RNA-Seq
- EBSeq 1.1.6 – RNA-Seq Differential Expression Analysis
- EBARDenovo 1.2.2 – Highly-accurate de novo Assembler of Paired-end RNA-Seq
- Trinity 20130225 – RNA-Seq De novo Assembly
- Cufflinks 2.1.1 – Transcript Assembler & Abundance Estimator for RNA-Seq
- Scotty – Power Analysis for RNA Seq Experiments
- isoform 0.99.1 – RNA Isoform Study using RNA-seq data
- asSeq 0.99.2 – Statistical Framework for eQTL Mapping using RNA-seq Data
- DiffSplice 0.1.1 – Discover Alternative Splicing Variants present in an RNA-seq dataset
- Grape 1.9.4 – Pipeline for Processing and Analyzing RNA-Seq data
- rSeq 0.1.0 – RNA-Seq Analyzer
- S-Mart 1.1.3 – Aid RNA-seq Data Analysis
- RobiNA 1.2.4 – Open Source Microarray and RNA-Seq Processing
- AltAnalyze 2.0.8 – Microarry and RNA-Seq Analysis
- GFold 1.0.8 – Generalized fold change for Rank Differentially Expressed Genes from RNA-seq data
- IsoEM 1.1.1 – Inferring Alternative Splicing Isoform Frequencies from High-Throughput RNA-Seq Data
- Myrna 1.2.0 – Cloud-scale Differential Gene Expression for RNA-seq
- RNAmapper v1 – Use of RNA-Seq data to Map and Identify Mutations in Zebrafish
- mseq 1.2 – Modeling non-uniformity in Short-read Rates in RNA-Seq data
- RNA-SeQC 1.1.7 – Quality Control Metrics for RNA-seq data
- Supersplat 1.0 – Spliced RNA-seq Alignment
- deFuse 0.6.0 – Gene Fusion Discovery using RNA-Seq Data
- RNASEQR 1.0.2 – Streamlined and Accurate RNA-seq Sequence Analysis program
- R-SAP 1.1 – RNA-Seq Analysis pipeline
- TrueSight 0.06 – Self-training Algorithm for Splice Junction Detection using RNA-seq
- FusionAnalyser – Detect Gene Fusions from paired-end RNA-Seq data
- BreakFusion 1.0.1 – Identify Gene Fusions from paired-end RNA-Seq data
- ERANGE 4.0a – Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq
- G-Mo.R-Se 2.0 – Gene MOdeling using RNA-Seq
- NSMAP 0.1.0 – Spliced Isoforms Identification and Quantification from RNA-Seq
- RACKJ 0.61 – Analyze and Compare RNA-seq data made by NGS Technologies
- RUM 1.11 – Comparative Analysis of RNA-Seq Alignment Algorithms and the RNA-Seq Unified Mapper
- 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
- RseqFlow – RNA-seq Data Analysis Workflow
- NOISeq – Differential Expression in RNA-seq
- RD – Statistical Estimation of Isoform Expression Levels using RNA-Seq Based on the Modeling of RNA Degradation
- CEDER – Detection of Differentially Expressed Genes by combining significance of exons using RNA-Seq
- SpliceMap 3.3.5.2 – Splice Junction Discovery Using RNA-Seq
- MISO 1.0 – RNA-Seq Experiments for Identifying Isoform Regulation
- deepBlockAlign 1.0 – Align RNA-seq Profiles of Read Block Patterns.
- Transcriptome Assembler – Transcriptome Assembly used in RNA-seq of 16 Mammalian Species
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