## ---- eval=FALSE---------------------------------------------------------
# install.packages("http://www.wisdom.weizmann.ac.il/~nettam/shaman/misha_3.4.3.tar.gz", repos=NULL) #Installs misha package from file
## ---- eval=FALSE---------------------------------------------------------
# source("https://bioconductor.org/biocLite.R")
# biocLite("Gviz")
## ---- eval=FALSE---------------------------------------------------------
# devtools::install_bitubucket("tanaylab/shaman", ref='default', vignette=TRUE)
# library(shaman)
## ---- eval=FALSE, warning=FALSE------------------------------------------
# shuffle_hic_track(track_db="db", obs_track_nm="obs", work_dir="work_dir")
## ---- eval=FALSE, warning=FALSE------------------------------------------
# score_hic_track(track_db="db", work_dir="work_dir", score_track_nm="score_track", obs_track_nms=c("obs"))
## ---- eval=FALSE, warning=FALSE------------------------------------------
# point_score = gextract("score_track", region, colnames="score")
# plot_map_score_with_annotations("hg19", point_score$points, region, misha_tracks=list("K56.k27ac", "rna-seq"), annotations=list("ctcf_pos", "ctcf_neg"), a_colors=c("#4572A7", "#AA4643"))
## ---- eval=FALSE, warning=FALSE------------------------------------------
# point_score = shuffle_and_score_hic_mat(obs_track_nms="obs", interval=interval, work_dir="work_dir")
## ---- eval=FALSE, warning=FALSE------------------------------------------
# plot_map_score_with_annotations("hg19", point_score$points, region, misha_tracks=list("K56.k27ac", "rna-seq"), annotations=list("ctcf_pos", "ctcf_neg"), a_colors=c("#4572A7", "#AA4643"))
## ---- eval=FALSE, warning=FALSE------------------------------------------
# grid = shaman_generate_feature_grid(feature1, feature2, obs_track, exp_track, range=25000, resolution=500)
# shaman_plot_feature_grid(grid, range=25000, grid_resolution=500, plot_resolution=1000)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.