最全面的转录组研究软件收集

能看到这个网站真的是一个意外,现在看来,还是外国人比较认真呀, 这份软件清单,能看出作者的确是花了大力气的,满满的都是诚意。from: https://en.wiki2.org/wiki/List_of_RNA-Seq_bioinformatics_tools
https://en.wiki2.org/wiki/List_of_RNA-Seq_bioinformatics_tools软件主要涵盖了转录组分析的以下18个方向,看我我才明白自己的水平的确没到家,印象中的转录组分析也就是差异表达,然后注释以下,最多分析一下融合基因,要不然就看看那些miRNA,和lncRNA咯,没想到里面的学问也大着呢,怪不得生物是一个大坑,来再多的学者也不怕,咱有的是研究方向给你。

    1 Quality control and pre-processing data
        1.1 Quality control and filtering data
        1.2 Detection of chimeric reads
        1.3 Errors Correction
        1.4 Pre-processing data
    2 Alignment Tools
        2.1 Short (Unspliced) aligners
        2.2 Spliced aligners
            2.2.1 Aligners based on known splice junctions (annotation-guided aligners)
            2.2.2 De novo Splice Aligners
                2.2.2.1 De novo Splice Aligners that also use annotation optionally
                2.2.2.2 Other Spliced Aligners
    3 Normalization, Quantitative analysis and Differential Expression
        3.1 Multi-tool solutions
    4 Workbench (analysis pipeline / integrated solutions)
        4.1 Commercial Solutions
        4.2 Open (free) Source Solutions
    5 Alternative Splicing Analysis
        5.1 General Tools
        5.2 Intron Retention Analysis
    6 Bias Correction
    7 Fusion genes/chimeras/translocation finders/structural variations
    8 Copy Number Variation identification
    9 RNA-Seq simulators
    10 Transcriptome assemblers
        10.1 Genome-Guided assemblers
        10.2 Genome-Independent (de novo) assemblers
            10.2.1 Assembly evaluation tools
    11 Co-expression networks
    12 miRNA prediction
    13 Visualization tools
    14 Functional, Network & Pathway Analysis Tools
    15 Further annotation tools for RNA-Seq data
    16 RNA-Seq Databases
    17 Webinars and Presentations
    18 References

 

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