Package: shaman 2.1.1.9000

Aviezer Lifshitz

shaman: Sampling Hi-C Contact Matrices for Aparametric Normalization

Generate expected Hi-C (genome-wide chromosome conformation capture) data maintaining marginal coverage, and the decay in contact probability with increasing genomic distance. Expected Hi-C data is used for normalization and graphical presentation of statistical significance of observed Hi-C contact enrichments. The method is described in Mendelson Cohen et al. (2017) <doi:10.1101/187203>.

Authors:Amos Tanay [aut], Netta Mendelson Cohen [aut], Aviezer Lifshitz [aut, cre], Weizmann Institute of Science [cph]

shaman_2.1.1.9000.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
shaman/json (API)

# Install 'shaman' in R:
install.packages('shaman', repos = c('https://tanaylab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/tanaylab/shaman/issues

Pkgdown/docs site:https://tanaylab.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • ctcf_forward - Human CTCF motifs found on forward strand on hg19 genome
  • ctcf_reverse - Human CTCF motifs found on reverse strand on hg19 genome

On CRAN:

Conda:

hi-cmishacpp

5.77 score 6 stars 49 scripts 10 downloads 16 exports 30 dependencies

Last updated from:20d2041c9b. Checks:15 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK202
linux-devel-x86_64OK232
source / vignettesOK232
linux-release-arm64OK189
linux-release-x86_64OK240
macos-release-arm64OK170
macos-release-x86_64OK329
macos-oldrel-arm64OK189
macos-oldrel-x86_64OK291
windows-devel-arm64OK269
windows-devel-x86_64OK106
windows-release-arm64OK188
windows-release-x86_64OK96
windows-oldrel-x86_64OK101
wasm-releaseOK125

Exports:shaman_generate_feature_gridshaman_get_test_track_dbshaman_gplot_mapshaman_gplot_map_scoreshaman_kk_normshaman_plot_feature_gridshaman_plot_map_score_with_annotationsshaman_plot_tracks_and_annotationsshaman_score_hic_matshaman_score_hic_mat_for_trackshaman_score_hic_pointsshaman_score_hic_trackshaman_score_palshaman_shuffle_and_score_hic_matshaman_shuffle_hic_mat_for_trackshaman_shuffle_hic_track

Dependencies:clicpp11curldata.tabledigestfarverggplot2gluegtableisobandlabelinglifecyclemagrittrmishaplyrpsR6RANNRColorBrewerRcppreshape2rlangS7scalesstringistringrvctrsviridisLitewithryaml

Import
Create misha database from ucsc | hg19 | hg38 | mm9 | mm10 | Import HiC observed contacts
Rendered fromimport.Rmdusingknitr::rmarkdown

Last update: 2026-10-06
Started: 2017-08-28

The shaman package - Sampling HiC contAct Matrices for Aparametric Normalization
Workflow | Distributed mode | Local mode | Analysis | Spatial contact enrichment - used to measure contact enrichment between two sets of genomic features. | Options | System parameters | Visualization parameters
Rendered fromshaman-package.Rmdusingknitr::rmarkdown

Last update: 2026-10-06
Started: 2016-08-02

Readme and manuals

Help Manual

Help pageTopics
Human CTCF motifs found on forward strand on hg19 genomectcf_forward
Human CTCF motifs found on reverse strand on hg19 genomectcf_reverse
Get params from saved varget_param
Get params from saved varget_param_list
Read params from filesinit_params
Calculate spatial enrichment of contacts between two featuresshaman_generate_feature_grid
Returns the example misha databaseshaman_get_test_track_db
Plot an observed or expected hic mapshaman_gplot_map
Plot a normalized hic mapshaman_gplot_map_score
Compute a score matrix for observed data based on the expected for a given set of pointsshaman_kk_norm
Plot spatial enrichment of contacts between two featuresshaman_plot_feature_grid
Plot a normalized hic map with annotationsshaman_plot_map_score_with_annotations
Plot misha 1D tracks and annotationsshaman_plot_tracks_and_annotations
Generate a score matrix for observed data based on the expected for a given 2D focus intervalshaman_score_hic_mat
Generate a score matrix for observed data based on the expectedshaman_score_hic_mat_for_track
Generate a score matrix for observed data based on the expected for a given set of pointsshaman_score_hic_points
Generate a score hic track based on observed and expected (shuffled) hic datashaman_score_hic_track
Returns the color palette used to display normalized scoresshaman_score_pal
Inline function for generating an expected matrix and computing the score for a given intervalshaman_shuffle_and_score_hic_mat
Generate an expected matrix from observed data as a process for generating an expected trackshaman_shuffle_hic_mat_for_track
Generate an expected hic track based on observed hic datashaman_shuffle_hic_track