Posts
- Category: Miscellaneous (continued)
- PIPE-CLIP 1.2.0 alpha - Comprehensive online tool for CLIP-seq Data Analysis
- PIPINO 0.3 - ProteIn Protein INteraction Optimizer
- PIPS 1.1.2 - Pathogenicity Island Prediction Software
- Piranha 1.2.1 - Peak-caller for CLIP- and RIP-Seq high-throughput Protein-RNA interaction data
- PIUMet - Network Integration of Untargeted Metabolomics
- PIVOT v1.0.1 - Platform for Interactive analysis and Visualization Of Transcriptomics data
- PKreport 1.5 - Reporting Pipeline for Checking Population Pharmacokinetic Model Assumption
- Planform 2.2.18 - software of Graph-encoded Planarian Regenerative Experiments
- PlantMAT v1.0 - Plant Metabolite Annotation Toolbox
- PlantSimLab 1.0 - A Simulation Laboratory for Plant Biology
- PlasmidTron 0.4.1 - Assembling the cause of Phenotypes and Genotypes from NGS data
- PLIC - Protein-ligand Interaction Clusters
- pLogo - Probability Logo Generator for Biological Sequence Motifs
- plshghmm - R Software for Fitting HGHMMs to Tiling Array data for Nucleosome Positioning
- PODKAT 1.18.0 - Association Testing Involving Rare and Private Variants
- POEAS - Plant Ontology Enrichment Analysis Server
- PointCloudXplore 2.0 - Visualization and analysis of the data in PointCloud and Virtual Embryo Files
- PolyaPeak 0.4 - ChIP-seq Peak Reranking tool using mixture of Multivariate Polya Ditributions
- PolyMarker 0.9.9 - Polyploid Primer Design
- PolySearch 2 - Text Mining system for extracting relationships between Human Diseases, Genes, Mutations, Drugs and Metabolites
- POPSCOMP v.3.2 - Automated Interaction analysis of Biomolecular Complexes
- Populous 1.2 beta - Populating Ontology Templates
- Portcullis 1.2.2 - Splice Junction Analysis and Filtering from BAM files
- PowerGet 3.5.8 - Software for liquid chromatography (LC) – high-resolution mass spectrometers (MS).
- POWSC - Power Evaluation and Sample Size Estimation in single cell RNA-seq.
- pPIC9 - Evaluation and Design for high-level Expression of Foreign Genes in pPIC9 Vector
- PPISURV - Cancer Survival Analyses
- preciseTAD 1.4.0 - Machine Learning framework for precise TAD Boundary Prediction
- PRECOG / iPRECOG - PREdiction of Clinical Outcomes from Genomic Profiles
- PrestoPlot 1.23 - 2D Plotting tool
- PRIME 0.9 - Mass Spectrum Data Mining Tool
- PrivGWAS - Preserving Privacy in Genomewide Association Studies
- PrivMAF - Privacy Loss and MAF
- pro Fit 7.0.18 - Scientific Application for Non-linear Curve-fitting
- Pro-origami - Protein Structure Cartoons
- PROBer v0.3.1 - Toolkit for Analyzing Sequencing-based 'Toeprinting' Assays
- ProCarDB - Prokaryotic Carotenoid DataBase
- PROcEED - Conduct Probabilistic Reverse Dosimetry Calculation
- ProMatch - Match Peptide and mRNA Sequences to Entries in NCBI RefSeq
- ProSig 1.1 - Designing Nucleic Acid-based Pathogen Detection Assays
- PROSSTT v1.4 - PRObabilistic Simulations of ScRNA-seq Tree-like Topologies
- Protege 5.5.0 / WebProtege 4.0.2 - Ontology Editor and Knowledge-base Framework
- ProtocolNavigator 1.0 - Open-source software for Designing, Documenting Biological Experiments
- ProtPhylo - Prediction of Protein-to-protein and Phenotype-to-protein Functional Associations based on Phylogenetic Profiling
- protTrace 1.0 - Estimate Evolutionary Traceability of Protein
- Provable / randGen - Software for the Closest Substring Problem and the Planted (L,d)-Motif Problem
- PRRDB 2.0 - Pattern Recognition Receptor Database
- Pse-in-One 1.0.6 - Generating various modes of Pseudo Components of DNA, RNA and Protein Sequences
- PSGInfer 1.2.1 - Inference of Alternative Splicing from RNA-Seq data with probabilistic Splice Graphs
- PsRRR - Pathways Sparse Reduced Rank Regression
- PsyGeNET v2 / Psygenet2r 1.4.0 - Knowledge Platform on Psychiatric Disorders and their Genes
- PTMcode 2 - Known and predicted PTM Functional Associations
- PTS 1.0.2 - Parallel Tagged Sequencing
- Pubcrawl - Networks of Literature-based Semantic Distances with Protein Domain Interactions
- PubCrawler 2.40 - Update Alerting Service for PubMed and GenBank
- pubmed2ensembl - Link Publications in PubMed to Genes in Ensembl
- PubNet - Publication Network Graph Utility
- PubSearch 0.8.1 - Literature Curation Management System
- PubTator - Text Mining tool for Assisting Biocuration
- PURE - Pubmed Article Recommendation System based on Content-based Filtering
- PuReD-MCL 20111130 - PubMed Document Clustering
- PurityEst - Estimating Purity of Human Tumor Samples using Next-generation Sequencing Data
- pVACtools 2.0.1 - Tools for Personalized Cancer Vaccine Design
- PyCorrFit 1.1.7 - Data Analysis software for Fluorescence Correlation Spectroscopy (FCS).
- PyFDAP 1.0 - Analysis of Fluorescence Decay After Photoconversion (FDAP) Experiments
- pymzML 2.5.0 - Python module to Parse mzML data based on cElementTree
- PyParaTools - Software for working with paramagnetic NMR data
- PyScanFCS 0.3.6 - Analysis of perpendicular Line Scanning FCS.
- Q v1.2.0 - Saturation-based ChIP-seq Peak Caller
- Q5 - Classification of Complete Mass Spectra of a Complex Protein Mixture
- QAPA 1.3.0 - RNA-seq Quantification of Alternative Polyadenylation
- QBiC-Pred - Quantitative Binding Change Prediction
- QChIPat - Comparing two Biological ChIP-seq Samples
- Qiita v0.2.0 - Microbiome Meta-analysis
- QiSampler 20111215 - Evaluate Prioritization Done by Scoring Schemes and Experimental Parameters of High Throughput Biological Datasets
- QMLGalaxyPortal 1.2.5 - A mobile QML app for interfacing with the Galaxy API
- qPMS9 - Parallel Algorithm for Quorum Planted Motif Search
- QRNAS - software tool for Refinement of Nucleic Acid structures
- QTModel 0.70Beta - Mixed Linear Model Analysis, Microarray Data Analysis and Diallele Cross Analysis
- QuantileMap - Visualization of Compactlydemonstrate Multiple Distributions in Genomic Applications
- QuantProReloaded 1.0 - Software for the Statistical Analysis of Microspot Immunoassays
- Quartz 0.2 - de novo Quality Score Compression tool
- QUASSI - Quantifying Significance of MHC II Residues
- QuateXelero - Fast Motif Detection algorithm
- QUERY_WIN - Retrieval Program with Graphical User Interface for ACNUC Databases
- QUOSA 1.22 - Manage Scientific and Technical Documents
- RABIT - Regression Analysis with Background InTegration
- RADinitio 1.1.1 - Simulation software for the Selection and Optimization of RADseq Experiments
- RAFSIL 0.2.5 - Lerning cell-cell similarities from scRNA-seq data
- RAIDA 1.0 - Identifying differentially Abundant Features in Metagenomic Samples
- RamiGO 1.20.0 - AmiGO Visualization Interface for R
- RamseyHAc 2010 - Prediction of Mammalian Transcription Factor Binding Sites
- RandProt - High-order Markov Random models for Protein Sequences
- RanSEPs - Framework for Bacterial Genome re-annotation and novel small proteins prediction
- RAP - Rank Aggregation-based data Fusion for Gene Prioritization
- RaPID 1.7 - Random Projection-based IBD Detection
- RAREVATOR - RAre REference VAriant annotaTOR
- RateLimit - Rate Limiting Steps in Transcription from RNA production times in live cells
- RaTrav 20130916 - Calculating Mean First Passage Times using Hill's and Monte Carlo algorithms
- RCADE 1.0 - Recognition Code-Assisted Discovery of Regulatory Elements
- Rchemcpp 2.24.0 - An R package for Computing the Similarity of Molecules
- REBACCA - Investigating Co-occurrence Patterns based on Meta-genomic compositional data
- References On Tap - Your reference manager for iOS
- Reflect - Automated Annotation of Biochemical Terms in web pages
- RefSense 1.2 - Search PubMed
- RefSeq 207 - NCBI Reference Sequence Database
- RegaDB 2.0 - A Viral Data and Analysis Management Environment
- Regression tree package - Implementation of Ensembles of Multiple output Regression Trees
- RegTools 0.5.2 - Integrated analysis of Genomic and Transcriptomic data for discovery of Splicing Variants in Cancer
- ReMap 2020 - ChIP-seq analysis of Regulatory Elements
- Renal Inner Medulla Free Energy Calculator
- RenBio 0.7d - Identify Gene and Protein Name in Textual Document
- Repbase Submitter 1.1.115 - Format & Annotate Repbase Entries
- RepeatedHighDim 2.0.0 - Global tests for Expression data of high-dimensional sets of Molecular Features
- RepExplore - Exploit Technical Replicate Variance in Omics Analysis
- REPIC - A Database for Epitranscriptomics
- Repitools 1.39.0 - Analysis of Enrichment-based Epigenomic Data
- ReportingTools 2.32.1 - Tools for Making Microarray and Sequencing Data Reports in various Formats
- RESCUE v1.0.3 - Imputing Dropouts in Single-cell RNA-sequencing data
- ResProx - Comparing the overall Quality of NMR Protein Structures
- REtools 5.0-101 - Assist in Restriction Enzyme Use
- RFMapp 20121217 - Ribosome Flow Model Application
- RHH 0.1 - Visualizing Chromosome Mosaicism and Detecting Ethnic Outliers
- RHybridFinder 0.2.0 - Identification of Hybrid Peptides in Immunopeptidomic Analyses
- Ribomap v1.2 - Isoform-level Ribosome Occupancy Estimation Guided by Transcript Abudance
- RiboVision 1.15 - Visualization and Analysis of Ribosomes
- RIPPLE - Regulatory Interaction Prediction for Promoters and Long-range Enhancers
- RLIMS-P 2.0 - Rule-based Literature Mining System for Protein Phosphorylation
- RNA-Scoop v1.0.1 - Interactive Visualization of Single-cell Transcriptomes
- RNAdbtool - Update and Cleanup of Structural RNA Databases
- RNANumbers - Estimation of RNA numbers of Spots Intensities
- RNApin - Prediction of Protein Interacting Nucleotides in a RNA Sequence
- RNASeqExpressionBrowser v1.22 - High-throughput Expression Data Analysis
- ROCCET - Receiver Operating Characteristic Curve Explorer & Tester
- ROCS 1.3 - Receiver Operating Characteristic Surface
- ROMA - Calculation of Gene Set Activities from Oomics data
- ROS-DET - Robust Detector of Switching Mechanisms in Gene Expression
- RPI-Pred - RNA-protein Interaction Prediction Server
- RRE 20040401 - Retrieval of Non-coding Regulative Elements from Annotated Genomic databases
- RReportGenerator 1.3.3 - Run Routine Statistical Analysis using R
- RseqFlow 2.2 - RNA-seq Data Analysis Workflow
- RSSS - Comparative Study of RNA-seq Analysis Strategies
- RTFBSDB 0.31 - Parse TF motifs from public databases, read into R, and scan using 'rtfbs'.
- rTRM 1.30.0 - Prediction of Transcriptional Regulatory Modules
- RUFUS V1.0 - K-mer based de novo Variant Calling
- RV-Typer - Typing of Rhinoviruses Using Alignment-Free Approach
- RVIS - Residual Variation Intolerance Score
- S4TE 2.0 - Searching Algorithm for Type IV Effector proteins
- SAD - Salmon Anomaly Detection
- SAFIR 1.3 - Small-angle Scattering Data Fitting with Tigid Bodies
- SAIGE 0.44.6.5 - Scalable and Accurate Implementation of GEneralized mixed model
- SAIL 1.0 - Sample avAILability system
- SAINT 3.6.3 - Significance Analysis of INTeractome
- SAINT2 - Cotranslational Protein Structure prediction
- Salmon v1.0.0 - Quantification of Transcript Abundance from RNA-seq reads
- SalmoNet - An Integrated multi-layered Network of Salmonella
- SalmonTE 0.4 - Ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances
- SamCluster - Discovery of Sample Classes using Gene Expression Profile
- Sampbias - Sampling Bias in Species Distribution Records
- SAPS 2.2.0 - Significance Analysis of Prognostic Signatures
- Satellog 1.0 - Database of Repeat Prioritization
- SATPdb - Database of Structurally Annotated Therapeutic Peptides
- SATuRNo - Supervised Prognostic Approach Through Regression Networks
- SC / SC-sample - Modeling Spatial Coalescent with Recombination Process
- SC1 - A web-based Single Cell RNA-seq Analysis Pipeline
- SC2P 1.0 - Two-phase differential Expression for single-cell RNA-seq
- SCAN-SNV - Single Cell Somatic Genotyper
- scAND - scATAC-seq data Analysis via Network Diffusion
- SCANMS 2.02 - Adjusting for multiple Comparisons in sliding window neutrality tests
- SCATE - Single-cell ATAC-seq Signal Extraction and Enhancement
- SCATS - Single Cell Analysis of Transcript Splicing
- SCENIC 1.1.2 / pySCENIC 0.11.2- Single-cell Regulatory Network Inference and Clustering
- SCG 0.3.1 - Inference of Clonal Genotypes
- SCHISM 1.1.3 - Subclonal Hierarchy Inference from Somatic Mutations
- scHMM 1.1.0 - Sparsely correlated hidden Markov model for ChIP-seq data Analysis
- SciClone 1.1 - Infer subclonal Architecture of Tumors
- sciCNV - Inferring CNVs from scRNA-seq
- ScoMAP 0.1 - Single-Cell Omics Mapping into spatial Axes using Pseudotemporall ordering
- SCORER 2.0 - Distinguish Parallel Dimeric and Trimeric Coiled-coil Sequences
- scPPIN v0.3-beta - Find active modules in PPINs
- SCRAT - Single-Cell Regulome Analysis Toolbox
- ScreenBEAM 1.0 - Functional Genomics Screens via Bayesian Hierarchical Modeling
- SCRMshaw - Genome-wide Supervised CRM Prediction
- SCUBA 1.0 - Single-cell Clustering Using Bifurcation Analysis
- SDAR 5.2 - Graphical Analysis of Two-dimensional Data
- sdef 1.7 - Synthesizing List of Differentially Expressed Features
- SDRF2GRAPH 1.0 - Visualization Tool of a Spreadsheet-based Description of Experimental Processes
- SEA 1.0.0 - Serial Expression Analysis
- SeDuS 1.10 - Segmental Duplication Simulator
- SEEK - Search-Based Exploration of Expression Compendium
- SEGtool 1.3 - Specifically Expressed Gene Detection
- Selfish - Discovery of Differential Chromatin Interactions via a Self-Similarity Measure
- Semantic Body Browser 1.6.2 - Graphically Exploring an Organism's Body
- SEMPPR 1.0.2 - Stochastic Evolutionary Model of Protein Production Rates
- SENT - Functional Interpretation tool based on Literature Analysis
- SeqCalc 1.0 - Portable software for Sequence Analysis
- Seqcrawler 0.6.2 - Biological Data Indexing and Browsing Platform
- SeqGL 1.1.4 - Identifies Context-dependent Binding Signals in ChIP-seq and DNase-seq profiles
- SeqHound 3.02 - Bioinformatics Database Warehouse Resource
- seqr v0.3.0 - Web-based Analysis tool for Rare Disease Genomics
- SeqSite 1.0.0 - ChIP-Seq Binding Site Identification
- SeroBA 1.0.1 - k-mer based Pipeline to identify the Serotype from Illumina NGS reads
- SeSAMe 1.11.0 - SEnsible Step-wise Analysis of Methylation data
- SGNNMD - Signed Graph Neural Network for Predicting Deregulation Types of MiRNA-disease Associations
- SGRP - Saccharomyces Genome Resequencing Project
- SGS v2 - Analysis of Spatial Genetic and Phenotypic Structures of Individuals and Population
- sGSCA - signature-based Gene Set Co-expression Analysis
- SHAPE 1.3 - Biological Shape Analysis with Elliptic Fourier Sescriptors
- SIAMCAT 1.5.0 - Statistical Inference of Associations between Microbial Communities
- sicegar 0.2.3 – Analysis of Single-cell Viral Growth Curves
- Sierra 0.3 - LIMS system designed for use by Small Sequencing Facilities
- Sight 3.2.0 beta - Automatic running of Bioinformatical Tools on Remote Servers
- SigMA - Signature Multivariate Analysis for low statistics SNV data
- SignaLink 2.0 - Multilayered Regulatory Networks
- SignalSpider - Probabilistic Modeling and Pattern Discovery on Multiple Normalized ChIP-Seq Signal Profile
- SigTools - Visualizing Genomic Signals
- silcLOD - Calculate Nominal Significance Levels and Critical LOD Scores
- SILP2 - ILP-based Maximum Likelihood Genome Scaffolding
- SimConcept - Hybrid approach for simplifying Composite Named Entities in Biomedical Text
- simDEF - Definition-based Semantic Similarity Measure of GO Terms for Functional Similarity Analysis of Genes
- SimGlycan 5.94 - Glycan & Glycopeptide MS/MS Data Analysis Tool
- simGWAS 0.2.0-2 - Simulation of case-control GWAS Summary Statistics
- SimLipid 6.06 - Characterize lipids using Data from MS, MS/MS and MSE
- SIMS 2.14 - Sample Information Management System
- SINC - Scale-invariant Deep Neural-network Classifier for Bulk and Single-Cell RNA-seq.
- Sincell 1.24.0 - Analysis of Cell State Hierarchies from Single-cell RNA-seq
- singlecellVR - Interactive Visualization of Single-Cell Data in Virtual Reality
- SitePainter 1.1 - Exploring Biogeographical Patterns
- Skylign - Creating Logos Representing both Sequence Alignments and profile hidden Markov models
- SLAM-DUNK 0.3.4 - Streamlining SLAMseq analysis with ultra-high sensitivity
- Sleipnir 3.0 / COALESCE - Library for Computational Functional Genomics
- SLIMS 1.0.0 - Sample-based Laboratory Information Management System
- SLR 0.1.9 - Performing Smoothed Logistic Regression for CGH data
- SMK 2011v4 - Mining Low-support Discriminative Patterns from Dense and High-dimensional Data
- SMLR 1.1.0 - Sparse Multinomial Logistic Regression
- SnackNTM v1.5.3 - Identification of Nontuberculous Mycobacterial Species
- Snakemake 6.4.1 - Scalable Bioinformatics Workflow Engine
- Sniffles 1.0.11 - Structural Variation Caller using Third Generation Sequencing
- SNOW - Standard Nomenclature Wizard
- Snpdat - A Simple High Throughput Analysis Tool for Annotating SNPs
- snpEnrichR - Automating Enrichment analysis of GWAS SNPs
- SoftPanel - Grouping Disorders for Generation of customized Panels
- Somalier v0.2.6 - fast Sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs
- southern_blot_design 20090825 - Automated Design of Genomic Southern Blot Probes
- spaMM 3.0.0 - Mixed Models, Particularly Spatial GLMMs
- sparseQuant 20130910 - Targeted Protein Quantification using Sparse Reference Labeling
- Spatial 1.0.0 - Model Animal Movement on Landscapes
- spatialTIME 1.2.0 / iTIME - Visualization and Analysis of Immunofluorescence data
- SPatt 2.1 - Statistic for Patterns
- Species 2000 Annual Checklist 2019 - Taxonomic Databases
- SpeciesGeoCoder 1.1.0 / speciesgeocodeR 2.0-10- Coding of Species into user-defined units
- Spectacle 1.4 - Spectral learning for Annotating Chromatin Labels and Epigenomes
- SpectFit 2.0 - Non-linear Data Fitting
- Spector II - Calculate Concentration of Oligonucleotides based on OD Values
- SPEID - Predict enhancer-promoter interactions based on Sequence-based features
- SPIA 1.1.0 - SNP Panel Identification Assay
- SpiceHit 2.2 - SIM-Peak Detection and Identification tool
- SPIKE - Database of highly curated human Signaling Pathways
- SPLASH - Structural Pattern Localization Analysis by Sequential Histograms
- SpliceGrapher 0.2.7 - Creat Splice Graphs from RNA-Seq data
- SpliceHetero - Measuring Spliceomic Intratumor Heterogeneity from bulk-tumor RNA-seq
- SpliceR v1.2.0 - Prediction of BE-splice sgRNAs for Base Editor mediated Knockout
- SPONGE 1.8.0 - Sparse Partial Correlations On Gene Expression
- SPoRE - Mathematical Model to Predict Double Strand Breaks and Axis Protein Sites in Meiosis
- sppPCA 1.0 - Sequential Projection Pursuit PCA
- Spresso 1.0.3 - Pre-screening Method Based on Compound Decomposition
- SPRINT 1.0.7 - Parallel Framework for R
- SQANTI 1.2 - Structural and Quality Annotation of Novel Transcript Isoforms
- SQUID v1.5 - Structural Variant Detection from RNA-seq
- SR4GN 1.0 - Species Recognition software tool for Gene Normalization
- SRAdb 1.52.0 - R tool to Query/ Download Short Read Archive
- SraTailor 1.0.7 - Processing and Visualizing ChIP-seq data
- SRM Collider 1.4.2 - Computes Interferences in SRM (Selected Reaction Monitoring) Experiments
- ssNPA 1.0 - subtyping samples based on Deregulation of their Gene Networks
- SSP 1.2.1 - Quality-assessment tool for ChIP-seq data
- st 1.2.5 - Shrinkage t Statistic and CAT Score
- stabs 0.6-4 - Stability Selection with Error Control
- stAIcalc - tAI Calculator based on Species-specific Weights
- StAR - Statistical Analysis of Receiver Operating Characteristic (ROC) Curves
- STAR 1.0 - Significance Tester for the Accumulation of Reads
- Stat-200 2.1 - General Statistics and Graphics Package
- STATegraEMS v0.9 - Experiment Management System (EMS) designed for Storage and Annotation of NGS experiments.
- Statius - Prediction of Individualized Therapeutic Vulnerabilities in Cancer from Genomic Profiles
- StatsDB 1.1 - Storage and Understanding of Next Generation Sequencing Run Metrics
- StemChecker - Discover and Explore Stemness Signatures in Gene Set
- stochprofML 2.0.3 - Stochastic Profiling using Maximum Likelihood Estimation
- STREAM v1.0 - Trajectory analysis from Single-cell RNAseq and ATACseq data
- STREE - Survival Analysis Trees
- Strut 0.1 - Protein Function Prediction
- SubcloneSeeker 1.0.0 - Computational Reconstruction of Tumor Clones
- SUMMON 1.8.10 - Visualization Prototyping and Scripting
- SUPERSMART / supersmartR - Estimating Rates of Speciation and Migration, Ages and Relationships of Taxa
- supraHex 1.24.0 - Tabular Omics data analysis using a Supra-hexagonal Map
- Survcomp 1.40.0 - Performance Assessment and Comparison for Survival Analysis
- SV-plaudit - Structural Variant Image Curation and Analysis
- SVEngine - Allele Specific and Haplotype Aware Structural Variants Simulator
- SVGMap 1.5.1 - Image Browser for Experimental data
- SWAN 0.3.0 - Statistical Structural Variation ANalyzer
- Swelfe - Detector of Internal Repeats in Sequences and Structures
- switchBox 1.22.0 - k-Top Disjoint Scoring Pairs
- sydSeq 1.1.7 - Various Functions for Gene Expression Analysis
- SYNBADm 20160206 - Toolbox for Automatic Optimal Design in Synthetic Biology
- SynBioWave 2.0 - Google Wave Implementation for Molecular Biologists
- Synergizer - Provide Translations of Biological Database Identifiers
- Synthaser v1.1.21 - Analysing Domain Architecture of Fungal Secondary Metabolite Megasynth(et)ases
- SynthEx 1.05 - CNA detection and Tumor Heterogeneity profiling
- systemPipeR 1.27.27 - NGS Workflow and report Generation Environment
- T-ACE 1.9.5 - Transcriptome Analysis and Comparison Explorer
- T-cep 1.0 - Transcription factor-associated Combinatorial Epigenetic Patterns
- T-WPPDC - Tree-based Weighted-Position Pattern Discovery and Classification
- T2DAG - Hotelling's T 2-type Test for detecting differentially Expressed Gene Pathways
- Tables 1.6 - X-ray Crystallographic Data Lookup
- tacg 4.1.0 - Finds Short Patterns and Specific Combinations of Patterns in Biological Strings
- TADKB - Topologically Associating Domain Knowledge Base
- TADtree - Identification of Hierarchical Topological Domains in Hi-C data
- TagGD - DNA Tag Generation and Demultiplexing
- TAMEE 1.1 - Tissue Array Management and Evaluation Environment
- TAP 1.8 - Calculate TAP and TAP-k to Evaluate Bioinformatics Retrieval Methods
- tappAS 0.99.15 - Understand the Functional Implications of Alternative Splicing
- Tardigrade Analyzer 2.00 - Tardigrade (Waterbear) Genome and Proteome Analysis
- TargetMine v1.8.5.0 - Data Warehouse for Candidate Gene Prioritisation and Target Discovery
- TASE 1.5.1 - Tag-counting and Analysis of Solexa Experiments
- Taverna 2.5 - Workflow Management System
- TaxMan 1.1 - Taxonomy Database Manager
- TaxonGap 2.4.1 - Compare and Select Individual Biomarkers.
- TaxonTree 1.2 - Interactive Tree Visualization for Kingdom Animalia
- TCC 1.32.0 - Differential Expression Analysis for Tag Count data with Robust Normalization Strategies
- Tclass - Tumor Classification System based on Gene Expression Profile
- TCLP - Online Cancer Cell Line Catalogue integrating HLA type
- tcR 2.2.4 - T Cell Receptor Repertoire Advanced data analysis
- tcsBU - Extend TCS Network Layout and Visualization
- Teaser 1.2 - Fast personalized Benchmarks and Optimization for NGS Read Mapping
- TEQC 4.12.0 - Quality Assessment of Target Enrichment Experiments
- TeXMed 2.0.7 - BibTeX interface to NCBI PubMed
- TEXMEX 0.3 - Treatment Effect eXplorer for Microbial Ecology eXperiments
- TeXP v1.0 - Quantifying Abundances of Transposable Elements transcripts from RNA-Seq data
- text2genome 0.4 - Extract DNA Sequences from Biomedical Text
- TF-Cluster - Identifying Regulatory Genes Controling Complex Traits
- TF-Finder - Idenitifying Regulatory Genes involved in a Biological Process
- TF-PathCo - Co-expression Analysis between Transcription Factors and Pathways
- TFBS Evo 1.0 - Tracing the Evolution of Lineage-specific Transcription Factor Binding Sites
- TFdiff 0.4 - Detection of Differential Gene Expression Factors
- TFM-CUDA 0.5 - CUDA tools for Position Weight Matrices (PWMs)
- TFM-Pvalue 0.0.8 - Efficient and Accurate P-value Computation for Position Weight Matrices
- TheorChromo 1.0 - Peptide and Protein Retention Time Prediction in Liquid Chromatography
- THPdb - Database of FDA approved Therapeutic Peptides and Proteins
- TI2BioP 2.0 - Topological Indices to BioPolymers
- Tibanna 1.7.1 - Running Genomic Pipelines on Amazon Web Services (AWS)
- TIgGER 0.4.0 - Infers Novel Immunoglobulin Alleles from Sequencing Data
- tigre 1.46.0 / tigreBrowser 1.1 - Transcription Factor Inference through Gaussian process Reconstruction of Expression
- TIME - Temporal Insights into Microbial Ecology
- Time-warp 3.2 - Generate Alignment Matrices
- TimeScape - Visualization tool for temporal Clonal Evolution
- TimeTP 1.0 - Influence Maximization in Time bounded network Identifies Transcription Factors Regulating Perturbed Pathways
- TiMEx 0.99 - A Waiting Time Model for Mutually Exclusive Cancer Alterations
- TitanCNA v1.17.1 - Analysis of subClonal CNA and LOH in Cancer
- TITINdb - Database of Titin Structure, Sequence, Isoform, Variant and Disease Information
- TMT-Integrator 1.0.8 - Extract and Combine Channel Abundances from multiple TMT samples
- tmVar 2.0 - Text Mining approach for Extracting Sequence Variants in Biomedical Literature
- TNM 1.0 - Compute Torsional Normal Modes
- TOBIAS 0.10.1 - Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
- TopicalPdb - Database of Topically Administered Peptide
- TopKCEMC 1.1 / TopKSpace 1.0 - Rank Aggregation Tool
- TPM - Temporal Pattern Mining Algorithm
- TrackSig - Reconstructing Evolutionary Trajectories of Mutations in Cancer
- TrackSM 1.00 - Associate Chemical Compound to Known Metabolic Pathway
- trackViewer 1.26.2 - Minimalist design for Plotting Elegant Track Layers
- Traitpedia - Collaborative Database of Species Traits
- TRAMPR 1.0-9 - TRFLP Species Identification
- tRanslatome 1.24.0 - Comparison between multiple levels of Gene Expression
- TransVar 2.4.0 - Multiway Annotator for precision Medicine
- TRAPID 2.0 - Rapid Analysis of Transcriptome Data
- Tree-HMM 0.1.0 - Clustering of Epigenetic Markers
- TreePlus 20060630 - Explore Large, Complex Food Webs
- Trend / jTrend 1.01 - Cellular Automata Simulation Environment
- TRES - Transcription Regulation in Embryonic Stem Cell
- tREX - Reconstruction of 3D structure of Chromatins using Hi-C data
- tRFTar - Prediction of tRF-target Gene Interactions
- TriDAMP - MathDAMP extension for Three-way Comparisons of Metabolite Profiles
- TrioVis 20130409 - Visualization approach for Filtering Genomic Variants of Parent-child Trios
- Tripal 7.x-3.6 - Construction of online Genetic and Genomic databases
- Tronco v2.26.0 - Inference of Cancer Progression Models
- TRRUST v2 - Curated TF-target Interaction Networks in Human and Mouse
- TRUmiCount v0.9.13 - Correctly Counting Molecules using UMIs
- TSSpredator 1.07.1beta - Comparative TSS prediction from RNA-seq data
- Tundra 0.1.1 - Interactive Piechart Editor
- Twease 20090512 - Web-based tool to Search Medline
- TWIGS - Three-Way module Inference via Gibbs Sampling
- UbiBrowser 2.0 - Proteome-wide Ubiquitin Ligase/Deubiquitinase-substrate Interactions in Eukaryotic species
- UGAHash - An algorithm for a Distributed Accession System
- UNICOR 2.0 - Species Connectivity and Corridor Network Simulator
- uORFs - Predicting Functional upstream Open Reading Frames
- UPDtool 0.2 - Detection of iso- and Heterodisomic Uniparental Disomy
- UPS-indel - Universal Positioning System of Indels
- UROPA 3.1.0 - Universal RObust Peak Annotation
- URSAHD - Unveiling RNA Sample Annotation for Human Diseases
- UST - Compression of K-mers
- Vacceed 1.1 - in silico Vaccine Discovery pipeline for Eukaryotic Pathogens
- VaccineDA - Designing Vaccine Adjuvants based on immunomodulatory DNA
- VacTarBac - Proteomic based Vaccine Design for Ptahogenic Bacteria
- validate - Omics Validation Calculator
- Validate GTF 1.0 - Check GTF file for Correctness
- VAMP 2.2.8 - Visualisation and Analysis of CGH arrays, transcriptome and other Molecular Profiles
- VanillaICE 1.52.0 - Hidden Markov model for inferring Copy Number Alterations from SNP Arrays
- VARIFI - Variant Identification, Filtering and Annotation of Amplicon Sequencing Data
- VarMatch - Matching Variants in VCF files
- VAtools - VCF Annotation Tools
- Vcfanno v0.3.2 - Annotate a VCF with other VCFs/BEDs/tabixed files
- VDA 0.1 - Design Minimal Validation Dataset to allow Reliable Comparisons
- VersaCount 1.02 / VersaCount Max! 0.6 - Assist with the Counting of Cells
- VESPUCCI - Exploring Patterns of Gene Expression in Grapevine
- VIBE 2.0 - Visual Integration for Bayesian Evaluation
- VIC - Variant Interpretation for Cancer
- ViewCommonPaths - Visualization of Sequences with the Same Start and End Elements
- Viola 1.0.0.dev10 - Structural Variant Signature Extractor
- VIPER v1.0.3 - Variant InsPector and Expert Rating tool
- Viroverse - Platform for Storage, Analysis of Experimental data for Laboratory Workflows
- Virtual Cat 3.0.0 - Simulation of an Anaesthetised Cat Experiment
- Virtual NMJ 2.1.9 - Simulation of an Experiment Recording the Electrical Potentials
- Virtual Rat 3.3.5 - Simulation of the Pithed Rat experiment
- Virtual Twitch 2.2.1 - Simulation of the Rat Phrenic Nerve-hemidiaphragm Preparation
- Virtual Worm 201202 - Recreate the nematode Caenorhabditis Elegans in Virtual form
- Virusbanker 1.0 - MySQL database of Virus Sequences and Alignments
- Voronto - Mapping Gene Expression to Ontologies with Voronoi Tessellations
- Vortex 10.5.5 - Population Viability Analysis software
- vPhyloMM 20090731 - Reconstructs Mutational Pathways of Drug Resistance
- VPMBench - Test Bench for Variant Prioritization methods
- VRMLGen 1.4.6 - An R Package for 3D Data Visualization on the Web
- VTAM 0.1.21 - Validation and Taxonomic Assignation of Metabarcoding Data
- Warpgroup 0.1.0 - Increased Precision of Metabolomic Data Processing by Consensus Integration Bound Analysis
- WaVPeak - Determining the location of Peaks in NMR spectra
- WEAT 1.0 - Weighted Enrichment Analysis Tools
- Web-gLV - Parameter Estimation and Simulation of Generalized Lotka Volterra models
- WebLogo 3.3 - Create Sequence Logos
- WebPSSM - Analyze V3 Loop Coreceptor Motifs
- WellReader 3.0 - Analysis of Fluorescence and Luminescence Reporter Gene data
- WExT - Weighted Exact Test for Mutually Exclusive Mutations in Cancer
- Whiteboard - C++ Framework for Programmatic Visualization of complex Biological Analysis
- Wigwams - Identifies Genes Working Across Multiple Biological Situations
- Wildfire/GEL 2.0 - Build Workflows
- WIlsON v2.3.1 - Webbased Interactive Omics visualizatioN
- WinEDR 3.9.5 - Electrophysiology Disk Recorder
- WinIAP - Ion Activities and Calcite Saturation Index
- WIST 1.1 - The Workflow Information Storage Toolkit
- Word Add-in for Ontology - Word add-in for Annotation of Word Documents based on terms that appear in Ontologies
- WormBase Converter - Conversion of any Gene ID into any other Gene ID
- WormGUIDES 2 - an in toto atlas of Embryogenesis and Neural Connectivity
- XAEM 0.1.1 - Pipeline to Estimate Isoform Expression from RNA-seq data
- XenoSite - Metabolism Prediction Web Server
- XIAPin - Predicting and Designing of XAIP Inhibitors
- XiP 3.0 - Construction of Workflows
- XMRF 1.0 - Fit Markov Networks to High-Throughput Genomics Data
- XperimentR - Ease the pain of Annotating Biological Experiments and Laboratory Processes
- xseq 0.2.1 - Assessing Functional Impact on Gene Expression of Mutations in Cancer
- xVis - Crosslink Analysis Webserver
- Y-Tools 3.1.1 - Construction of Antibody Repertoire and Immunoproteogenomics Analysis
- Yabi 9.9.7 - Online Research Environment for Grid, High Performance and Cloud Computing
- YEASTRACT / YEASTRACT-DISCOVERER - Yeast Search for Transcriptional Regulators And Consensus Tracking
- YETI2 - Your Evidence Tailored Integration
- ZENBU 2.11.2 - Data Integration, Data Processing, and Visualization Web system
- ZikaVR - Integrated Zika Virus Resource
- Zodiac - Depiction of Genetic Interactions in Cancer by integrating TCGA data
- Category: PCR / Primer Design
- 3PD - Primer design for Chromosome Conformation Capture Assays
- AAScan 2.2 / MutantChecker 1.3 / PCR Cloning 1.5 - Primer Design and Sequence Analysis for High-throughput Scanning Mutagenesis
- AlignPrimer 1.0 - Dynamic programming Alignment for PCR Primers
- AlleleID 7.85 - Assay Design for Bacterial Identification
- Amplicon b09 - Software for Designing PCR Primers on Aligned DNA Sequences
- AmpliconNoise 1.29 - Noise Removal from Pyrosequenced Amplicons
- AmplifX 2.1.1 - Manage & Design Primers for PCR
- AMUSER 1.0 - Design of Optimal PCR Primers for USER Cloning
- Assembly PCR Oligo Maker - Design Oligodeoxynucleotides For Constructing Long DNA Molecules
- Auto-qPCR - Process Spreadsheet output directly from qPCR Thermocycler
- AutoDimer 1.0 - Screening Tool for Primer-dimer & Hairpin Structures
- BatchPrimer3 1.0 - High Throughput Web Application for PCR and Sequencing Primer Design
- Beacon Designer 8.21 - Automate Real Time PCR Primer & Probe Design
- BiSearch 2.69 - Primer Design and Search Tool
- chipPCR 1.0-2 - Toolkit of helper Functions to pre-process Amplification data
- CloneAssistant 1.0 - automated Cloning Primer Design
- CloningBench 3.2.0 - Guide of Cloning Experiments for iPhone / iPAD
- CSGM Designer - Cross Species Genic Marker Designer
- CutSPR - Construction of Mutagenesis Vector based on the pJoe8999 plasmid system
- DART-PCR 1.0 - Quantitative Real-time PCR Data Analysis
- DefiningTheRain - Automatically analysing BioRad's Digital Droplet PCR Output
- DEODAS 0.2.0 -DEgenerate Oligo Nucleotide Design & Analysis System
- DesignPrimer - Design PCR Primer Pairs for the SciRoKo output using Primer3
- Disperse 1.0.3 - Design of Selector Assays for Targeted Resequencing Applications
- DNA-BAR - Select DNA Probes
- dnaMATE 1.0 - Consensus Melting Temperature Prediction server for short DNA sequences
- DualPrime 1.1 - Whole-genome Primer Design software
- Ex-Ex Primer - Designing Oligonucleotides Spanning Spliced Nucleic Acid Regions
- Expeditor 2 - Design Primers using Human Gene Structure and EST information of your Species
- FastPCR 6.7.50 - PCR Primers or Probe Design
- FindProbe v2 - Design Probes for Microarrays
- G-POT 1.0 / PRIMER-ILP 1.0 - Multiplex-PCR Primer Set Selection
- GenEx 7.0 - Analyze Real-time qPCR Data
- GenoFrag 2.1 - Design Primers Optimized for Whole Genome Scanning by Long-range PCR Amplification
- GenomeMasker 1.3 / GenomeTester 1.3 / SNPmasker 1.1 - Design Unique Genomic PCR Primers
- GLAPD - Whole Genome based LAMP Primer Design for a set of Target Genome
- GPLVM - Time-structured Gene-expression data
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