Introduction | Motivation | Quick start | Installation | Load library | Initial the database | Start shiny app | Create a new data | by administrator | via R session | Add downloadable file | Distribute to a shiny server | SessionInfo | References

Introduction | Installation | Quick start | SessionInfo

Introduction | Installation | Quick start | SessionInfo

Introduction | Quick start | Installation | Load library | Details about vennCount | Plot for overlapping peaks output by ChIPpeakAnno | GLEAM test | Session Info

Introduction | Installation | Quick start | Prepare the inputs | Generate the 3D coordinates from contact matrix | Add gene informations | Add additional signals along the strand | view the data by rgl | view the genomic interaction data | Plot chromatin interactions data as loopBouquet or MDS plot | Plot single cells in 3d | Advanced usage of threeJsViewer | layout | Create objects from raw | Session Info

Introduction | Installation | Step 1, prepare target enhancer sequences. | Step 2, download candidate regions of enhancers from ENCODE by H3K4me1 marks | Step 3, get alignment score for target enhancer and candidate enhancers. | Step 4, filter the candidate regions. | Step 5, alignment for the enhancer and the orthologs | Step 6a, for quick evolution enhancers, check the conserved motifs in the orthologs | Step 6b, for slow evolution enhancers, export the multiple alignments in order. | Session info

Introduction | Motivation | Quick start | Installation | Load library | Prepare binding sites | TFEA | View results | Do TFEA step by step. | Counting reads | Filter the counts | Normalize the counts by width of count region | Get weighted binding scores | Differential analysis | Filter the DB results | TF enrichment analysis | SessionInfo | References

Introduction | Installation | Quick start | Session Info

Introduction | Safe colorsets | Color vision deficiency (CVD) simulator | How to use this package | Use safe color to plot | replace the color of a plot to safe color | Best approach to make figures | Collection of safe colors | replacePlotColor effect for Ishihara Color Test. | Session Info | References