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資源導航

  • 資源導航
  • Alternative Splicing
1. CuffLinks
Cufflinks assembles transcripts and estimates their abundances in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support ...
標簽：RNA-Seq Alignment,?RNA-Seq Quantitation,?Alternative Splicing,?Transcriptome,?RNA-Seq
2. ALEXA-Seq
Alternative Expression Analysis by massively parallel RNA sequencing
標簽：RNA-Seq Quantitation,Alternative Splicing
3. Solas
Given gene annotation the major questions addressed by the package are: prediction of alternative exons in a single condition / cell sample, prediction of differential alternative exons between two conditions / cell samples, quantification of alternative splice forms in a single conditi...
標簽：RNA-Seq Quantitation,Alternative Splicing
4. IsoEM
Expectation maximization algorithm for estimating alternative splicing isoform frequencies
標簽：Alternative Splicing
5. RNASEQR
a streamlined and accurate RNA-seq sequence analysis program
標簽：Alternative Splicing
6. SpliceTrap
SpliceTrap is a statistic tool for quantifying exon inclusion ratios in paired-end RNA-seq data. Instead of full transcript quantification, SpliceTrap approaches to exon inclusion level estimation as a Bayesian inference problem. For every exon it quantifies the extent to which it is in...
標簽：Alternative Splicing,?RNA-Seq Quantitation,?RNA-Seq
7. SeqSaw
A package for mapping of spliced reads and unbiased detection of novel splice junctions from RNA-seq data.
標簽：RNA-Seq,?Alternative Splicing
8. DSGseq
This program aims to identify differentially spliced genes from two groups of RNA-seq samples.
標簽：RNA-Seq,?Differential Expression,?Alternative Splicing
9. RDiff
rDiff is an open source tool for accurate detection of differential RNA processing from RNA-Seq data. It implements two statistical tests to detect changes of the RNA processing between two samples. rDiff.parametric is a powerful test, which can be applied for well annotated organisms t...
標簽：Alternative Splicing,?RNA-Seq,Transcriptomics
10. Partek Genomics Suite
Easy to use software providing A to Z analysis for all Next Generation Sequencing and Microarray data.
標簽：Allele-specific transcription,RNA-Seq Quantitation,Epigenomics,?Functional Genomics,?ChIP-Seq,Alternative Splicing,?SNP discovery,?Small RNA transcriptome
11. BBMap
BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.
標簽：Resequencing,?Alignment,Quality Control,?RNA-Seq Alignment,?Alternative Splicing,?Whole Genome Resequencing,?SNP discovery,Phylogenetics,?Metagenomics,Read Binning
12. SpliceGrapher
SpliceGrapher is a package for creating splice graphs from RNA-Seq data, guided by gene models and EST data (when available).
標簽：Alternative Splicing
13. Subjunc
The Subread read aligner and Subjunc junction detector employ a novel read mapping paradigm called "seed-and-vote" to achieve a fast mapping speed and a high mapping accuracy. The seed-and-vote paradigm is particularly powerful in detecting indels. Subjunc can be used to discover exon-e...
標簽：Alternative Splicing,?Next-generation sequencing,?RNA-Seq Alignment
14. CRAC
CRAC is a mapping software specialized for RNA-Seq data. It detects mutations, indels, splice or fusion junctions in each single read. We propose a novel way of analyzing reads that integrates genomic locations and local coverage, and delivers all above mentioned predictions in a singl...
標簽：Mapping,?RNA Seq analysis,RNA-Seq Alignment,?Alternative Splicing,?Fusion genes,?Fusion transcripts,?SNP discovery,InDel discovery
15. IQSeq
Integrated Isoform Quanti?cation Analysis based on A Partial Sampling Framework
標簽：RNA-Seq Quantitation,Alternative Splicing
16. SplicePlot
RNA sequencing has provided unprecedented resolution of alternative splicing and splicing quantitative trait loci (sQTL). However, there are few tools available for visualizing the genotype-dependent effects of splicing at a population level. SplicePlot is a simple command line utility ...
標簽：Alternative Splicing