RNA Analysis
- EBSeq 1.1.6 – RNA-Seq Differential Expression Analysis
- pairedBayes 20130514 – Bayesian modeling of paired RNA-seq experiment
- AStalavista 3.1 – Alternative Splicing Transcriptional Landscape Visualization tool
- miRTRAP 20120110 – Identification of miRNAs from High Throughput Sequencing data
- Scotty – Power Analysis for RNA Seq Experiments
- isoform 0.99.1 – RNA Isoform Study using RNA-seq data
- LocARNA 1.7.6 – Global and Local Alignment of RNA
- SplamiR – Predicting miRNAs in Plants
- RCAT 3.0 – RNA Comparative Analysis Tools
- RNA2DMap v2 – Visual Exploration of RNA Structure
- CID-miRNA – miRNA Prediction Webserver
- RNA-eXpress 1.4.3 – Extract & Annotate Transcripts from Next Generation RNA sequencing data
- AbundantOTU+ 0.92b – Identification and Quantification of Abundant Species from Pyrosequences of 16S rRNA
- RCoS – Compute Rank Consistency Score
- NetUTR 1.0b – Web server for Prediction of Splice Site in 5′ UTRs
- miTEA – miRNA Target Enrichment Analysis
- SFmap 1.7 – Motifs Analysis and Prediction of Splicing Factors
- SARA 1.0.7 – Server for Function Analysis of RnA structures
- CIMS 1.0.0 – Crosslinking Induced Mutation Site analysis
- OLego 1.1.1 – Senstive and fast Splice Mapping for mRNA-seq reads
- DiffSplice 0.1.1 – Discover Alternative Splicing Variants present in an RNA-seq dataset
- ncFANs v2 – non-coding RNA Function Annotation Server
- Grape 1.9.4 – Pipeline for Processing and Analyzing RNA-Seq data
- RSEM 1.2.4 – RNA-Seq Expression Estimation by Expectation-Maximization
- SARA 1.0.7 – Server for Function Annotation of RNA Structures
- FR3D 20120611 – Find Structural Motifs in RNA 3D Structures
- SpliceSeq 1.2.1 – Investigate alternative mRNA Splicing in Next Generation mRNA Sequence data
- r-make 1.0b – Process RNA Sequencing Reads
- RIsearch 1.0 – Fast search for RNA-RNA interactions
- RNAstructure 5.5 – Prediction & Analysis of RNA Secondary Structure
- miRPara 6.2 – SVM-based miRNA Prediction tool
- TopHat 2.0.8b – Short Read Aligner for RNA-Seq Experiments
- Sylamer 1.0 – Fast Assessment of microRNA Binding and siRNA off-target effects from Expression data
- rSeq 0.1.0 – RNA-Seq Analyzer
- kinfold 2.2 – Analysis of Time-Resolved RNA Folding
- Circles 0.1.1 – Analysis of RNA Secondary Structure
- GraphClust 0.7.4 – Structural Clustering of local RNA Secondary Structures
- ExpaRNA 1.0 – Exact Matching of Sequence-structure
- RNAclust 1.3 – Cluster RNAs based on Secondary Ctructures
- BarMap 20080919 – RNA Folding on Dynamic Energy Landscapes
- Treekin 0.3.1 – Computation of RNA Folding Dynamics
- Vienna RNA Package 2.1.1 – RNA Secondary Structure Prediction & Comparison
- SnoReport 1.2.3 – Computational Identification of snoRNAs with unknown Targets
- RNAmicro 1.1.3 – Hairpins in a Haystack
- NanoTiler 0.11.1 – Design of RNA Nanostructures
- KNetFold 1.4.4b – RNA secondary structure prediction
- MPGAfold / MPGAfold Visualizer – Massively Parallel Genetic Algorithm that Predicts RNA Secondary Structure
- StructureLab 4.5.0 – RNA Structure Analysis
- SMART TOOLS – Implementation of a de novo Genome-wide Computational approach for updating Brachypodium miRNAs
- RNASeqBias 1.0 – Bias Detection and Correction in RNA-Sequencing Data
- S-Mart 1.1.3 – Aid RNA-seq Data Analysis
- TAPIR 1.1 – Prediction of Plant microRNA Targets
- Oxfold 20120925 – Implementation of RNA Folding
- fRNAkenstein 20130115 – Python program for Multiple Target Inverse RNA Folding
- Evolving SCFGs 2.0 – RNA Secondary Structure Prediction
- RAmiRNA – Viral mature MicroRNA prediction Toolkit
- ComiR – Combinatorial miRNA target prediction tool
- MiRmat – Predict mature microRNA from pri-microRNA
- ProbRNA 1.0 – Modeling RNA Structure Probing data
- GAISR – Genomic Analysis Illuminating RNA Structure
- mRNA optimiser 1.0 – Redesign mRNA Sequences to Optimise the Secondary Structure
- piRNApredictor 1.0 – Predict piRNA Sequences
- miRNA-MATE – A mapping pipeline for SOLiD miRNA data
- Myrna 1.2.0 – Cloud-scale Differential Gene Expression for RNA-seq
- CURE 1.1 – Cytidine-to-Uridine RNA Editing Predictor
- RNA-SeQC 1.1.7 – Quality Control Metrics for RNA-seq data
- WAR – Webserver for Aligning structural RNAs
- Starfold – Predict RNA Secondary Structures
- RNAbor – Compute Structural Neighbors of an RNA Secondary Structure
- rnapagenumber – Compute Optimal “page number” of an RNA Structure
- rnaifold – RNA Inverse Folding and Molecular Design
- DIAL – 3-Dimensional RNA Structural Alignment and Motif Detection
- VARNA 3-9 – Java pplet for Drawing the Secondary Structure of RNA
- Assemble2 1.0 beta1 – Construct & Study RNA Architectures
- PORTRAIT 1.2 – Prediction of transcriptomic ncRNA by ab initio methods
- UNAFold 3.8 / mfold 3.5 / MFold Interface 1.18 – Nucleic Acid Folding & Hybridization Package
- GenemiR 1.0 – Unified Search of Mammalian microRNA Target Predictions
- OrientationChecker 1.0 – Check Orientation of 16S rRNA Gene Sequences
- Pintail 1.1 – Analyse 16S rRNA Chimera & Anomalies
- Mallard 1.02 – Screen 16S rRNA Clone Libraries contain Chimeras
- RNASEQR 1.0.2 – Streamlined and Accurate RNA-seq Sequence Analysis program
- RNASeqR 1.1 – RNAseq Expression Analysis
- Tarsier – Testing and Analysing RNA gene Software, Including Evolutionary Relationships
- RNA draw 1.1b2 – RNA Secondary Structure Calculation & Analysis
- loopDloop 2.07b – Draw RNA Secondary Structures
- miRNAkey 1.2 – Analysis of microRNA Deep Sequencing data
- R-SAP 1.1 – RNA-Seq Analysis pipeline
- get_size_NN v1 – Neutral Network Size Estimation
- RLooM – RNA Loop Modeling
- TrueSight 0.06 – Self-training Algorithm for Splice Junction Detection using RNA-seq
- NAbind – RNA Binding Prediction Package
- smyRNA 1.2 – Discover Novel ncRNAs in Given Genome
- piRNA 3.3 – RNA Interaction Search Engine
- inteRNA 3.3 – Predict Joint Secondary Structure of two RNA Sequences
- GraPPLE – Graph Property based Predictor and Likelihood Estimator
- TargetScan 6.2 – Prediction of microRNA Targets
- TargetRank 1.0 – Rank Conserved and non-conserved microRNA Targets and siRNA off-targets
- MiRScan 1.0 – Predict microRNA Genes from pairs of Conserved Sequences
- ExonScan 1.0 – Simulating the RNA Splicing Pattern of a Primary Transcript Sequence
- RNAAnalyzer – Identify Regulatory RNA Elements
- Riboswitch finder – Identification of Riboswitch RNAs
- TaLasso – Quantification of miRNA-mRNA interactions
- RNAmap2D 1.7.5 – Visualization of 2D maps of RNA Structures
- RNAprofile 2.2 – Secondary structure motif discovery in RNA sequences
- rnalocopt 20101116 – Compute Partition Function of Locally Optimal RNA Secondary Structures
- GTfold 3.0 – Scalable Multicore Code for RNA Secondary Structure Prediction
- RNABOB 2.2 – Fast Pattern Searching for RNA Secondary Structures
- snoGPS 1.0 – H/ACA snoRNA predictions
- Snoscan 1.0 – C/D box snoRNA Predictions
- SoupViewer 0.7.5.2 – Graphical Analysis tool for Output of RNAsoup program
- PPfold 3.0 – Predict Consensus Secondary Structure of RNA Alignments
- FindtRNA 1.0 – tRNA Prediction tool
- SStructView 1.2.2 – RNA Secondary Structure Viewing Java Applet
- INSEGT 1.0 – Analyse Alignments of RNA-Seq reads using Gene Annotations
- SnowShoes-FTD – Find Fusions from RNA-Seq data
- FusionAnalyser – Detect Gene Fusions from paired-end RNA-Seq data
- RILogo 1.0 – Visualise RNA-RNA interactions
- Context Fold 1.0 – RNA Secondary Structure Prediction tool
- STRMS 0.5.2 – Structural RNA Motif Search
- TargetPrediction – Target mRNAs Prediction
- RNAMute – RNA Secondary Structure Mutation Analysis Tool
- ILM 20030728 – Predict RNA Secondary Structures with Pseudoknots
- CG-seq – Comparative Genomics-seq
- 4SALE 1.7 – Synchronous RNA Sequence and Secondary Structure Alignment and Editing
- MultiMiTar – Predict mRNA Targets of a Given microRNA
- TargetMiner – microRNA Target Prediction
- SSPcompare – Takes a Library of known RNA Sequence-structure Pairs
- RNAwolf 0.3.2 / MC-Fold-DP – RNA Secondary Structure Prediction.
- CMCompare 0.0.1 – Discriminatory Power of RNA Family Models
- Bcheck 0.6 – rnpB gene prediction
- barriers 1.5.2 – Basin Structure of RNA Energy Landscapes
- Oligomap 1.01 – Identification of nearly-perfect matches of small RNAs in Sequence databases
- miRFinder 4.0 – MicroRNA Prediction
- expected5to3distance – Compute Expected Distance between Terminal Nucleotides of RNA
- Dishuffle – RNA Dinucleotide Shuffle
- RDP Classifier 2.5 – Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
- miRDeep 2.0.0.5 – Discovering Known and Novel miRNAs from Deep Sequencing Data
- ESPRIT – Estimating Species Richness Using Large Collections of 16S rRNA Pyrosequences
- ModeRNA 1.7.1 – Comparative RNA 3D Modeling
- RACKJ 0.61 – Analyze and Compare RNA-seq data made by NGS Technologies
- SpliceTrap 0.90.5 – Exon Inclusion Ratio Estimation from Paired End RNAseq data
- ReadSpy – Assessment of Uniformity in RNA-Seq reads
- tRNAcc 1.0 – Identify Genomic Islands Associated with tRNA Genes
- riboPicker 0.4.3 – Identification and Removal of rRNA-like Sequences.
- SI-FI 3.1 – RNAi (RNA interference) Off-target Prediction
- nocoRNAc 1.23 – Predict & Characterise ncRNA Transcripts in Bacteria
- miRComp – Composite MicroRNA Target Prediction
- RNAmotifs 3 – Predict a motif for your own set of RNAs
- PITA 6 – microRNA prediction tool
- SeqSaw 1.0.8 – Short Spliced Sequence Mapping Tool
- MapMi 1.5.0-b01 – Automated Mapping of miRNA loci
- ShortFuse 0.2 – Gene Fusion Detection using Ambiguously Mapping RNA-Seq Read Pairs
- Chimerascan 0.4.5a – Detect Gene Fusions in Paired-end RNA Sequencing (RNA-Seq) Datasets
- RSEQtools 0.6 – Analyze RNA-Seq data using Compact and Anonymized data summaries
- IQSeq 1.0 – Isoform Quantification with RNA-seq data
- FRASS 1.0 – RNA Structure Comparison
- CASHX 2.3 – Process Read data output from Illumina and other HTS technologies
- CleaveLand 3.0.1 – Find Cleaved Small RNA Targets
- Targetfinder 1.6 – Predict Small RNA Targets in a Sequence Database
- RNAmutants 1.1.0 – Exploring the Effects of Mutations on the Secondary Structure of RNAs
- RNApathfinder – Analyze Near-optimal Folding Pathways between RNA Secondary Structures
- RNA-WL – Thermodynamics of RNA structures by Wang-Landau sampling
- RNAborMEA – Maximum Expected Accurate Structural Neighbors of an RNA Secondary Structure
- RD – Statistical Estimation of Isoform Expression Levels using RNA-Seq Based on the Modeling of RNA Degradation
- RNACluster 1.0 – RNA Secondary Structure Comparison and Clustering
- ParaRNA 1.0 – Computing Parametric Alignment of Two RNA Structures
- BBSeq 1.0 – Analysis of RNA Sequence Count Data
- FDM 1.0 – Analyze Differential Transcription
- MapSplice 1.15.2 – Mapping of RNA-seq reads for Splice Junction Discovery
- SimTree 1.2.3 – Compute Similarity between RNA Secondary Structure
- ESSA – Analyse RNA Secondary Structure
- SpliceMap 3.3.5.2 – Splice Junction Discovery Using RNA-Seq
- MiRfold 0.2b – Search for a good miRNA-like Folding in Sequence
- RNAML 1.1.2 – Syntax for Exchanging RNA Information
- LeARN 1.5.0 /smallA – Platform for Annotating, Clustering and Editing ncRNA
- miRanalyzer 0.2 – microRNA Detection Tool for Next Generation Sequencing Experiments
- rQuant 2.1 – Transcriptome Quantitation from RNA-seq Experiments
- PKNOTS 1.07 – RNA Pseudoknot Prediction
- QRNA 2.03d – Prototype Noncoding RNA Genefinder
- RSEARCH 1.1 – Sequence Database Searching with RNA Structure Queries
- Trnascan-SE 1.3 – Search for tRNA Genes in Genomic Sequence
- Randfold 2.0 – RNA Minimum Free Energy of Folding Randomization Test
- MIRO 2.9 – Analyze microRNAs using Next-generation Sequencing Data
- SPLITS 1.1 / SPLITSX – tRNA Detection in Genome Sequence
- Novel miRNA detection 1.0 – Identification of novel miRNA genes
- MiRNA Profiling 0.2.6 – Profile Content of miRNA Sequencing Run.
- BLISS 0.7 – Identify Batch Effects in RNA Expression Data
- RSpredict – Predict Secondary Structures of multiple RNA Sequence Alignments
- RSfold – Predict Secondary Structures of Single RNA Sequence
- RADAR 2.0 – RNA Data Analysis and Research
- Erpin 5.5.4 – RNA Motif Search program
- MISO 1.0 – RNA-Seq Experiments for Identifying Isoform Regulation
- Darn 1.0 – Non-protein-coding RNA Detection
- comrad 0.1.3 – Discovery of Gene Fusions using Paired End RNA-Seq and WGSS
- MEMERIS 1.0 – MEME in Rna’s Including Secondary Structures
- MARNA 100729 – Server for Multiple Alignment of RNAs
- LocalFold 1.0 – Local Folding of RNA
- INFO-RNA 2.1.2 – A Server for Inverse Folding of RNA
- IntaRNA 1.2.5 – RNA-RNA Interaction Prediction
- RNAsoup 1.0a – Structural Clustering Pipeline for Structured RNAs
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