Posts
- Category: RNA Analysis (continued)
- miRge 3.0 0.0.9 - Rational and Efficient Approach to miRNA-seq
- Mirinho 1.0.0 - Prediction of pre-miRNAs
- miRlastic 1.0 - Integrative Analysis of miRNA and mRNA Expression data
- miRLocator - Machine Learning-based mature miRNAs within pre-miRNA Sequences
- miRMaid 1.0 - microRNAs data structured for easier access and integration
- miRmap 1.1 / miRmap web - Comprehensive Prediction of microRNA Target Repression Strength
- MirMark - Prediction of microRNA Targets both at Site-level and UTR-level
- MiRmat - Predict mature microRNA from pri-microRNA
- miRMOD 0.4 - miRNA Modification Identification tool
- miRModule - Identification of miRNA modules from high-throughput miRNA-mRNA Binding Experiments
- miRNA Digger - Genome-wide novel miRNA Mining
- MiRNA Profiling 0.2.8 - Profile Content of miRNA Sequencing Run
- miRNA-deKmer - Identification of microRNA precursor with the degenerate K-tuple or Kmer strategy
- miRNA-MATE - A mapping pipeline for SOLiD miRNA data
- miRNACon - Influence of Confounding Factors Age and Sex on microRNA
- mirnaDetect - Predict possible microRNA Precursors within Genome data
- miRNAFold - Ab initio miRNA Precursor Search in Genomes
- miRNAgFree - microRNA prediction using sRNAseq/miRNAseq/sncRNAseq
- miRNAkey 1.2 - Analysis of microRNA Deep Sequencing data
- miRNALasso - microRNA Target Prediction
- miRNAminer - microRNA Homology Search
- miRNAmRNA 1.0 - miRNA mRNA Expression Integration
- mirnaTA 1.2.3 - miRNA Temporal Analyzer
- MIRO 2.9 - Analyze microRNAs using Next-generation Sequencing Data
- miRPara 6.3 - SVM-based miRNA Prediction tool
- miRPD - miRNA Protein Disease Associations
- MIRPIPE 1.2.1 - miRNA detection and quantification pipeline
- miRPlant v6 - An Integrated Tool for Identification of Plant MiRNA from RNA Sequencing Data
- MiRPlex 0.1 - microRNA Prediction from High-throughput Sequencing data
- miRpp 1.0 - Plant microRNA Precursor Prediction Tool
- miRPredictor - miRNA Target Predictor based on Support Vector Machine
- mirPRo 1.1.4 - Tool for miRNA-seq Analysis
- miRQuest - Integration of tools on a Web Server for microRNA Research
- miRror 2.0 - A Dual View on Sets of MicroRNAs and their Targets
- MiRScan 3 - Predict microRNA Genes from pairs of Conserved Sequences
- miRSel - Automated Extraction of Associations between microRNAs and Genes from the Biomedical Literature
- miRseqViewer 1.0 - Visualization of Sequence, Structure and Expression for Analysis of microRNA Sequencing data
- Mirsynergy 1.23.0 - Detect Synergistic miRNA Regulatory Modules by Overlapping Neighbourhood Expansion
- miRSystem 20160511 - miRNA integrated System for Target Genes Prediction
- miRTarBase 8.0 - microRNA-target Interactions database
- mirTarPri 1.0alpha - miRNA Target Prioritization method
- mirTarVis - Analysis tool for microRNA-mRNA Expression Profile data
- miRtest 1.8 - Combined miRNA- and mRNA-testing
- MiRTif - MicroRNA:Target Interaction Filter
- mirTools 2.0 - non-coding RNA Discovery, Profiling and Functional Annotation based on High-throughput Sequencing
- MirtronPred - Intronic miRNAs Predictor
- miRUPnet - A System Biology Approach to Infer the Function of miRNAs
- miRviewer - Multispecies microRNA Homologous Viewer
- MISIM 2.0 - miRNA Functional Similarity Measuring
- MISO 0.5.4 - RNA-Seq Experiments for Identifying Isoform Regulation
- miTEA - miRNA Target Enrichment Analysis
- MiTie 1.0.0 - Simultaneous RNA-Seq-based Transcript Identification and Quantification in Multiple Samples
- miTRATA v1.3 - microRNA Truncation and Tailing Analysis
- MixMir - Mixed linear models for microRNA Motif Finding
- MMAPPR 0.83 - Mutation Mapping Analysis Pipeline for Pooled RNA-seq
- ModeRNA 1.7.1 - Comparative RNA 3D Modeling
- MPGAfold / MPGAfold Visualizer - Massively Parallel Genetic Algorithm that Predicts RNA Secondary Structure
- mRIN 1.2.0 - direct Assessment of mRNA integrity from RNA-Seq data
- mRNA optimiser 1.0 - Redesign mRNA Sequences to Optimise the Secondary Structure
- MS2distance - Minimum Length MS2 Folding Trajectories
- MSARi - Detecting Conservation of RNA Secondary Structure
- MTide - Identification of miRNA-target Interaction in Plants
- multiMiR 1.0.1 - Integration of microRNA-target Interactions along with their Disease and Drug Associations
- MultiMiTar - Predict mRNA Targets of a Given microRNA
- MultiRNAFold 2.0 - Secondary Structure Prediction of RNA/DNA
- MULTo - Identify Unique Resource
- MutualFold - Simultaneous Folding of Alternative RNA Structures with Mutual Constraints
- Myrna 1.2.3 - Cloud-scale Differential Gene Expression for RNA-seq
- nagnag 1.0.3 - Identifyng and Quantifying NAGNAG Alternative Splicing
- NAMS 2.0 - Noncoding Assessment of long RNAs in Magnoliophyta Species
- NanoTiler 0.11.1 - Design of RNA Nanostructures
- NASSAM - 3D Pattern Searching in Nucleic Acid Structures
- NASTIseq 1.0 - Detection of Natural Antisense Transcripts using Strand-specific RNA Sequencing data
- ncFANs v2 - non-coding RNA Function Annotation Server
- ncRNAClassifier 1.2 - Identify TE and TE-derived ncRNAs from other ncRNAs
- ncRNAscout - Discovering non-coding RNA in Genome Sequences
- netSmooth v0.1.0 - A Network smoothing based method for single cell RNA-seq
- NetUTR 1.0b - Web server for Prediction of Splice Site in 5' UTRs
- NEXT-RNAi 1.31 - Design and Evaluation of RNAi Sequences on a Genome-wide scale
- nocoRNAc 1.23 - Predict & Characterise ncRNA Transcripts in Bacteria
- NOFOLD 1.0.1 - RNA Structure Clustering without Folding or Alignment
- Noncoder - Exon Array-based Detection of Long non-coding RNA
- NorahDesk 1.4 - Detecting small non-coding RNA(ncRNA) from Deep Sequencing data (RNA-seq)
- noRNAlize 1.0 - RNA SHAPE Data Normalization software
- novoMiRank - Prioritizing novel predicted miRNA Precursors for Experimental Validation
- Oasis 1.0 - small RNA Classification
- OEFinder 0.0.2 - Identify Ordering Effect Genes in Single Cell RNA-seq data
- OLego 1.1.7 - Senstive and fast Splice Mapping for mRNA-seq reads
- Oligomap 1.01 - Identification of nearly-perfect matches of small RNAs in Sequence databases
- OligoWalk 2 - Select Efficient siRNA using Hybridization Thermodynamics
- omiRas - Differential Expression Analysis of miRNAs
- OrientationChecker 1.0 - Check Orientation of 16S rRNA Gene Sequences
- ORMAN 1.3 - Optimal Resolution of Ambiguous RNA-Seq Multi-mappings in the Presence of Novel Isoforms
- P-SAMS - the Plant Small RNA Maker Suite
- PACCMIT-CDS / PACCMIT - MicroRNA Target Predictions
- PACES - Prediction of ac4C(N4-acetylcytidine) sites in mRNA
- PAI - Predicting Adenosine to Inosine sites
- pairedBayes 20130514 - Bayesian modeling of paired RNA-seq experiment
- PAL 1.31 - Pseudoknot Aligment for RNA Sequences
- pAliKiss 1.0.7 - Predict Kissing Hairpin Motifs from Aligned Sequences
- PANGEA 1.0.2 - Pipeline Analysis for Next GEneration Amplicons
- PAR-CLIP HMM 0.1.0 - Bayesian hidden Markov models to identify RNA-protein interaction sites in PAR-CLIP
- ParaRNA 1.0 - Computing Parametric Alignment of Two RNA Structures
- PARma 1.0 - PAR-CLIP data microRNA Assignment
- Parseq rev02 - Infer Transcription level from RNA-Seq Read Counts
- PBLR 1.0 - Single-cell RNA-seq data Imputation tool
- PCAGO 1.0.0 - Principal Component analysis for RNA-Seq Read Counts
- PcircRNA_finder - circRNA Prediction in Plants
- PCS 1.5 - Identify and Analyze Conserved K-mers in Pairwise Alignment
- PennSeq - Isoform-specific Gene Expression Quantification in RNA-Seq
- PEPPRO v0.9.11 - A Modular, Containerized pipeline for PRO-seq Data Processing
- PETfold 2.0 / PETcofold 3.2 - Folding of Multiple Alignment of RNA sequences
- PhaseTank 1.0 - Genome-wide Computational Identification of phasiRNAs
- PHDcleav - Prediction of Human Dicer Cleavage
- PhyloQFold - Bayesian Sampling of Evolutionarily Conserved RNA Secondary Structures with Pseudoknot
- PhyloRNAalifold v1 - Predicting Consensus Structures in RNA Alignments by incorporating RNAalifold with Phylogenetic information
- Piano - Predicting piRNAs
- Pibomd - A web-server Predictor for Identifying piRNAs
- Pintail 1.1 - Analyse 16S rRNA Chimera & Anomalies
- piPipes 1.5.0 - piRNA Pipeline Collection
- PIPmiR 1.1 - Pipeline for the Identification of Plant miRNAs
- piRNA 3.6 / biRNA 3.6 - RNA Interaction Search Engine
- pirnaPre 1.0.0 - piRNA Targets on mRNAs in Mouse
- piRNApredictor 1.0 - Predict piRNA Sequences
- piRPred 1.0 - piwi interacting RNA (piRNA) Prediction
- PITA 6 - microRNA prediction tool
- pKiss 2.2.12 - Folding RNA Secondary Structures
- PKNOTS 1.07 - RNA Pseudoknot Prediction
- PLATA 1.01 - Probe Level Alternative Transcript Analysis
- PLEK 1.2 - Predictor of Long Non-coding RNAs and mRNAs based on K-mer Scheme
- PLEXY - Target Pprediction for Box C/D snoRNAs
- PLNseq 1.0 - Poisson Lognormal Distribution for High-throughput matched RNA-sequencing Read Count data
- PmiREN 2.0 - A comprehensive Encyclopedia of Plant miRNAs
- polyester 1.28.0 - Simulate RNA-seq Reads
- POME - Possion Mixed-Effects Regression for RNA-seq Data
- PORTRAIT 1.2 - Prediction of transcriptomic ncRNA by ab initio methods
- PPUS - Predict PUS-specific Pseudouridine sites
- PRADA 1.2 - Pipeline for RNA-Sequencing Data Analysis
- PRI-Modeler 1.3 - Extract RNA Structure elements from PDB files of Protein-RNA Complexes
- pRNAm-PC - Predicting N6-methyladenosine sites in RNA sequences
- ProbeAlign 0.3 - ncRNA Homology Search
- ProbRNA 20131213 - Modeling RNA Structure Probing data
- PROmiRNA v2 - Annotating miRNA Promoters in Human
- ProMISe 1.24.0 - Infer miRNA-mRNA interactions using paired expression data from a single sample
- PROPER 1.24.0 - PROspective Power Evaluation for RNAseq
- PseudoViewer 3.0 - Visualization of RNA Pseudoknots of any type
- PSMAlign - Progressive Stem Matching Alignment
- psRNATarget - Plant small RNA Target Analysis Server
- psRobot v1.2 - Plant Small RNA Analysis Toolbox
- pssRNAMiner - A Plant short small RNA Regulatory Cascade Analysis Server
- PSTAG 2.1.4a - Model Pseudoknot RNA Structure
- pulseR 1.0.3 - Analysis of RNA Metabolic Kinetics from RNAseq data
- PVAAS 0.1.5 - Identify Variants Associated with Aberrant Splicing from RNA-seq
- pVsupPred 1.0 - Predict Viral Suppressors of RNA Silencing
- pydca 1.0 - Direct Coupling analysis software for Protein and RNA sequences
- QRNA 2.03d - Prototype Noncoding RNA Genefinder
- QRNAseq 0.1.0 - for Functional Isoform, Driver Mutation Gene and Fusion Gene Detection
- QuaCRS 1.2 - Quality Control for RNA-Seq
- Quantas 1.0.9 - Analyze alternative Splicing using RNA-Seq
- r-make 1.0c - Process RNA Sequencing Reads
- R-SAP 1.1 - RNA-Seq Analysis pipeline
- R3D-BLAST - A Search Tool for Similar RNA 3D Substructures
- RACKJ 0.95- Analyze and Compare RNA-seq data made by NGS Technologies
- RactIP 2.1.0 - Joint Secondary Structure Prediction
- RAmiRNA - Viral mature MicroRNA prediction Toolkit
- RAMPred - Identifying the N1-methyladenosine sites in Eukaryotic Transcriptomes
- Randfold 2.0 - RNA Minimum Free Energy of Folding Randomization Test
- RASER 0.521 - Reads Aligner for SNPs and Editing sites of RNA
- RASP 1.0.1 / WebRASP - Assessing the Stability of RNA Structures
- RBPSpot - Learning on Appropriate Contextual Information for RBP Binding Sites Discovery
- RBSDesigner 1.0.78 - Design Synthetic Ribosome Binding Sites (RBS) to control Gene Expression levels
- RCARE - RNA-Seq Comparison and Annotation of RNA Editing
- RCAS 1.18.0 - RNA Centric Annotation System
- RCAT 3.0 / CATUI 3.51 - RNA Comparative Analysis Tools
- Rcorrector 1.0.4 - Error Correction for Illumina RNA-seq Reads
- RCoS - Compute Rank Consistency Score
- Rcount - Simple and Flexible RNA-Seq Read Counting
- RD - Statistical Estimation of Isoform Expression Levels using RNA-Seq Based on the Modeling of RNA Degradation
- rddChecker - software for Detecting RNA-DNA Differences
- RDDpred 1.1 - Random Forest RDD Classifier
- RDiff 0.3 - Accurate Detection of Differential RNA Processing
- RDP Classifier 2.13 - Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
- Read-Split-Walk - Identifying Non-canonical Spliced Regions for RNA-Seq data
- READemption 1.0.1 - A RNA-Seq Analysis Pipeline
- REAPR 1.0 - Realignment for Prediction of Structural Non-coding RNA
- RED 0.0.3 - RNA Editing sites Detector
- REDItools 1.2.1 / REDItools2 - RNA editing detection by NGS data
- RefLnc - comprehensive Annotation for human long noncoding RNAs(lncRNAs)
- Regliss - RNA Energy Landscape and Saturated Structures
- remuRNA - Measurement of Single-Nucleotide Polymorphism-induced Changes of RNA Conformation
- repRNA - Web Server for Generating Various Modes of RNA Sequences
- Rfold 0.1.2 - Compute local base pairing Probabilities
- RIblast 1.2.0 - RNA-RNA Interaction prediction
- riboPicker 0.4.3 - Identification and Removal of rRNA-like Sequences.
- Riboswitch finder - Identification of Riboswitch RNAs
- Ribothrypsis - Key tools for Ribothrypsis analysis
- RILogo 1.0 - Visualise RNA-RNA interactions
- RIPSeeker 1.26.0 - de novo RIP Peak Predictions based on HMM.
- RIscoper - RNA Interaction Extraction from Literatures
- RIsearch 1.2 - Fast search for RNA-RNA interactions
- RLooM - RNA Loop Modeling
- rlsim 1.4 - Simulating RNA-seq library Preparation with Parameter Estimation
- rMAPS 2.0.0 - RNA Map analysis and Plotting server for alternative Exon Regulation
- rMATS 4.1.1 - replicate Multivariate Analysis of Transcript Splicing
- RME 1.1 - RNA Secondary Structure Prediction incorporating Experimental Constraints
- RMfam 0.3 - Multiple Alignments and Probabilistic Models of RNA Motifs
- RNA - RNA Consensus Secondary Structure Prediction Software
- RNA draw 1.1b2 - RNA Secondary Structure Calculation & Analysis
- RNA FRABASE 2.0 - RNA FRAgment Search Engine & Database
- RNA Self Containment - Calculates the Self-Containment Index
- RNA-CODE - Noncoding RNA Classification tool
- rna-dm 0.9 - Minimum or Optimal Free Energy Landscape for a RNA sequence
- RNA-DV 1.0 - Design & Visualization Tool for RNA Secondary Structure
- RNA-eXpress 1.4.3 - Extract & Annotate Transcripts from Next Generation RNA sequencing data
- RNA-Pareto 20130814 - Interactive Analysis of Pareto-optimal RNA Sequence-Structure Alignments
- RNA-Redesign - Web server for Fixed-backbone 3D Design of RNA
- RNA-SeQC 1.1.8 - Quality Control Metrics for RNA-seq data
- RNA-Skim - RNA-Seq Quantification at Transcript Level
- rna-sm beta1 - Mine RNA Structure Elements
- RNA-unchained v1.0 - Chaining sequence/structure seeds for computing RNA Similarity
- RNA-WL 1.5 - Thermodynamics of RNA structures by Wang-Landau sampling
- RNA22 v2 - microRNA Target Detection
- RNA2DMap v2 - Visual Exploration of RNA Structure
- RNAalishapes 2.4.7 - Secondary Structure Prediction using Shape Abstraction
- RNAAnalyzer - Identify Regulatory RNA Elements
- RNABOB 2.2 - Fast Pattern Searching for RNA Secondary Structures
- RNAbor - Compute Structural Neighbors of an RNA Secondary Structure
- RNAborMEA - Maximum Expected Accurate Structural Neighbors of an RNA Secondary Structure
- RNAclust 1.3 - Cluster RNAs based on Secondary Structures
- RNACluster 1.0 - RNA Secondary Structure Comparison and Clustering
- RNAcommender v0.1-beta.1 - Genome-wide Recommendation of RNA-protein Interaction
- RNAcompete / RNAcompete-S - Analysis of RNA Sequence/structure preferences for RNA binding proteins
- RNAComposer 1.0 - RNA Structure Modeling Server
- RNAcon 1.0 - Classification of non-coding RNAs (ncRNA)
- RNAConSLOpt 1.2 - Predicting Consensus stable local optimal Structures for Aligned RNA Sequences
- RNAcontext - Predict the Sequence and Structure Preferences of RNA-binding proteins
- RNAcop 1.0.3 - Optimizing RNA structures by Sequence Extensions
- RNAEAPath 1.0 - Predicting Folding Pathways between RNA Conformational Structures Guided by RNA Stacks
- RNAenn - Energy Parameters and novel algorithms for Extended nearest Neighbor Energy Model of RNA
- RNAentropy 1.0 - Compute RNA Secondary Structure Conformational Entropy
- RNAex - RNA Secondary Structure Prediction Server
- RNAexinv - Extended Inverse RNA Folding from Shape and Physical Attributes to Sequences
- RNAexpNumNbors - Expected Number of Structural Neighbors
- RNAfamily - Java Viewer for RNA Secondary Structures
- RNAfdl 1.1.3 - RNA Force Directed Layout
- RNAfitme - Reconstruction & Remodeling of Full-Atom RNA Structure
- RNAFold - Create Batch files for the FOLD module of the GCG
- RNAG - Block Gibbs Sampler for RNA Prediction
- RNAgraphdist 1.0 - Calculation of Graph-distance Distribution of the Boltzmann ensemble of RNA Secondary Structures
- RNAHeliCes 2.0.14 - RNA Folding Space Analysis
- RNAhybrid 2.1.2 - Find Minimum Free Energy Hybridisation of RNA
- rnaifold 3.1 - RNA Inverse Folding and Molecular Design
- Rnall 2.0 - RNA Local Secondary Structure Prediction
- RnallViewer 1.0.1 - RNA Analysis Visualization Tool
- RNAlocmin 2.1 - Finds local Minima of RNA + Constructs Barrier Tree
- rnalocopt 20101116 - Compute Partition Function of Locally Optimal RNA Secondary Structures
- RNALYZER - RNA Structural Comparison Framework
- RNAmap2D 1.7.5 - Visualization of 2D maps of RNA Structures
- RNAmigos - RNA Small Molecule Ligand Prediction
- RNAMiner - Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data
- RNAML 1.1.2 - Syntax for Exchanging RNA Information
- RnamlView 1.0 - Manipulation, Storage & Visualisation of RNA Data
- RNAmmer 1.2 - Ribosomal RNA Sub Units
- RNAMoIP 1.1 - Automated Prediction Framework for RNA Tertiary Structures
- RNAMotif 3.1.1 - Find Structural Motifs in RNA
- RNAmotifs 3 - Predict a motif for your own set of RNAs
- RNAMotifScan 5.3 - Automatic Comparing and Searching for RNA Tertiary Motifs
- RNAMotifScanX 0.0.5 - Graph Alignment approach for RNA Structural Motif Identification
- RNAmountAlign - RNA Sequence/Structure Alignment
- RNAmutants 2.0 - Analysis of RNA Mutational Landscapes
- RNAMute / XRNAmute - RNA Secondary Structure Mutation Analysis Tool
- rnapagenumber - Compute Optimal "page number" of an RNA Structure
- RNAparametric - Computing the Probability of RNA Hairpin and Multiloop Formation
- RNApasta 1.6 - RNA Structural Alignment & Statistical Analysis
- RNApathfinder - Analyze Near-optimal Folding Pathways between RNA Secondary Structures
- RNApdbee 2.0 - RNA Secondary Structures Extraction from PDB Files
- RNAplex 0.2 - Search for Short Interactions between two long RNAs
- RNAprofile 2.2 - Secondary structure motif discovery in RNA sequences
- RNApyro - Detect and Correct Pyrosequencing Errors in Noncoding RNAs
- RNArobo 2.1.0 - RNA Structural Motif Search tool
- RNASampler 1.3 - Predict RNA Secondary Structure Motifs
- RNAsc - RNA Secondary Structure Prediction using SHAPE or inline-probing data
- RNAscf 1.1 - Consensus Folding of Unaligned RNA sequences
- RNASeqBias 1.0 - Bias Detection and Correction in RNA-Sequencing Data
- RNASeqBrowser V3.1 - A Genome Browser for Strand Specific RNAseq Reads
- RNASeqGUI 1.1.2 - GUI for the Identification of Differentially Expressed Genes
- RNASeqMut 0.7 - RNA-Seq Mutation Detection
- RNASeqPowerCalculator - Calculate the Power and Sample size for RNA-Seq Differential Expression
- RNASEQR 1.0.2 - Streamlined and Accurate RNA-seq Sequence Analysis program
- RNASeqR 1.1 - RNAseq Expression Analysis
- RNASeqReadSimulator - A Simple RNA-Seq Read Simulator
- RNAshapes 3.3.0 - RNA Analysis Package based on Abstract Shapes
- RNAsifter 1.0 - RNA Shape Index Filter
- RNASim 1.0 - RNA Evolution Model
- RNASLOpt - Predicting stable local optimal Structures for RNAs
- RNAsnoop 0.2 - Target Prediction for H/ACA snoRNAs
- RNAsnp 1.2 - Identifying local RNA Structures Disrupted by SNPs
- RNAsoup 1.0a - Structural Clustering Pipeline for Structured RNAs
- RNAspace 1.2 - Platform for Non-protein-coding RNA Annotation
- RNAssess - Quality Assessment of RNA 3D Structures
- RNAstrand 2.0.0 - Predict Reading Direction of Structured RNAs in Multiple Sequence Alignments
- RNAstructure 6.3 - Prediction & Analysis of RNA Secondary Structure
- RNATOPS 1.2 - RNA Pseudoknot Search in Genomes
- RNAv - Search Genomes for RNA Secondary Structure Variation
- rNAV 2.0 - Visual Exploration of sRNA mediated Regulatory Network
- RNAView - Generates 2-dimensional Displays of RNA/DNA Secondary Structures
- RNAvista - Prediction of RNA Secondary Structure with Non-canonical Base Pairs
- RnaViz 2.0.3 - Secondary Structure Drawings of RNA Molecules
- RNAwolf 0.3.2 / MC-Fold-DP - RNA Secondary Structure Prediction.
- RNAxs - Design Potent siRNAs
- RNAz 2.1 - Predict Structural Noncoding RNAs
- RP-BP 2.0.0 - Ribosome Profiling with Bayesian Predictions
- RPASuite v0.02 - RNA Processing Analysis Suite
- rpkmforgenes.py - Calculating Gene Expression for RNA-Seq data
- rPredictor - Prediction of Ribosomal RNA Secondary Structure
- rQuant 2.1 - Transcriptome Quantitation from RNA-seq Experiments
- RSEARCH 1.1 - Sequence Database Searching with RNA Structure Queries
- RSEM v1.3.3 - RNA-Seq Expression Estimation by Expectation-Maximization
- rSeq 0.2.1 - RNA-Seq Analyzer
- RSeQC v3.0.1 - RNA-seq Quality Control package
- rSeqDiff 0.1 - Detecting differential Isoform Expression from RNA-seq data
- rSeqNP 1.0 - Detecting Differential Expression and Splicing from RNA-Seq data
- RSEQtools 0.6 - Analyze RNA-Seq data using Compact and Anonymized data summaries
- Rsite2 - Predict the Functional Sites of ncRNAs
- RSmatch 2.0 - Comparison of RNA structures
- RSSVM 1.0 - Discover cis-Regulatory RNAs
- RSVP - RNA-seq Variant Prediction
- Rtools - Secondary Structural analyses on single RNA sequence
- RVboost 0.1 - RNA-seq Variant Prioritization approach for Illumina Next-generation Sequencing data
- S-Mart 1.1.4 - Aid RNA-seq Data Analysis
- Sailfish 0.9.2 - Ultrafast Isoform Abundance Estimation from RNA-seq Reads
- SARA 1.0.7 - Server for Function Annotation of RNA Structures
- SARSE 1.37 - RNA Sequence Editor
- SAVoR - Sequencing Annotation and Visualization of RNA structures
- SbacHTS v5 - Spatial background correction for High-Throughput RNAi Screening
- scds 1.2.0 - In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data
- SCFG Structural Entropy 20120907 - Calculate RNA Structural Entropies through Stochastic Context Free Grammars
- Scirpy v0.10.1 - Scanpy Extension for analyzing Single-cell T-cell Receptor-sequencing data
- scLVM 0.1 - Modelling framework for Single-cell RNA-seq data
- SCmut - Detect Cell-level Mutation from single-cell RNA-sequencing
- Scotty - Power Analysis for RNA Seq Experiments
- SCRIP 1.0.0 - An Accurate Simulator for Single-Cell RNA Sequencing Data
- scRNABatchQC v0.10.3 - multi-samples Quality Control for single cell RNA-seq data
- scvis 0.1.0 - Dimension Reduction of high-dimensional Biological data.
- Sebnif 1.3rc - Comprehensive Novel lincRNA Filter from RNA-seq data
- SECISDesign - Design SECIS-Elements within the Coding Sequence
- SEECER 0.1.3 - SEquencing Error CorrEction for Rna reads
- segmentSeq 2.26.0 - Identifying small RNA loci from High-throughput Sequencing data
- SePIA - RNA Sequence Processing, Integration, and Analysis
- seq2HLA 2.3 - HLA typing from RNA-Seq sequence reads
- SEQBIAS 1.40.0 - Estimation of Per-position Bias in High-throughput Sequencing data
- SeqBuster 3.5 - small RNA analysis of deep Sequencing data
- SeqGSEA 1.33.0 - Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
- SeqSaw 1.0.8 - Short Spliced Sequence Mapping Tool
- SETTER / MultiSETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm
- SFmap 1.8 - Motifs Analysis and Prediction of Splicing Factors
- Sfold 2.2 - Statistical Folding and Rational Design of Nucleic Acid
- sgRNA online 1.2 - Identifies efficient sgRNAs for CRISPR editing of mouse and human Genomes
- sgRNA-PSM - Predict sgRNAs on-target Activity based on Position Specific Mismatch
- ShortFuse 0.2 - Gene Fusion Detection using Ambiguously Mapping RNA-Seq Read Pairs
- ShortStack 3.8.5 - Comprehensive Annotation and Quantification of small RNA genes
- SI-FI 1.2.3 - RNAi (RNA interference) Off-target Prediction
- siDirect 2.0 - Target Specific siRNA online Design Site
- SIM - Analyzing long-range RNA-RNA interactions in Viral Genomes and structured RNAs
- SimiRa - Identify Coregulation between microRNAs and RNA-binding proteins
- SimRNA 3.20 - Simulations of RNA Conformational Dynamics
- SimSeq 1.4.0 - Nonparametric Simulation of RNA-Seq Data
- SimTree 1.2.3 - Compute Similarity between RNA Secondary Structure
- siPRED - Predicting siRNA Efficacy using Various Characteristic Methods
- SIREs 2.0 - Iron Responsive Elements Prediction Server
- SMART TOOLS - Implementation of a de novo Genome-wide Computational approach for updating Brachypodium miRNAs
- SMiRK - an Automated Pipeline for miRNA Analysis
- SNAPR - Scalable Nucleotide Alignment Program RNA-seq
- snoGPS 1.0 - H/ACA snoRNA predictions
- SnoReport 1.2.3 - Computational Identification of snoRNAs with unknown Targets
- Snoscan 1.0 - C/D box snoRNA Predictions
- SnowShoes-FTD - Find Fusions from RNA-Seq data
- SNPfold 1.01 - Identify RiboSNitches by leveraging GWAS data and an Analysis of the mRNA Structural Ensemble
- SNPlice 1.8.0 - Find SNPs influencing splicing in NGS mRNA data
- Solas 0.2.1 - Analysis of RNA-Seq data
- SoMART - Server for plant miRNA/tasiRNA Analysis Tools
- SortMeRNA 2.1 - Filter rRNA Fragments from Metatranscriptomic data
- SoupViewer 0.7.5.2 - Graphical Analysis tool for Output of RNAsoup program
- Spanki 0.5.0 - Analysis of Alternative Splicing from RNA-Seq data
- SPARCS - Structural Profile Assignment of RNA Coding Sequences
- sPARTA 1.27 - small RNA-PARE Target Analyzer
- SPF 1.1 - Find Structurally Significant Regions in RNA Sequences
- SplAdder 2.4.0 - Detection and Quantification of Alternative Splicing Events from RNA-Seq data
- SplamiR - Predicting miRNAs in Plants
- SpliceJumper - Splicing Junction Calling from RNA-Seq data
- SpliceMap 3.3.7 - Splice Junction Discovery Using RNA-Seq
- SpliceSeq 2.1 - Investigate alternative mRNA Splicing in Next Generation mRNA Sequence data
- SplicingCompass 1.0.1 - Differential Splicing Detection using RNA-Seq data
- SplicingTypesAnno 1.0.2 - Annotation tool for alternative Splicing Types by RNA-Seq data
- SplicingViewer 1.1.0 - Detection, Annotation and Visualization of the Alternative Splicing from RNA-Seq Data
- SPLITS 1.1 / SPLITSX - tRNA Detection in Genome Sequence
- spongeScan - Detecting microRNA Binding Elements in lncRNA Sequences
- SPuNC - RNA Structure Prediction using Nucleotide Composition
- SRAMP - Sequence-based RNA Adenosine Methylation Site Predictor
- srnaloop - Search long DNA/RNA Strings for small RNA Hairpin Loops
- sRNAscanner 20100831 - intergenic small RNA Detection in Bacterial Genomes
- sRNAtoolbox 1.3.1 - Collection of small RNA Analysis tools
- SSC 0.1 - Sequence Scan for CRISPR
- SSCA - Sequences Selection for the Comparative Approach
- SSCprofiler - miRNA Gene Prediction
- sSeq 1.1 - Detection of Differentially Expressed Genes in RNA-seq Experiments
- SSPcompare - Takes a Library of known RNA Sequence-structure Pairs
- SStructView 1.2.2 - RNA Secondary Structure Viewing Java Applet
- sTAM - Single Sample microRNA Set Enrichment Analysis
- Starfold - Predict RNA Secondary Structures
- Stem Kernels 193 - Directed acyclic graph kernels for structural RNA analysis
- StringTie 2.0.3 - Transcript Assembly and Quantification for RNA-Seq
- Structator 1.1 - Fast Index-based Search for RNA Sequence-structure Patterns
- StructureLab 4.7 - RNA Structure Analysis
- SurvMicro v0.9 - Assessment of Prognostic miRNA Signatures
- SVMicrO 20100315 - Mammalian MicroRNA Target Prediction
- Sylamer 1.0 - Fast Assessment of microRNA Binding and siRNA off-target effects from Expression data
- TaLasso - Quantification of miRNA-mRNA interactions
- TAM 2.0 - Annotations of meaningful human miRNAs Categories
- TAPIR 1.2 - Prediction of Plant microRNA Targets
- Targetfinder 1.7 - Predict Small RNA Targets in a Sequence Database
- TargetMiner - microRNA Target Prediction
- TargetProfiler - miRNA Target Prediction tool
- TargetRank 1.0 - Rank Conserved and non-conserved microRNA Targets and siRNA off-targets
- TargetRunningSum 1.0 - Rank-based method to Detect key microRNA Regulators
- TargetS - microRNA Target Prediction in Different Gene Regions
- TargetScan 7.2 - Prediction of microRNA Targets
- TargetScore 1.24.0 - Infer microRNA Targets using microRNA-overexpression data and Sequence Information
- TargetSpy 1.0 - microRNA Target Prediction
- TargetThermo - microRNA Target Prediction under relaxed seed and no conservation requirements
- TarPmiR - microRNA Target Site Prediction
- Tarsier - Testing and Analysing RNA gene Software, Including Evolutionary Relationships
- TASR 1.1 - Annotate Transposable Elements using siRNAs Mapping
- Tax4Fun 0.3.1 - Predicting Functional Profiles from Metagenomic 16S rRNA data
- TBI - Predicting Ion Effects in RNA Folding
- TEISER 1.0 - de-novo Motif Discovery tool for Finding Informative Structural Elements in RNA
- TEMT 1.0 - Transcripts Abundances Estimation from Heterogeneous Tissue sample of RNA-Seq data
- TERA-Seq - True end-to-end Sequencing of native RNA molecules for Transcriptome Characterization
- TERIUS 1.0.1 - Prediction of lncRNA via High-throughput Sequencing data
- TFmiR 1.2 - Disease-specific miRNA/Transcription Factor Co-regulatory Networks
- TFold - RNA Secondary Structure Prediction
- TIGAR 2.1 - Estimate Transcript Isoform abundances from RNA-Seq data
- TopHat 2.1.1 - Short Read Aligner for RNA-Seq Experiments
- TRAP 2.3 - Time-series RNA-seq Analysis Package
- Traph 0.7.2 - Transcript Identification and Quantification with RNA-Seq
- Treekin 0.4 - Computation of RNA Folding Dynamics
- TRFolder / TRFolder-W - Telomerase RNA Structure Prediction
- tRNAcc 1.0 - Identify Genomic Islands Associated with tRNA Genes
- tRNAmod - Prediciton of tRNA Modifications
- tRNAmodpred - Predicting Posttranscriptional Modifications in tRNAs
- Trnascan-SE 2.0.8 - Search for tRNA Genes in Genomic Sequence
- TrueSight 0.06 - Self-training Algorithm for Splice Junction Detection using RNA-seq
- TRUP 0.1 - Tumor-specimen suited RNA-seq Unified Pipeline
- TSCAN 1.0 - Pseudo-time Reconstruction and Evaluation in Single-cell RNA-seq Analysis
- TSMDA - Target and Symptom-based computational model for miRNA-disease Association Prediction
- tsRFun - A Web Server to Detect tRFs and their expression in multiple Cancers
- TSSAR 1.0.1 - Transcription Start Site Annotation Regime
- TSSpredator 1.1 beta - Comparative TSS Prediction from RNA-seq data
- tweeDEseq 1.30.0 - Analyzing RNAseq Count data
- UEA sRNA Workbench 4.6 ALPHA - Analysing micro RNA and other small RNA data from High-Throughput Sequencing devices
- UNAFold 4.0 / mfold 3.6 / MFold Interface 1.18 - Nucleic Acid Folding & Hybridization Package
- V-RevComp 1.1 - Detect and Re-orient Reverse Complementary SSU and LSU rRNA Sequences
- V-Xtractor 2.1 - Extraction of Variable Subregions from SSU or LSU rRNA Sequences
- VARNA 3-93 - Java pplet for Drawing the Secondary Structure of RNA
- VARUS 1.0.0 - Drawing Diverse Samples from RNA-Seq Libraries
- VASC - Variational Autoencoder for Single Cell RNA-seq datasets
- VDJSeq-Solver - in Silico VDJ Recombination Detection tool
- VeRNAl - Discovering Flexible Motifs in RNA Graphs
- VERSE v1.0.5 - Versatile and Efficient RNA-Seq Read Counting Tool
- Vfold 2.0 - RNA Structure and Folding Thermodynamics Prediction
- Vienna+P - Modeling the interplay of Single-stranded Binding Proteins and Nucleic Acid Secondary Structure
- ViennaRNA 2.5.0 - RNA Secondary Structure Prediction & Comparison
- VIPER 1.0 - Variability-preserving imputation for Single-cell RNA-seq
- viRome 0.10 - Analysis of Viral small RNA Sequence datasets
- VirTect - Detection of Viruses from RNA-Seq on human samples
- WAR - Webserver for Aligning structural RNAs
- WASP v1.0 - Web-Accessible Single Cell RNA-Seq Processing Platform
- WemIQ - Isoform Quantification method for RNA-seq data
- WMD 3.2 - Web MicroRNA Designer
- WU-CRISPR - WashU gRNA Designer for CRISPR/Cas9 Knockout
- XRNA 2.0 - Creation, Annotation & Display of RNA Secondary Structure Diagrams
- Yanagi - Segment-based RNA-seq analysis
- ZINBWaVE 1.16.0 - Zero-Inflated Negative Binomial based Wanted Variation Extraction
- Category: System Biology & Modeling
- 3DProIN - Protein-Protein Interaction Networks and Structure Visualization
- 3Omics - Web based Systems Biology Visualization tool
- ABC-SysBio 2.08 - Parameter Inference and Model Selection
- ABM-TKI 0.11 - Multi-scale Agent-Based Brain Tumor Modeling
- ACIB PGDB Toolbox 1.0 - Create, Maintain and Query Pathway/Genome Databases
- Acorn 0.3 - Visualation of Genome Scale Metabolic Reaction Networks
- ACRE - Absolute Concentration Robustness Exploration in Module-based Networks
- ADAM 1.1 - Analyze the Dynamics of Discrete Biological Systems
- AIRnet 0.9 - Infer Gene Regulatory Networks
- AlignNemo 1.1 - Local Network Alignment method to integrate Homology and Topology
- ALSYSTA 1.07 Beta - Analysis of different Aspects of Biological Systems
- AMBIENT 1.3 - Find Active Modules in Metabolic Networks using High-throughput data
- AMEBA 1.0 - Advanced MEtabolic Branchpoint Analysis
- AMIGO2 R2019b - Advanced Modelling and Identification using Global Optimization
- AminoNet 2.0 - Create, Visualize and Analyse Protein Network
- AMOUNTAIN 1.18.0 - Active modules for multilayer weighted Gene co-expression networks
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