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Alignment Allele-specific transcription Alternative Splicing Barcoding Bisulfite Sequencing Cancer biology ChIP-exo ChIP-on-chip ChIP-Seq Clone verification Comparative genomics Comparative transcriptomics Comparison Conversion Copy number estimation De novo assembly De novo sequencing De-novo assembly DNA methylation DNA-Seq Epigenomics Evaluation and validation Exome and whole genome variant detection Framework Functional Genomics Gene expression Gene regulatory network analysis General bioinformatics (pipeline) Genomic Assembly Genomic Assembly Evaluation Genomic Assembly Validation Genomics Identification InDel discovery Infrastructure Mapping Mass Accuracy Metagenomics Metatranscriptomics Next Generation Sequencing Nucleic acid sequence analysis Nucleic acid structure comparison Pairwise structure alignment Peptide identification (DB) Peptide identification (De novo) Peptide identification (lib match) Personal genomics Phylogenetics Population genetics Population Genomics Protein Inference Quality Control Quantitation Raw Data Raw Data / Conversion Read alignment Reference assembly Regulatory genomics Regulatory genomics epigenomics Resequencing Results processing RNA structure prediction RNA-Seq RNA-Seq Alignment RNA-Seq Quantitation Search and retrieval Sequence analysis Sequence database search Sequence functional annotation Sequence motif discovery Sequence motif recognition Sequence Quality Control Sequencing Small RNA transcriptome SNP Annotation SNP discovery SNPs Somatic mutations Structural variation Targeted assembly Targeted resequencing Transcription Factor Binding Site identification Transcriptome Viral genomics Whole gene prediction Whole Genome Resequencing Whole Genome Resequencing Analysis  Alignment  Alternative Splicing  Bisulfite Sequencing  ChIP-on-chip  ChIP-Seq  De novo assembly  De novo transcriptome assembly  De-novo assembly  DNA methylation  DNA-Seq  Exome and Whole genome variant detection  Fusion finding  Fusion genes  Fusion transcripts  Genomic Assembly  Genomics  Genotyping  High-throughput sequencing  In vitro selection  InDel discovery  Mapping  Metagenomics  MiRNA  MiRNA-Seq  Motif analysis  Next Generation Sequencing  Personal genomics  Phylogenetics  Population genetics  Population genomics  Read alignment  Reference assembly  Regulatory genomics  RNA Seq analysis  RNA-Seq  RNA-Seq Quantitation  Sequence analysis  Sequence annotation  Sequencing  Small RNA transcriptome  SNP discovery  Structural variation  Targeted resequencing  Transcription Factor Binding Site identification  Transcriptomics  Whole Genome Resequencing  Whole Genome Resequencing Analysis 基因组注释 基因预测 多重序列比对 多重比对 序列拼接 推荐 比较基因组 重复序列
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  • RNA-Seq
81. FusionCatcher
FusionCatcher searches for novel/known fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq).
标签：RNA-Seq, Fusion finding
82. Geneious
Search, organize and analyze genomic and protein information of any size via desktop program that provides publication ready images to enhance the impact of your research.
标签：Phylogenetics, Sequence analysis, De-novo assembly,Genomics, Population genetics,Metagenomics, Structural variation, RNA-Seq,Epigenomics
83. GenoMiner
A proprietary NGS analysis solution. Powerful hardware comes with preinstalled software, organized in workflows.
标签：Reference assembly, De-novo assembly, ChIP-Seq, RNA-Seq
84. Goby framework
Goby is a next-gen data management framework designed to facilitate the implementation of efficient next-gen data analysis pipelines.
标签：RNA-Seq
85. Goseq
An R package to detect Gene Ontology (GO) categories and other categories of genes (such as KEGG pathways) that are over/under represented in an RNA-seq data.
标签：RNA-Seq Quantitation
86. HeliSphere
Open-source LINUX software package intended for use in analyzing data produced by the HeliScope Single Molecule Sequencer.
标签：Genomics, Whole Genome Resequencing, RNA-Seq, SNP discovery
87. Inchworm
Employs the Kmer graph method to reconstruct (in many cases full-length) transcripts from Illumina RNA-Seq (preferrably strand-specific) reads.
标签：RNA-Seq, De novo transcriptome assembly
88. IOmics
iOmics is a cloud based workflow analysis framework for managing, analyzing and visualizing NGS data.
标签：Genomics, Transcriptomics,Epigenomics, RNA-Seq, Exome and Whole genome variant detection
89. IQSeq
Integrated Isoform Quantification Analysis based on A Partial Sampling Framework
标签：RNA-Seq Quantitation,Alternative Splicing
90. mapsembler
Mapsembler is a targeted assembly software. It takes as input a set of NGS raw reads and a set of input sequences (starters). It first determines if each starter is read-coherent, e.g. whether reads confirm the presence of each starter in the original sequence. Then for each read-cohere...
标签：Metagenomics, Transcriptomics,DNA-Seq, RNA-Seq Quantitation,Targeted assembly
91. MeV
Visualization of genomic data, Differential Gene Expression based on DEGseq, DESeq and edgeR
标签：RNA-Seq
92. MochiView
Hybrid genome browser and motif visualization/analysis/management desktop software.
标签：Genomics, ChIP-Seq, ChIP-on-chip, RNA-Seq, Motif analysis
93. QSeq
QSeq is DNASTAR's Next-Gen application for RNA-Seq,ChIP-Seq, and miRNA alignment and analysis.
标签：ChIP-Seq, RNA-Seq, MiRNA
94. SOAPfusion
SOAPfusion is a novel tool for fusion discovery with paired-end RNA-Seq reads. The tool follows a different strategy by “finding fusions directly and verifying them”, differentiating it from all other existing tools by “finding the candidate regions and searching for the fusions afterwa...
标签：Transcriptome, RNA-Seq
95. SplicingViewer
SplicingViewer is an integrated tool developed to enable users to detect the splice junctions, annotate alternative splicing events, and visualization of the patterns of alternative splicing events.
标签：RNA-Seq, Genomics
96. Subread
Subread is a general-purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. It uses a new mapping paradigm called "seed-and-vote" to achieve fast, accurate and scalable read mapping. It automatically determines if a read should be globally or locally...
标签：Next Generation Sequencing,RNA-Seq Alignment, Read alignment
97. Syapse
Syapse is a platform and application suite for bringing together omics and clinical data.
标签：Allele-specific transcription,DNA methylation, DNA-Seq,InDel discovery, SNP discovery, Structural variation, RNA-Seq, Small RNA transcriptome, ChIP-Seq,Comparative genomics,Comparative transcriptomics,Epigenomics, Genomics,Personal genomics, Population ge
98. UnoSeq
UnoSeq is a Java library to analyze next generation sequencing data (e.g. data generated by Illumina's mRNAseq method) and especially perform expression profiling in organisms where no well-annotated reference genome exists.
标签：RNA-Seq Alignment, De novo transcriptome assembly
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