Perl 5 and R source codes for next generation (the second generation) sequencing data analysis by integrating lots of open-source softwares.
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CISDA: ChIP-Seq Data Analyzer (also contains MNase-Seq, DNase-Seq, ChIP-exo and all ChIPseq-like data). -
starCISDA: small-scale TELP-assisted rapid ChIP-Seq Data Analyzer. -
BSDA: Bisulfite Sequencing (BS-Seq) Data Analyzer (such as RRBS, MethylC-seq, PBAT and Single-cell BS-seq data). -
MeDIP: MeDIP-seq and hMeDIP-seq Data Analyzer. -
RASDA: RNA-Seq Data Analyzer. -
small_RASDA: small or micro RNA-seq Data Analyzer. -
long_RASDA: long non-coding RNA-seq Data Analyzer. -
HISDA: Hi-C Data Analyzer.
To use all the above pipelines, the recent versions of some softwares and packages must be available in your Linux OS:
https://github.com/CTLife/Top10
The required softwares and packages of each script are also available in its help message.