Posts
- Category: Protein Sequence Analysis (continued)
- X!TandemPipeline 0.4.34 - Peptide / Protein Identifications from MS/MS Mass Spectra
- XDIA - Extended Data-independent Acquisition
- XSTREAM - Variable Sequence Tandem Repeats Extraction and Architecture Modeling
- XtalPred - Prediction of Protein Crystallizability
- YinOYang 1.2 - O-(beta)-GlcNAc Glycosylation and Yin-Yang Sites
- ZincExplorer - Predictor of Protein Zinc-binding Sites
- Category: proteomics
- Abacus 20160720 - Extracting Spectral Counts from MS/MS Data Sets.
- aLFQ 1.3.6 - Estimating Absolute Protein Quantities from Label-free LC-MS/MS Proteomics data
- ALL-P - Including shared Peptides for Estimating Protein Abundances
- APEX 1.1.0 - Quantitative Proteomics Tool
- ATAQS - Automated and Targeted Analysis with Quantitative SRM
- atBioNet - Network Analysis Tool for Genomics and Proteomics
- BatMass 0.3.1 - Mass Spectrometry data Visualization
- BayesMix-MS - Analysis of Mass Spectrometry Proteomics data.
- BICEPS 1.0.3 - Novel Error Tolerant Search Strategy for Cross-Species Proteomics
- CHAMPS - Complete Homology Assisted MS/MS Protein Sequencing
- CIG-P 1.1 - Circular Interaction Graph for Proteomics
- compomics-rover 2.3.14 - Visualize and Validate Quantitative Proteomics data
- Compomics-utilities 5.0.9 - Java Library encompassing shared code of various Proteomics research projects
- CPhos 1.3 - Calculate and Visualize Evolutionarily Conserved Functional Phosphorylation Sites
- Cromwell 1.0 - The New Model Processor for Mass Spectrometry Data
- Crux 4.0 - Tandem Mass Spectrometry Analysis
- dagLogo 1.28.1 - Identifying and Visualizing differential Amino Acid group usage in Proteomics data
- DecoyDatabaseBuilder 1.5.47 - Generation of Decoy Sequences for Amino Acid Databases
- DeepRescore - Rescore PSMs leveraging Deep Learning-derived Peptide Features
- DIA-Umpire 2.2.2 - Computational Analysis pipeline for DIA Proteomics data
- DiagnoProt 1.4 - Discovery of new Molecules by Mass Spectrometry
- DIAlignR v1.1.2 - Chromatogram Alignment for Targeted Proteomics
- DIAproteomics 1.2.4 - Automated Quantitative Analysis of DIA Proteomics Mass Spectrometry Measurements
- Dintor - Functional Annotation of Genomic and Proteomic data
- EBprot 1.1.1 - Bayesian Analysis of labeling-based Quantitative Proteomics Data
- FragmentationAnalyzer 1.5.17 - Analyze MS/MS Fragmentation Data
- GenoMS 20120110 - Sequencing Whole Proteins using a Template Databases
- GOfact 20051017 - An Integrated Strategy for Functional Analysis in Large-scale Proteomic Research by Gene Ontology
- GoMiner Build454- Resource for Biological Interpretation of Genomic and Proteomic data
- IDEAL-Q 1.065 - Mass Spectrometry Protein Quantitation
- IKAP - Inference of Kinase Activities from Phosphoproteomics
- InSilicoSpectro 1.3.24 - Open-source Proteomics Library
- InsPecT 20120109 - Proteomics Search Toolkit
- JAMSS - A GUI Java Mass Spectrometry Simulation Suite
- LC-IMS-MS Feature Finder v2.2.6487 - Detecting Multidimensional Liquid Chromatography, Ion Mobility and Mass Spectrometry features
- LFQuant 20120114 - Label-free Quantitative Analysis Tool for LC-MS/MS Proteomics Data
- Luciphor2 - PTM-site localization on MS/MS data
- MAPDIA 3.1.0 - Model-based Analysis of quantitative Proteomics data in DIA-MS
- MapQuant 2.1.1 - Large-scale Protein Quantification
- Mass-Up 1.0.14 - Mass Spectrometry Utility for Proteomics
- Mass++ Ver.4 beta - Analysis Tool for Mass Spectrometry
- MassShiftFinder 1.09 - Blind search for Post-translational Modifications and Amino Acid Substitutions
- MassSorter 3.1 - Administrating and Analyzing data from Mass Spectrometry experiments on Proteins
- MassSpec 1.1 - Peak list Extraction from Proteomic Mass Spectra
- MassyTools 1.0.0 - High-Throughput Targeted Data Processing Tool
- MaXIC-Q v1 - MS/MS- and MS-based Quantitation Analysis
- MaxQuant v2.0.1.0 - Quantitative Proteomics software package
- Mayu 1.08 - Protein Identification False Discovery Rates
- MetaPepSeq 0.8 Beta - Protein Identification in Mass Spectrometry Experiments.
- MetaSPS 7.332 - De novo Protein Sequencing
- MixDB 1.0r - Identify Mixture MS/MS Spectra from more than one Peptide
- MixGF 1.0r - Computing Statistical Significance of Peptide-spectrum-matches for multiplexed MS/MS Spectra
- mMass 5.5.0 - Open Source Mass Spectrometry Tool
- MOTIPS - Motif Analysis Pipeline
- MRMPlusGUI 20151104 - Quality Control and Assessment tool for SRM/MRM Assay development
- ms-data-core-api 2.0.5 - Metadata-oriented Library for Computational Proteomics
- MS-Deconv 0.8.0.7370 - Deconvolution of Top-down Spectra
- MS-GF+ 20140630 - Database search for Peptide Identification
- ms-lims 7.7.7 - Mass Spectrometry based Proteomics Information Management System
- MSAcquisitionSimulator 1.0.2 - Data-dependent Acquisition Simulator for LC-MS Shotgun Proteomics
- MSBayesPro - Bayesian Protein Inference for LC-MS/MS Proteomics experiment
- MSblender - Integrating Peptide Identifications from multiple database search engines
- MSFragger / FragPipe 16.0 - Peptide Identification in Mass Spectrometry-based Proteomics
- MSnbase 2.19.1 - Base Functions and Classes for MS-based Proteomics
- mspire 0.10.8 - Mass Spectrometry Proteomics in Ruby
- MSPLIT 1.0 - Multiplexed Spectral Library Search
- MUDE 1.0 - Assess MS/MS Spectra Assignments
- MUMAL - Multivariate Analysis in Shotgun Proteomics
- myProMS 3.9.3 - Management, Validation and Interpretation of MS-based Proteomic data
- mzMatch/PeakML 2.0 - Metabolomics Data Analysis
- mzqLibrary 1.0.1 - Java Library supporting the HUPO-PSI Quantitative Proteomics Standard
- NeoFlow - Proteogenomics Pipeline for Neoantigen discovery
- NITPICK 2.0 - Peak Identification for Mass Spectrometry Data
- NOmESS - Homology-driven Assembly of NOn-redundant protEin Sequence Sets
- OMSSA Parser 2.0.1 - Java based Parser for OMSSA omx files
- Open2Dprot 20060607 - Proteomics Exploratory Data Analysis Software
- OpenMS / pyOpenMS 2.6.0 - C++ / Python Framework for Proteomics
- PAnalyzer 1.1 - Protein Inference in Shotgun Proteomics
- PatternLab for proteomics V - tool for analyzing Shotgun Proteomic data
- peakANOVA - Stronger Findings from Mass Spectral data through Multi-peak Modeling
- PeakQuant 1.5.47 - Proteomics Software Suit
- PepDistiller 1.26 - Improve Sensitivity & Accuracy of Peptide Identifications in Shotgun Proteomics
- Peppy – Proteogenomic, Proteomic search tool
- PeptideReranking - Peptide Re-ranking with Protein-peptide Correspondence and Precursor Peak Intensity Information
- PeptideShaker v2.0.33 - Interpretation of Proteomics Identifications from multiple search engines
- Perseus v1.6.15.0 - Shotgun Proteomics Data Analysis
- pFind Studio 2.8.8 - Mass Spectrometry-based Proteomics
- PGx - Tool for Proteogenomics Mapping
- Philosopher 4.0.0 - Toolkit for Shotgun Proteomics data analysis
- PhosphoLogo - Calculate Position-specific Amino Acid Preferences and Anti-preferences
- PhosphoSiteAnalyzer 1.4 - Bioinformatical tool for Analyzing (Quantitative) Phosphoproteome datasets
- PhosSA - Phosphorylation Site Assignment Algorithm for Mass Spectrometry Data
- PIA 1.3.15 - Protein Inference Algorithms
- PIQMIe 1.0 - Proteomics Identifications & Quantitations Data Management & Integration Service
- pLink-SS - Identification of Disulfide Bond Peptides
- pLSA - Probabilistic Latent Semantic Analysis of Imaging Mass Spectrometry Data
- POSTMan 2.0a - POST-translational Modification analysis
- ProClassify 1.4.2 - Proteomic data Classification
- ProHits v4.0.3 - LIMS for Interaction Proteomics.
- ProLiC 1.2 - Protein List Comparator
- ProMS - Proteome Analysis using Mass Spectrometry
- ProSight Lite 1.4.7 - Analyze Top-down Mass Spectrometry data
- ProteinDecision 1.0 - Protein Identification using Peptide-Mass Fingerprinting Data
- ProteinInfer - A Combinatorial Perspective of the Protein Inference Problem
- Proteios 2.19.0 - Multi-user Platform for Analysis and Management of Proteomics data
- ProteoCombiner v1.0 - Integrating Top-down, Bottom-up and Middle-down Proteomics data
- ProteomeScout - Visualization and Analysis Framework for Proteins
- ProteoSAFe 1.2.6 - Proteomics Environment
- ProteoWizard 3.0.21193 - Proteomics Data Analysis
- ProtMAX - Analyzing Large Shotgun Proteomics Mass Spectrometry data sets
- Protter 1.0 - Interactive Protein Feature Visualization
- ProtViz 0.6.8 - Proteomics Data Analysis & Visualization
- PSS 20091105 - Protein Profile Similarity Screening
- PTM-Shepherd v1.1.1 - A tool for Summarizing Open Search Results
- PWIMS 2.3 - Proteomics Workflow and Information Management System
- Pyteomics 4.4.2 - Python Framework for Exploratory Data Analysis and Rapid Software Prototyping in Proteomics
- QARIP - Quantitative Analysis of Regulated Intramembrane Proteolysis
- QPROT 1.3.5 - Differential Protein Expression using Spectral Count and Intensity data.
- QUILTS 2.0 - Proteogenomic Data Integration tool
- sapFinder 1.20.1 - Variant Peptides Detection and Visualization in Shotgun Proteomics.
- ScreenCap3 - Screening of Caspase-3 substrates and Cleavage site prediction
- SearchGUI 4.0.41 - GUI for Proteomics Identification Search Engines
- SimTandem 1.1.96 - Protein Sequence Identification
- Sipros 3.0 - Proteomics Data Analysis software
- SIRIUS 4.9.3 - Identification of Metabolites using single and Tandem Mass Spectrometry
- SPC Proteomics Tools 060107 - CDROM Image for SPC tools
- Specialize 1.0 - Identification of Peptides with complex PTM from Tandem Mass Spectra
- specL 1.26.0 - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
- SpectroGene 1.0 - Genome Annotation using Top-down Mass Spectrometry
- SpliceDB 1.0 - Splice Graph Proteomics Tools
- SpotLink 1.0 - Proteomics tool for Organization and Visualization
- SRMstats 1.7 - Protein significance analysis in SRM measurements
- SRPI - Score Regularization for Peptide Identification
- STRAP 1.5 - Software Tool for Rapid Annotation of Proteins
- TAPIR 1.2 - Visualization of Targeted Proteomics data
- TBnovo - De novo Protein Sequencing by combining Top-down and Bottom-up Mass Spectrometry
- TDFragMapper 1.0 - Visualization tool for Evaluating Experimental parameters in top-down Proteomics
- Thermo MSF Parser 2.0.5 - Parser and Viewer for Thermo msf files
- Topograph 2 - Precursor Enrichment corrected global Protein Turnover Measurements
- TopPIC 1.6 - TOP-Down Mass Spectrometry Based Proteoform Identification and Characterization
- TPP 5.2 - Collection of integrated tools for MS/MS Proteomics
- Tremolo 20130821 - Spectral Library Search
- UniNovo 20130520 - Universal tool for de novo Peptide Sequencing
- Unipept 4.3.1 - Web Services for Metaproteomics Analysis
- UPF 0.912 - Unique Peptide Finder
- VESPA 1.1.1 - Visual Analytics Platform for Exploring Proteogenomics data
- XGlycScan 20140527 - Quantification of Glycosite Associated Spectra Counts
- xiNET 1.1.13 - Crosslink Viewer
- xQuest/xProphet 2.1.5 - Analysis of Cross-linked Peptides
- XTandem Parser 1.13.0 - Java based parser for X!Tandem output xml files
- Category: RNA Analysis
- 16S classifier - Fast and Accurate Taxonomic Classification of 16S rRNA Sequences
- 4SALE 1.7 - Synchronous RNA Sequence and Secondary Structure Alignment and Editing
- AbundantOTU+ 0.93b - Identification and Quantification of Abundant Species from Pyrosequences of 16S rRNA
- aCMs 1.2.1 - Stochastic Homology Search tools
- ActMiR - Activity of miRNAs
- AIRlINER - Assessment of A-to-I RNA Editing Sites in Non-repetitive Regions
- ALEXA-Seq 1.17 - Alternative Expression Analysis by massively parallel RNA Sequencing
- ALIDOT 2.0.6 - Detect Conserved Secondary Structure Motifs
- ALTSCAN 1.0 - ALTernative Splicing SCANner
- Annocript 1.1.3 - Annotation of Transcriptomes
- AnnoLnc 2.1 - Annotate human lncRNAs
- antaRNA 2.0.1.2 - Ant Colony Optimized RNA Sequence Design
- ApolloRNA 1.11.8 - Apollo for non Protein Coding RNA (ncRNA) Identification
- ARAGORN 1.2.41 - tRNA (and tmRNA) Detection
- aRNhAck 1.0 - Prediction of RNA-binding interfaces using SHAPE data and MSA
- ArrayExpressHTS 1.42.0 - RNA-seq data Processing and Quality Assessment
- ARWEN 1.2.3 - tRNA Detection in Metazoan Mitochondrial Sequences
- ASARP 0.9 - Identification of Allele-Specific Alternative mRNA Processing in RNA-Seq data
- ASprofile - Extracting, Quantifying and Comparing Alternative Splicing (AS) Events from RNA-seq data
- Assemble2 2.3 - Construct & Study RNA Architectures
- AStalavista 4.0.1 - Alternative Splicing Transcriptional Landscape Visualization tool
- AveRNA - Ensemble-based Prediction of RNA Secondary Structures.
- Ballgown - Isoform-level Differential Expression Analysis in R
- BarMap 20080919 - RNA Folding on Dynamic Energy Landscapes
- Barnacle 1.0.4 - Detecting and Characterizing Tandem Duplications and Fusions in Transcriptome Assembly
- barriers 1.8.0 - Basin Structure of RNA Energy Landscapes
- Barrnap 0.9 - Bacterial ribosomal RNA predictor
- BASiNET 0.0.4 - Classification of RNA Sequences using Complex Network Theory
- BASIS v1 - Bayesian Analysis of Splicing IsoformS
- BayesPairing - Identifying the presence of 3D Structural Modules from RNA sequences
- BBSeq 1.0 - Analysis of RNA Sequence Count Data
- Bcheck 0.6 - rnpB gene prediction
- BEERS - Benchmarker for Evaluating the Effectiveness of RNA-Seq Software
- Bellerophontes 0.4.0 - RNA-Seq Data Analysis Framework
- BioVLAB-MMIA-NGS - miRNA mRNA Integrated Analysis
- BkTree 20160124 - Prediction of RNA Nucleotide Interactions with Backbone k-Tree Model
- BlastR 2.2 - Searching and Clustering RNA
- BLISS 0.7 - Identify Batch Effects in RNA Expression Data
- BM-DE 2 - Bayesian Method of Calling Differential Expression
- BosFinder - pre-microRNA Gene prediction algorithm in Bos taurus
- BoulderALE 1.0.0 - Web-based RNA Alignment Tool
- BPLA kernel 1.1 - Structural RNA Analysis
- BPSC v0.99.2 - Beta-Poisson model for single-cell RNA-seq data analyses
- BRAKER v2.1.6 - RNA-seq based Eukaryotic Genome Annotation pipeline
- C-mii 1.11 - Computational miRNA Identification
- C2Analyzer - Cotarget-Cofunction Analyzer
- CADBURE 20151031 - Evaluating Aligner performance on your RNA-Seq dataset
- CAMUR - Classifier with Alternative and MUltiple Rule-based models
- CAP-miRSeq - Analysis Pipeline for deep microRNA Sequencing
- CapR 1.1.1 - Revealing Structural Specificities of RNA-binding protein Target Recognition
- CARNA 1.3.3 - Alignment of RNA Structure Ensembles
- Carnac 0.98 - Predict Secondary Structure for a set of Homologous RNA Sequences
- CaRNAval - Catalog of RNA Recurrent Interaction Networks (RIN)
- Cartaj r14 - Classification Of RNA Threeway Junctions
- Cas-Designer 2.4 - A Bulge-allowed quick guide-RNA Designer for CRISPR/Cas derived RGENs.
- Cas-OFFinder 2.4.1 - Off-target Searching tool
- casper 2.26.0 - Characterization of Alternative Splicing based on Paired-End Reads
- CATCh v1 - Ensemble Classifier for Chimera Detection in 16S rRNA Sequencing Studies
- CCmiR - Prediction of miRNA Competitive / Cooperative Binding
- CCTop 1.0.0 - CRISPR/Cas9 Target Online Predictor
- cellHTS2 2.57.0 - Analysis of Cell-based RNAi Screens
- CentroidFold 0.0.16 - Predict RNA Secondary Structure from RNA Sequence
- CG-seq - Comparative Genomics-seq
- Chain-RNA 20120225 - Comparative ncRNA Search Tool Based on the Two-dimensional Chain Algorith
- ChangePoint 0.1.1 - Change-point model for detecting 3'UTR Changes by RNA-Seq
- Chimerascan 0.4.5a - Detect Gene Fusions in Paired-end RNA Sequencing (RNA-Seq) Datasets
- Chimira 1.5 - Analysis of small RNA Sequencing data and microRNA modifications
- CHIP-RNA-SEQPRO 1.1 - ChIP-RNA-sequencing-processing
- ChiRA 1.4.3 - Chimeric Read Analyzer
- CICERO v1.8.1 - Clipped-reads Extended for RNA Optimization
- Circall v0.1.0 - Discovery of Circular RNAs from Paired-end RNA-sequencing data
- CircTest 0.1.0 / DCC 0.5.0 - Identification and Quantification of Circular RNAs from Sequencing Data
- CIRCTOOLS 1.2.0 - a one-stop software solution for circular RNA research
- cisASE - Detecting Putative Cis-regulated Allele-specific Expression in RNA Sequencing data
- CisRNA-SVM - Identification of Structured Cis-regulatory Elements in the 3’UTRs of human Protein-coding mRNAs
- CLASS 2.1.7 - Constraint-based Local Assembly and Selection of Splice Variants
- CleaveLand 4.5 - Find Cleaved Small RNA Targets
- CLRNASeq 1.00 - RNA-Seq Analysis
- CMCompare 0.0.1 - Discriminatory Power of RNA Family Models
- CodingMotif - Determination of Overrepresented Nucleotide Motifs in Coding Sequences
- CodingQuarry 2.0 - Fungal Gene Prediction
- COGNAC - COnnection Tables Graphs for Nucleic ACids
- ComiR 20151020 - Combinatorial miRNA target prediction tool
- CompAnnotate 1.5 - Annotate base-pairing Interactions in RNA 3D Structures.
- comPARE - PARE Validated miRNA Targets
- compcodeR 1.26.1 - Benchmarking Differential Expression Methods for RNA-seq data
- comrad 0.1.3 - Discovery of Gene Fusions using Paired End RNA-Seq and WGSS
- comRNA 1.80 - Common RNA Secondary Structure Predictor
- comTAR - Conserved Plant miRNA Target Prediction Tool
- ConsAlifold - Prediction Accuracy of RNA Consensus Secondary Structures
- consexpression - Tool for RNA-Seq analysis
- ConStruct 3.2.5 - RNA Alignment Editor and Consensus Structure Prediction Tool
- contamDE 1.0 - Differential Expression analysis of RNA-seq data for Contaminated Tumor Samples
- Context Fold 1.0 - RNA Secondary Structure Prediction tool
- ContextMap 2.7.9 - Context-based mapping of RNA-seq data
- CONTRAfold 2.02 - RNA Secondary Structure Prediction
- CONUS 1.0 - Exploration of Lightweight Stochastic Context Free Grammars
- CopraRNA 2.1.3 - sRNA Target Prediction utilizing Homology
- CoRAL 1.1.1 - Classification of RNAs by Analysis of Length
- CORNA 1.3 - Testing Gene Lists for Regulation by microRNAs
- corRna - Prediction of Deleterious Mutations in Structural RNAs
- CovaRNA / CovStat 1.16.0 - Detecting Long-range Covariations in Nucleotide Alignments
- CPAT 2.0.0 - RNA Coding Potential Assessment Tool
- CPC 2 - Assess Protein-coding Potential of Transcripts
- CPSS 2.0 - Computational Platform for analysis of Small RNA Deep Sequencing data
- CRAC 2.5.2 - An Integrated RNA-Seq Read Analysis
- CracTools 1.24 / digitagCT 1.0.2 - Integrated pipelines for RNA-Seq Analysis using CRAC
- CRISPR-ERA 1.2 - Fast and Comprehensive Guide RNA Design Tool
- CRISPRDirection 2.0 - Accurate Computational Prediction of Transcribed Strand of CRISPR non-coding RNAs
- CRISPRmap 2.1- CRISPR Repeat Conservation and Diversity Analysis
- CRISPRseek 1.30.1 - Design of Target-specific Guide RNAs in CRISPR-Cas9, Genome-editing Systems
- CRISPRTarget - A Tool to Explore Targets of CRISPR RNAs
- CROSS / CROSSalign / CROSSalive - Recognition of RNA Secondary Structure
- CSZ 1.0 - Characterization of small RNAome for Zebrafish
- CTK v1.1.3 - CLIP Tool Kit, previously known as CIMS
- DAFS 0.0.3 - Simultaneous Aligning and Folding of RNA Sequences by Dual Decomposition
- DaPars 0.9.1 - Dynamic analysis of Alternative PolyAdenylation from RNA-seq
- DARIO / plantDARIO - Web Server for the analysis of (Plant) Short RNAs
- Darn 1.0 - Non-protein-coding RNA Detection
- DASHR – Database of small human noncoding RNAs
- dCLIP 1.7.3 - Comparative CLIP-seq Analyses
- ddbRNA - RNA Secondary Structure Prediction
- DeAnnIso - Detection and Annotation of IsomiR from small RNA sequencing data
- deepBlockAlign 1.3.1 - Align RNA-seq Profiles of Read Block Patterns.
- DegPack - Identifying DEGs in multiclass RNA-seq data
- deGPS 2.0 - Detecting Differential Expression in RNA-sequencing Studies
- DEGseq 1.38.0 - Differentially Expressed Gene Identification for RNA-seq data
- Degust v4.1.1 - Interactive web-based Visualization of RNA-Seq DGE Results
- derfinder v0.0.42 / regionReport 0.0.1 - Fast Differential Expression Analysis of RNA-seq data at Base-pair Resolution
- DESeq2 1.36.0 - Differential Expression Analysis for Sequence Count Data
- DEsi - Design Engine of siRNA
- desiRm - Designing siRNA for Silencing a Gene
- DEXSeq 1.38.0 - Inference of Differential Exon usage in RNA-Seq
- DEXUS 1.26.0 - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions
- DIAL - 3-Dimensional RNA Structural Alignment and Motif Detection
- DiffSplice 0.1.2beta - Discover Alternative Splicing Variants present in an RNA-seq dataset
- Dishuffle - RNA Dinucleotide Shuffle
- DotcodeR 1.0.1 - Alignment-free comparative Genomic Screen for structured RNAs
- DREAM - Detecting RNA Editing Association with MiRNAs
- DrivAER - Identification of driving Transcriptional programs in single-cell RNA sequencing data.
- DRME - Differential RNA Methylation Analysis
- dsCheck — Off-target Search website for dsRNA-mediated RNAi
- DSIR - Designer of Small Interfering RNA
- DSSR 2.3.2 - Dissecting the Spatial Structure of RNA
- DyNB 20150501 - Analyze RNA-seq Time Series data
- E-miR - miRNA analysis and Expression Profiling pipeline
- E-RNAi 3.2 - Design Optimized RNAi Constructs
- Ebbie 3.0.9 - Analysis & Storage of Small RNA Cloning Data
- Ebbie-MM 4.3 - Analyze Single Mismatches of Small RNAs to the genome
- EBChangePoint 0.1.0 - Empirical Bayes Change-point Model
- EBSeq 1.33.0 / EBSeq-HMM 1.26.0 - RNA-Seq Differential Expression Analysis
- EditPredict - Prediction of RNA editable sites with convolutional Neural network
- EmpiricalGO - Measure Enrichment using an Empirical Sampling Approach
- EMSAR v2.0.1 - Quantify Transcripts from RNA-seq data
- Ensemble Calc - Script to Compute Equilibrium Concentrations & Free Energy Change
- EnsembleClust 1.0 - Fast and Accurate Clustering of noncoding RNAs
- ERD - Evolutionary RNA Designer
- EricScript 0.5.5 - Identify Chimeric Transcripts in RNA-seq data
- eRNA 1.01 - RNA Data Analysis Tool
- ernwin 1.0.1 - RNA Structure Prediction
- Erpin 5.5.4 - RNA Motif Search program
- ESPRIT 201102 - Estimating Species Richness Using Large Collections of 16S rRNA Pyrosequences
- ExomePeak 2.17.0 - Exome-based Analysis for RNA Epigenome Sequencing Data
- ExonScan 1.0 - Simulating the RNA Splicing Pattern of a Primary Transcript Sequence
- ExpaRNA 1.0 - Exact Matching of Sequence-structure
- expected5to3distance - Compute Expected Distance between Terminal Nucleotides of RNA
- FDM 1.0 - Analyze Differential Transcription
- FFTbor / FFTbor2D 2.0.2 - 2D Energy Landscape of / RNA Secondary Structures
- FindtRNA 1.0 - tRNA Prediction tool
- FlaiMapper 3.0.0 - Fragment Location Annotation Identification Mapper
- FLAM-seq 1.0.0 - Full-length poly(A) and mRNA Sequencing
- FlipFlop 1.8.0 - Fast Lasso-based Isoform Prediction as a Flow Problem
- forna 20150415 - RNA Secondary Structure Visualization Using a Force Directed Graph Layout
- FR3D 20120611 / WebFR3D - Find Structural Motifs in RNA 3D Structures
- fragrep 2 - Efficient Search for Fragmented Patterns in RNA
- fRNAkenstein 20130115 - Python program for Multiple Target Inverse RNA Folding
- FUCHS 0.3.0 - FUll circular RNA CHaracterization from RNA-Seq
- FuMa 3.0.0 - Reporting Overlap in RNA-seq Detected Fusion Genes
- FuSeq 1.1.4 - Discover Fusion Genes from paired-end RNA Sequencing data
- FusionAnalyser - Detect Gene Fusions from paired-end RNA-Seq data
- FusionCatcher 1.33 - Fusion Genes Finder for RNA-seq data
- FusionFinder 1.2.1 - Finding Gene Fusions In RNA-Seq Data
- FusionQ v.5 - Detection and Quantification of Chimerical RNAs from Paired-end RNA-seq
- FX 1.0.5 - RNA-Seq analysis tool on the Cloud
- GAISR - Genomic Analysis Illuminating RNA Structure
- Galaxy RNA workbench 19.01 - The RNA Analyses Workbench
- Gardenia - Compare & Align RNA Structures
- GENE-counter 0.4.4 - Analysis of RNA-Seq data for Gene Expression Differences
- GenemiR 1.0 - Unified Search of Mammalian microRNA Target Predictions
- GESS 1.0 - Exon-skipping Scanner Detection program for RNA-seq data
- get_size_NN v1 - Neutral Network Size Estimation
- GETUTR 2.0.0 - Global Estimation of the 3' UTR landscape based on RNA sequencing
- GIIRA 01_3 - RNA-Seq driven Gene Finding Incorporating Ambiguous Reads
- GIREMI 0.2.1 - Genome-independent Identification of RNA Editing by Mutual Information
- GORAP 2.4.0 - Genomewide ncRNA Annotation Pipeline
- GOseq 1.44.0 - Performing Gene Ontology (GO) based tests on RNA-seq data
- GPSeq 0.5 - Using the Generalized Poisson distribution to model sequence read counts from high throughput sequencing experiments
- Grape 1.1.0 - Pipeline for Processing and Analyzing RNA-Seq data
- GraphClust 0.7.6 - Structural Clustering of local RNA Secondary Structures
- GraPPLE - Graph Property based Predictor and Likelihood Estimator
- GRM 0.2.1 - Single Cell RNA-seq De-noise Tools
- GTfold 3.0 - Scalable Multicore Code for RNA Secondary Structure Prediction
- GUUGle 1.2 - Fast Exact Matching under RNA Base Pairing Rules
- HALO 1.3 - Precise RNA de novo Transcript Half-life Determination
- HAMR 1.2.0 - High-throughput Annotation of Modified Ribonucleotide
- HDMC - Hierarchical Distribution Matching and Contrastive learning
- HelixPSO - Particle Swarm Optimizer for RNA Secondary Structure Prediction
- HITS-CLIP - Detect RNA-protein Binding Sites
- homoTarget - Prediction of microRNA targets in Homo Sapiens
- HotKnots 2.0 - Predict Secondary Structures of RNA with or without Pseudoknots
- htSeqTools 1.31.0 - Quality Control, Visualization and Processing for High-Throughput Sequencing data
- iCircDA-LTR - Identification of circRNA-disease Associations based on Learning to Rank
- ICQ-lincRNA - Identification, Characterization, and Quantification of Long Intergenic Non-Coding RNAs
- iFoldRNA V2.0 - Interactive RNA Folding
- iKNN - Classifier for Non-coding RNA Identification in Organelle Genome level
- ILM 1.0 - Predict RNA Secondary Structures with Pseudoknots
- iLncRNAdis-FB - Identify potential lncRNA-disease Associations
- iLoc-LncRNA - Predict the subcellular locations of LncRNAs
- IM-TORNADO 2.0.3.2 - Illinois Mayo Taxonomy Operations for RNA Database Operations
- iMcRNA / miRNA-dis - microRNA Precursor Identification based on Distance Structure Status Pairs
- iMiRNA-PseDPC - microRNA Precursor Identification with a Pseudo Distance-pair Composition Approach
- IMMP - Integration of MicroRNA, mRNA, and Protein Expression Data for the Identification of Cancer-Related MicroRNA
- imRNA - Prediction of Immunomodulatory RNA
- incaRNAfbinv / RNAfbinv 2.0 - Fragment-based design of RNA sequences
- IncaRNAtion - Design of RNA Sequences with Targeted Secondary Structure and Nucleotide Distribution
- INFO-RNA 2.2.0 - A Server for Inverse Folding of RNA
- INSCT - scRNAseq Integration with Triplet Neural Networks
- INSEGT 1.0 - Analyse Alignments of RNA-Seq reads using Gene Annotations
- IntaRNA 3.2.1 - RNA-RNA Interaction Prediction
- IntSplice 1.1 - Prediction of the Splicing Consequences of Intronic Single-nucleotide Variations in the Human Genome
- iPARTS 2 - A Tool of Improved/ Pairwise Alignment of RNA Tertiary Structures
- IPED v1.1 - Sequencing Error Correction in 16S rRNA Illmina paired-end Sequencing Reads
- iPiDi-PUL - Identifying Piwi-interacting RNA-disease Associations based on Positive Unlabeled Learning
- IPknot 1.4.1 - RNA Secondary Structure Prediction including Pseudoknots
- IPMiner - Identification for Influenza A Virus
- IQSeq 1.0 - Isoform Quantification with RNA-seq data
- IRESPred - Prediction of Cellular and Viral Internal Ribosome Entry Site (IRES)
- IRFinder-S v2.0-beta - Detecting Intron Retention
- iRNA-2OM - Identifying the position of the 2'-O-methylation site in the H. sapiens.
- iRNA-3typeA - Identifying 3-types of Modification at RNA’s Adenosine Sites
- iRNA-AI - Identifying Adenosine to Inosine Editing Sites
- iRNA-m2G - Identifying N2-methylguanosine sites
- iRNA-Methyl / iRNA(m6A)-PseDNC - Identifying N6- methyladenosine sites
- iRNA-PseColl - Identifying Occurrence Sites of different RNA Modifications
- iRNAD - Identifying D Modification Sites in RNA sequence
- iSeeRNA 1.2.2 - Accurate and Extra-fast lincRNA/mRNA Classifier
- isoform 0.99.2 - RNA Isoform Study using RNA-seq data
- IsoInfer 0.9.1 - Inference of Isoforms from Short Sequence Reads
- isomiR-SEA 1.60 - RNA-Seq analysis tool
- ISOP 0.99.1 - Isoform-level expression patterns in single-cell RNA-sequencing data
- ISP 0.3 - Accurate Inference of Isoforms from Multiple Sample RNA-Seq Data
- ITSx 1.1.3 - Extraction of ITS1 and ITS2 from Ribosomal ITS Sequences
- IUTA 1.0 - Detecting Differential Isoform usage from RNA-Seq data
- iwa-miRNA - Interactive Annotation of Plant MiRNAs
- JACUSA v2.0.2-RC - JAVA framework for accurate SNV Assessment
- JAR3D - Predicting RNA 3D Motifs in Sequences
- jViz.Rna 4.0 - Visual Comparison of RNA Secondary Structure
- K2N - Service to Get from Knotted to Nested RNA Structures
- Kinefold - RNA/DNA Folding Predictions
- kinfold 2.2 - Analysis of Time-Resolved RNA Folding
- Kinwalker - Algorithm for Prediction of RNA Folding Trajectories
- KNetFold 1.4.4b - RNA secondary structure prediction
- KnotInFrame 2.0.8 - Prediction of -1 Ribosomal Frameshift Events
- Knotted2Nested - Remove Pseudoknots from RNA
- L_RNA_scaffolder - Long Transcriptome Reads to Scaffold Genome
- lara 1.3.2a - Sequence-structure Alignment of RNA Sequences
- LINDEL - Integrated Design system for LincRNA deletion
- LncADeep - ab initio lncRNA Identification and Functional Annotation tool
- LncDisease 1.41 - Predicting lncRNA-disease Associations
- lncFunTK - Functional Characterization of lncRNA by integrative network analysis
- LncRNA-ID - Long non-coding RNA IDentification using Balanced Random Forest
- LncTar 1.0 - Predicting RNA targets of lncRNAs
- LocalFold 1.0 - Local Folding of RNA
- LocARNA 1.9.2.1 - Global and Local Alignment of RNA
- LocARNAscan 1.0 - Homology Search for Structured RNAs
- Locomotif - Visual Design of RNA Motifs
- loopDloop 2.07b - Draw RNA Secondary Structures
- LR50 1.0 - Assessing Insect Transcriptomes
- LRIscan - Predict Conserved, Genome-wide Long range RNA-RNA Interactions
- m6Apred - Identification and Analysis of the N6-methyladenosine in Saccharomyces Cerevisiae Transcriptome
- M6ATH - Identifying N6-methyladenosine sites
- Magnolia - Classification of Coding and Noncoding RNAs
- Mallard 1.02 - Screen 16S rRNA Clone Libraries contain Chimeras
- MAP-RSeq 1.2.1 - System for RNA-Sequencing Data Analysis
- MapFold - Predicting Secondary Structure of RNA using Chemical and Enzymatic Mapping data
- MapSplice 2.1.8 - Mapping of RNA-seq reads for Splice Junction Discovery
- MARIO 0.4 - Mapping RNA-RNA interactome and RNA Structure
- MARNA 100729 - Server for Multiple Alignment of RNAs
- MateRNAl - RNA Evolutionary Simulation Framework
- MatureBayes - Web-based tool for the Computational Identification of Mature miRNAs
- MBSTAR - microRNA Binding Site Prediction tool
- mCarts 1.2.0 - Hidden Markov model to predict Clustered RNA Motif sites
- McGenus / TT2NE - Prediction of RNAs Secondary Structures with Pseudoknots
- MDCAP - MiRNA-Disease Causal Association Predictor
- mEAT 1.0 - microRNA Enrichment Analysis Tool
- Megraft 1.0.2 - Graft Ribosomal Small Subunit (16S/18S) Fragments onto full-length SSU Sequences
- MEMERIS 1.0 - MEME in Rna's Including Secondary Structures
- meRanTK 1.2.1b - Methylated RNA Analysis ToolKit
- MetaDiff - Differential Expression Analysis on RNA-Seq
- MetalionRNA - Metal Ion Binding Site Predictor
- MetAmp - Meta-amplicon Analysis
- metaRNASeq 1.0.5 - Meta-analysis of RNA-seq data
- Metaxa2 2.2.3 - Identification and Classification of Small Subunit (SSU) rRNA Sequences
- MethyRNA - Identificationof N6-methyladenosine Sites
- MIC - MicroRNA Importance Calculator
- microDoR - Prediction of Human miRNA-Mediated Gene Silencing
- MicroLive - Design of live attenuated Virus Vaccine based on microRNA-mediated Gene Silencing
- MicroTar 0.9.6 - microRNA Target Prediction from RNA Duplexes
- miES - Predict microRNA Essentiality Score
- MIfold 2 - Predicting RNA Structure using Mutual Information
- miFRame - Analysis and Visualization of miRNA sequencing data in Neurological Disorders
- Migal 2.2 - Compare RNA Secondary Structure
- MIMEAnTo - Profiling functional RNA in Mutational Interference Mapping Experiments
- mimiRNA - microRNA Expression Profiler
- MinoTar - Predict microRNA Targets in Coding Sequence
- MINTbase V2 - Exploration of Mitochondrial and Nuclear tRNA Fragments
- miR_Path - Inferring Cancer-related miRNAs based on Gene Expression data
- miR-AT! 1.6 - Prediction of Combinatorial Activity of microRNAs
- miR-PREFeR 0.24 - microRNA PREdiction From small RNA-seq data
- miR2GO - Comparative Functional analysis for microRNAs
- miRA 1.2.0 - micro RNA Identification tool
- miRanda 1.9 - microRNA Target Detection Software
- miRbiom - A Machine Learning Approach to Profile miRNAs
- miRBoost 1.0 - MicroRNA Precursor Classifier using Boosting SVM
- MiRCat 1.2 - miRNA Sequence Profiling
- MirCheck - Identify Plant miRNA Genes
- miRClassify 1.0 - miRNA Family Classification and Annotation
- miRComp - Composite MicroRNA Target Prediction
- MirCompare 2.0 - Algorithm to Compare Plant and Mammalian miRNAs
- miRD - pre-microRNA Detection
- miRDeep-P 1.3 / miRDP2 1.1.5 - Analyzing the microRNA Transcriptome in Plants
- miRDeep2 0.1.3 / miRDeep* 3.8 - Discovering Known and Novel miRNAs from Deep Sequencing Data
- MiRdup 1.4 - Prediction of the Localization of microRNAs within their pre-miRNA
- MiRduplexSVM - MiRNA-Duplex Prediction and Evaluation Methodology
- miRe2e - Finding pre-miRNA sequences in raw Genome-wide data
- miReduce - Correlate the logarithm of Expression Fold Changes
- miREE - miRNA Recognition Elements Ensemble
- MIReNA 2.0 - Find microRNAs with high Accuracy and No Learning
- MIReStruC 1.0 - A tool to find microRNA Structural Clusters
- miREval 2.0 - microRNA Prediction in Genome Sequences
- miRFinder 4.0 - MicroRNA Prediction
- MiRGator 3.0 - microRNA portal in Deep Sequencing era
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