Chippeakanno manual

Bioconductor version: The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. Starting , new functions have been added for biocViews: Annotation, ChIPSeq, ChIPchip, Software. The input of ChIPpeakAnno is a list of called peaks identified from ChIP-seq experiments. The peaks are represented by GRanges in ChIPpeakAnno. We implemented a conversion functions toGRanges to convert commonly used peak file formats, such as BED, GFF, or other user defined formats such as MACS (a popular peak calling program) output file to.  · The binding sites annotated with ChIPpeakAnno can be viewed easily as a table, a pie chart or plotted in histogram form, i.e., the distribution of Estimated Reading Time: 7 mins.

The binding sites annotated with ChIPpeakAnno can be viewed easily as a table, a pie chart or plotted in histogram form, i.e., the distribution of distances to the nearest genes for each set of peaks. 使用ChIPpeakAnno进行peak注释. 欢迎关注”生信修炼手册”! ChIPpeakAnno是一个bioconductor上的R包，针对peak calling之后的下游分析，提供了以下多种功能. 查找与peak区域最相邻的基因, 也支持自定义查找的特征，可以是exon,miRNA等. peak相邻基因的GO富集分析. conda install -c bioconda/label/cf bioconductor-chippeakanno Description The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users.

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