordered data
- DASS-GUI 1.4 - Pattern Search in Non-sequential Data
- Database Manager 2.1 - FASTA Database Manager
- Datasets2Tools - Repository and Search Engine for Bioinformatics Datasets, Tools and Canned Analyses
- DBC - Predict Genomic Markers using Imaging Features
- dbcAmplicons 0.6.7 - Analysis of Double Barcoded Illumina Amplicon Data
- dbEM - Database of Epigenetic Modifiers
- DBRandomizer - Randomizes DNA and protein databases
- dbVOR 1.12 - Phenotype and Genotype Database System
- DCGL 2.1.2 - R package for unveiling differential Regulation from Differential Co-expression
- dcGOR 1.0.6 - Analysing Ontologies and Protein Domain Annotations
- dCMA - differential Chromatin Modification Analysis
- DCOEX 0.9.9.7 - Finding Groups of Differentially Coexpressed Genes
- DDSClassifier - Deconvoluted Disease-Specific Classifier
- DE-SAGE - Analyze SAGE Library data
- DeepArk - Deep Learning models of Regulatory Activity for Model Species
- DeepFun - Tissue and Cell Type specific Deep Learning Sequence-based model to Decipher Noncoding Variant Effects.
- DeepInsight - Transform Non-image data to Image
- DeepSynergy - Predicting Anti-cancer Drug Synergy with Deep Learning
- deepTS - Exploring Transcriptional Switches from pairwise, temporal, and population RNA-Seq data
- DeLorean 1.5.0 - Estimates Pseudotimes for Single Cell Expression Data
- DelPhi Force - Electrostatic Force Calculation Web Server
- DelPhiPKa - Protonation and pKa Calculation Websever
- DeMixT 1.6.0 - Deconvolution on Transcriptome data from a mixture of two or three components
- dendsort 0.2 - Optimize Ordering of Nodes in a Dendrogram
- DensityFit 1.0 - Analysis of Electronic Density Map for Protein
- DESCHRAMBLER - Reconstructs Ancestral order of Syntenic Fragments
- destiny 2.14.0 - R library for Diffusion Maps
- deTS v1.0 - Tissue-Specific Enrichment Analysis
- DextMP - Moonlighting Protein Prediction by Deep Dive into Text
- DGIdb v2.22 - Rails Frontend to The Genome Institute's Drug Gene Interaction Database
- diCal 1.3 / diCal-IBD 1.0 - Predicts Identical by Descent Tracts using Sequence data
- diffReps 1.55.6 - Finding Differential Chromatin Modification Sites from ChIP-seq data
- DigSee v2.01 - Disease Gene Search Engine with Evidence Sentence
- diHMM v0.1 beta - multi-scale Chromatin State Annotation from ChIPseq data
- DIME 1.2 - Identifying Differential ChIP-seq Based on an Ensemble of Mixture Models
- DIMERO - Data Integration for Molecular Reconstruction
- DiPCell - Designing of Inhibitors against Pancreatic Cancer Cell Lines
- DiPhiSeq 0.2.0 - Robust Comparison of Expression levels
- Discordant - A Novel Approach for Differential Correlation
- DISEASES - Disease-gene Associations Mined from Literature
- DisVis 2.0 - Visualisation of Conformational Space Restriction by Distance Restraints
- DIVE 1.0 - Data Intensive Visualization Engine
- Djeen 1.5.1 - A Joomla! Component to Manage Scientific data
- DLTCount - Counting and Sampling Gene Family Histories
- DMAN 5.3 - Differential Scanning Fluorimetry Melting Data analysis
- dms_tools 1.2.2 - Analysis and Visualization of Deep Mutational Scanning
- DNASIZE - Computation of size of DNA and Protein Fragments from Their Electrophoretic Mobility
- dnet 1.1.5 - Integrative Analysis of Omics data in terms of Network, Evolution and Ontology
- DNorm 0.0.7 - Disease Name Normalization
- DoDoMa - Analytical tool to Identify Transcription Factors with matching DNA Binding Domains
- dotplot 0.3 - Simple Shaded DotPlotter
- Dotter 20131114 - Dot-matrix Program with Interactive Greyscale Rendering
- DoubleTree 0.7 - Compare Two Trees using Coupled Interaction
- DPS 1.4.0 - Predict and Prioritize Pairs of Drugs
- DR_bind1 - DNA and RNA Binding Residue Prediction Server
- DROMPA 3.7.2 / DROMPAplus 1.10.0 - Peak-calling and Visualization Tool for Multiple ChIP-seq Data
- Drug Gene Budger 1.0 - Identify Drugs and Small Molecules to Regulate Expression of Target Genes
- DrugThatGene - Streamlines Analysis of potential Therapeutic Targets identified from Functional Genetic Screens
- DRUID 1.02.1 - Deep Relatedness Inference utilizing Identity by Descent
- DSA 1.0 - Digital Sorting Algorithm for Heterogeneous Samples
- dSpliceType 2.0.0 - Detect various types of differential Splicing Events using RNA-Seq
- Dsuite 0.4 - Fast D-statistics and related Admixture Evidence from VCF files
- DTome - Drug-Target Interactome
- DTWave 201405 - Dynamic Time Warping for Spectrogram Alignment and AVErage Sequence Computation
- Duphold v0.2.1 - Annotation and Curation of high-confidence Structural Variant Calls
- DWLS - Cell-type Deconvolution using Single-cell RNA-sequencing data
- DynBin - Binning Microbial Community Profiles
- e!DAL 3.0.4 - Electronic Data Archive Library
- EasyFRAP - Quantitative and Qualitative Analysis of FRAP data
- easym6A v1.0.0 - A pipeline for m6A Sequencing data pre-processing
- Easyworm 20141001 - Determine the Mechanical Properties of Worm-like Chains.
- EbolaVCR - Ebola Virus Computational Resources
- ECLAIR - Robust Lineage Reconstruction from Single-cell Gene Expression data
- EcoLens 20051212 - Browse through a Large Database of Information about Food Webs
- EcologIE PMCMiner 0.1 - Extract Information about Species Interactions from the Ecological Literature
- ECplot v2.0 - Making Standardized Plots from large datasets for Bioinformatics Publications
- EdgeExpressDB 0.954 - Integrated database of Promoters, Genes, microRNAs, Expression Dynamics and Regulatory Interactions.
- edira 1.2.3 / ediraAMLdata 1.0.6 - Equally Directed Abnormalities / of Acute Myeloid Leukemia plus reference data
- EditR 1.0.8 / MultiEditR 1.1.0 - Multiple Edit Deconvolution by Inference of Traces in R
- EGFRIndb - Epidermal Growth Factor Receptor Inhibitor Database
- EGFRpred - Classification of Active and Inactive Anti-egfr Compounds
- eggNOG 5.0 - Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups
- EgoNet - Identification of human Disease Ego-network Modules
- EhecRegNet v2 - Database of Pathogenic E. coli Transcriptional Gene Regulatory Networks
- EHR-Phenolyzer v1.0.1 - takes Clinical notes from EHRs and Generate Phenotype terms, then generate ranked Gene List
- eigenR2 1.0 - Dissecting Variation in High-dimensional studies
- ELL 3.2.4 - Platform for Generic Algorithms
- ellipsoidFN 0.0.1 - Identifying a Heterogeneous set of Cancer Biomarkers based on Gene Expressions
- ELN 4.05 - Electronic Lab Notebook
- EMDomics 2.22.0 - Earth Mover's Distance for Differential Analysis of Genomics Data
- EMEN 2.2b7 / EMDash 2.2b5 - Object Oriented Database and Electronic Lab Notebook / Client Utilities
- EMPANADA - Evidence-based Assignment of Genes to Pathways in Metagenomic data
- EMVC 0.3 - Entropy Minimization over Variable Clusters
- Enlight - Integrating GWAS Results with Biological Annotations
- EntrezAJAX 20100216 - An AJAX Endpoint for NCBI's Entrez Service
- EP-sim - Multiple-resolution Alignment-free Measure based on Entropic Profiles
- ePEST 1.0 - ChIP-exo Paired-ends Sequencing Processing Toolkit
- Epi-Seq 1.0.0 - Predicting Tumor Specific Epitopes from RNA-Seq data
- EPIG-Seq v1.0 - Extracting Patterns and Identifying co-expressed Genes from RNA-Seq
- EPIP - Condition-specific Enhancer–promoter Interaction prediction
- Eurexpress Browser Menu - Get Fast Access to Eurexpress Database
- ExactNumCI 1.2.1 - Exact Numerical Confidence Interval for Binomial Proportions
- ExAtlas - Meta-analysis of Gene Expression data
- Exchanger 1.0 - Send files to a Bioinformatician and Receive analyses
- exim - Compare Time-series Expression Profiles
- EXIMS 20141021 - EXploring Imaging Mass Spectrometry data
- ExonDel 1.07 - Detection of Internal Exon Deletion with Exon Del
- ExonHunter 1.07 - Comparative Gene Finder
- ExPecto - Tissue-specific Gene Expression Effect Prediction for human Mutations
- Expitope - Expression of Epitope
- expVIP 20180914 - RNA-seq Data Analysis and Visualization Platform
- Eyediagram - Visualization Probabilistic Decompositions
- ezFreezer 1.5.10 - Samples and Specimens Storage Management
- FACTA+ 0.8.1 - Text Mining from MEDLINE
- FARAO 1.0b – The Flexible All-Round Annotation Organizer
- Fastbreak - Structural Variant Detection in Genomic data
- FastDMA 1.2.1 - Humanmethylation450 Beadchip Analyzer
- fastLSA 1.0 - Implementation of the Local Similarity Analysis
- FastPairMI - Fast Calculation of Pairwise Mutual Information Based on Kernel Estimation
- FCOP - Discover Frequent Combinatorial Occupancy Patterns
- FCSM - Frozen Cell Stock Monitor
- fdrtool 1.2.15 - Estimation of (local) False Discovery Rates and higher Criticism
- FEBio 1.5 - Finite Elements for Biomechanics
- FEMER 1.0 - noninvasive Reconstruction of Placental Methylome
- Fenrir - Tissue-specific Enhancer Functional Networks for Associating Distal Regulatory Regions to disease
- FFLtool - Web Server for TF-miRNA-target Feed Forward Loop analysis
- Fido - MS/MS Protein ID Software
- FigSys 2.4 - Publication Quality Graph Plotting and Data Analysis
- findGSE - Estimating Genome Size Variation using k-mer Frequencies
- FireProt 1.2 - Automated Design of Thermostable Proteins
- FisHiCal 1.1 - Iterative FISH-based Calibration of Hi-C Data
- Fizzy v1.4 - Feature Selection for Biological Data Formats
- FlashMotif - Finding Statistically Significant colored Motifs
- FlexSA 1.0 - Flexible Sequence Analysis system
- FluxEs 2.0 - Metabolic Flux Estimation
- FMTP - Fingerprint-based Minimal Tiling Path
- FOCS - Analyzing Enhancer and Gene Activity Patterns
- FoCuS-point 1.16.197 - Python TCSPC FCS data Visualiser
- fourSig 2.2 - Analyze 4C-seq data
- FoXS - Fast SAXS Profile Computation with Debye Formula
- FRED 1.0 - Framework for T-cell Epitope Detection
- FretTrace 1.0 - Maximum Likelihood Trajectories from Single-molecule FRET Experiments
- FuncAssociate 2.0 - Gene Sets Characterizing & Functional Trend Analysis
- FuncEpiMod 2.7 - Identification of Functional Epigenetic Modules (FEM)
- FunCoup 4.0 - Explore comprehensive Protein networks of Functional Coupling
- FunRich 3.1.4 - Functional Enrichment analysis tool
- FunSys 20120525 - Transcriptome and Proteome Analyzes for Prokaryotes
- funtooNorm 1.00.1 - Normalization of Illumina Infinium Human Methylation 450 BeadChip
- FusionSeq 0.7.0 - Detect Chimeric Transcripts from Paired-end RNA-seq Experiments
- G-NEST - Gene Neighborhood Scoring tool
- GA2GAQ - GO Annotation Quality(GAQ) Score
- Galaxy LIMS - LIMS for Next-generation Sequencing
- GARM 1.0 - Genetic Algorithm for creation of Resistance Maps
- GCAligner 1.0 - Alignment of Chemical data obtained by Gas Chromatography
- Gcorr - FTMS Signal Suppression Processing software
- GDASC - A GPU Parallel based Server for Detecting Batch Factors
- GDISC - Gene-Drug Interactions for Survival in Cancer
- GDPC 2.0 - Access to Genomic Diversity and Phenotype data
- GECES - Gene Expression Classification
- GEDS - Gene Expression Display Server
- Gee Fu 0.1.2 - Database tool for Genomic Assembly and Feature data
- GEM 3.4 - Study Protein-DNA interaction using ChIP-Seq/ChIP-exo data
- GEMINI - The Genomic Search Engine
- Gemvid 0.8c - Monitoring System for Rodents
- GEN3VA - Gene Expression and Enrichment Vector Analyzer
- Gencount 1.0 - Counts the Number of different Multilocus Genotypes
- Gencrypt 1.0.0 - One-way Cryptographic Hashes to Identify Overlapping Individuals
- GeneCT - Cancerous Status and Tissue Origin Classifier for Pan-cancer Biopies
- GeneExpressionSignature 1.38.0 - Gene Expression Signature based Similarity Metric
- Genefu 2.23.1 - Computation of Gene Expression-Based Signatures in Breast Cancer
- GeneHub-GEPIS - Expression Profiling for Normal and Cancer Tissues based on an integrated Gene Database
- GeneLink 1.7 - Data Management System to Facilitate Genetic Studies of Complex Traits
- GeneMatcher - Matching Tool for Connecting Investigators with an Interest in the Same Gene
- GeNemo - Web-based Search Engine for Functional Genomic Data
- GeneNomenclatureUtils - Tools for Annotating Genes and Comparing Gene Lists with Community Resources
- GeneNotes 1.0 - FireFox Extension of Collecting and Managing Biological Information
- GenePEN - Network Analysis of Omics Data
- Generategenelistvariants 0.1.4 - Generate Gene Listvariants from Gene file
- GeneRave 3.0.9 - Fitting Sparse Response Models to very high Dimensional data
- Genes2WordCloud - Create Biologically-relevant-content WordClouds
- GeneScissors - Detecting and Correcting Spurious Transcriptome Inference due to RNAseq reads misalignment
- GeneSet2Diseases - Calculate Enrichment of Associations to Diseases on sets of human Genes
- Geneshot - Submit Biomedical Terms to Receive Ranked Lists of Relevant Genes
- geneSLOPE 0.37.0 - Genome-Wide Association Study with SLOPE
- GeneTerrain - Next-generation Panel Biomarker Discovery and Validation software
- GeneTIER - Expression-based Candidate Gene Prioritisation
- GeneValorization - Gene List significance at-a-glance
- GeneVenn - Gene list Venn Diagram
- GENIA tagger 3.0.1 - Part-of-Speech Tagger for Biomedical Text Mining
- GenoClone 0.1 - subClone inference and studying Tumor Heterogenity
- GenoGUARD 20110320 - Biosecurity of Gene Synthesis
- GenomicSQLite v0.9.1 - Genomics Extension for SQLite
- GenoQuery - Querying Genomic Data Warehouse
- GeoAssign 0.4.1 - Assignment of Origin using Genetic, Phenotypic and Geographic information
- GEOquery 2.58.0 - Get data from NCBI Gene Expression Omnibus (GEO)
- GeoStaS 1.2 - Divides a biomolecule into Dynamic Domains
- GermlineFilter 1.2 - Encrypted Filtering of Germline Calls from Somatic vcf
- GetCrosses 0.5b - Simulation of Offspring Genotypes from a SNPs file
- Getgo - A Simple Gene Enrichment analysis tool
- GETM 20100519 - Gene Expression Text Miner
- GExposer 1.0 - Differential Expression analysis in RNA-Seq
- GFAsparse 1.0.3 - Elementwise Sparse Group Factor Analysis
- GFtbox 20210716 - Quantitative Understanding of Growing Shapes
- GGSD 2.19 - Generic Genetic Studies Database
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