Package: HiCBricks 1.25.0

Koustav Pal

HiCBricks: Framework for Storing and Accessing Hi-C Data Through HDF Files

HiCBricks is a library designed for handling large high-resolution Hi-C datasets. Over the years, the Hi-C field has experienced a rapid increase in the size and complexity of datasets. HiCBricks is meant to overcome the challenges related to the analysis of such large datasets within the R environment. HiCBricks offers user-friendly and efficient solutions for handling large high-resolution Hi-C datasets. The package provides an R/Bioconductor framework with the bricks to build more complex data analysis pipelines and algorithms. HiCBricks already incorporates example algorithms for calling domain boundaries and functions for high quality data visualization.

Authors:Koustav Pal [aut, cre], Carmen Livi [ctb], Ilario Tagliaferri [ctb]

HiCBricks_1.25.0.tar.gz
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HiCBricks.pdf |HiCBricks.html✨
HiCBricks/json (API)
NEWS

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

Peer review:

On BioConductor:HiCBricks-1.25.0(bioc 3.21)HiCBricks-1.24.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

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4.48 score 1 packages 9 scripts 278 downloads 1 mentions 49 exports 80 dependencies

Last updated 2 months agofrom:51b1cc8712. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winOKNov 29 2024
R-4.5-linuxOKNov 29 2024
R-4.4-winOKNov 29 2024
R-4.4-macOKNov 29 2024
R-4.3-winOKNov 29 2024
R-4.3-macOKNov 29 2024

Exports:Brick_add_rangesBrick_call_compartmentsBrick_export_to_sparseBrick_fetch_range_indexBrick_fetch_row_vectorBrick_get_bintableBrick_get_chrominfoBrick_get_entire_matrixBrick_get_matrixBrick_get_matrix_mcolsBrick_get_matrix_within_coordsBrick_get_rangesBrick_get_values_by_distanceBrick_get_vector_valuesBrick_list_matricesBrick_list_matrix_mcolsBrick_list_mcool_normalisationsBrick_list_mcool_resolutionsBrick_list_rangekeysBrick_list_ranges_mcolsBrick_load_cis_matrix_till_distanceBrick_load_data_from_mcoolBrick_load_data_from_sparseBrick_load_matrixBrick_local_score_differentiatorBrick_make_rangesBrick_matrix_dimensionsBrick_matrix_existsBrick_matrix_filenameBrick_matrix_isdoneBrick_matrix_issparseBrick_matrix_maxdistBrick_matrix_minmaxBrick_mcool_normalisation_existsBrick_rangekey_existsBrick_return_region_positionBrick_vizart_plot_heatmapBrickContainer_change_experiment_nameBrickContainer_change_output_directoryBrickContainer_get_path_to_fileBrickContainer_list_chromosomesBrickContainer_list_experiment_nameBrickContainer_list_filesBrickContainer_list_output_directoryBrickContainer_list_resolutionsBrickContainer_unlink_resolutionCreate_many_BricksCreate_many_Bricks_from_mcoolload_BrickContainer

Dependencies:askpassBHBiocGenericsBiocParallelbitbit64clicliprcodetoolscolorspacecpp11crayoncurldata.tabledigestfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegridExtragtablehmshttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeopensslpillarpkgconfigplyrprettyunitsprogressR.methodsS3R.ooR.utilsR6RColorBrewerRcppreadrreshape2rhdf5rhdf5filtersRhdf5librlangS4VectorsscalessnowstringistringrsystibbletidyselecttzdbUCSC.utilsutf8vctrsviridisviridisLitevroomwithrXVectorzlibbioc

Introduction To HiCBricks

Koustav Pal, Ilario Tagliaferri, Carmen Maria Livi

Rendered fromIntroductionToHiCBricks.rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2020-02-25
Started: 2019-02-03

Readme and manuals

Help Manual

Help pageTopics
Store a ranges object in the Brick store.Brick_add_ranges
Identify compartments in the Hi-C dataBrick_call_compartments
Export an entire resolution from a given BrickContainer as a upper triangle sparse matrixBrick_export_to_sparse
Returns the position of the supplied ranges in the binning table associated to the Hi-C experiment.Brick_fetch_range_index
Return row or col vectors.Brick_fetch_row_vector
Returns the binning table associated to the Hi-C experiment.Brick_get_bintable
Get the chrominfo for the Hi-C experiment.Brick_get_chrominfo
Return an entire matrix for provided chromosome pair for a resolution.Brick_get_entire_matrix
Return a matrix subset.Brick_get_matrix
Get the matrix metadata columns in the Brick store.Brick_get_matrix_mcols
Return a matrix subset between two regions.Brick_get_matrix_within_coords
Fetch the ranges associated to a rangekey or chromosome.Brick_get_ranges
Return values separated by a certain distance.Brick_get_values_by_distance
Return a N dimensional vector selection.Brick_get_vector_values
List the matrix pairs present in the Brick store.Brick_list_matrices
List the matrix metadata columns in the Brick store.Brick_list_matrix_mcols
Get all available normalisations in an mcool file.Brick_list_mcool_normalisations
Get all available normalisations in an mcool file.Brick_list_mcool_resolutions
List the ranges tables stored within the Brick.Brick_list_rangekeys
Find out what metadata columns are associated to a ranges with a certain nameBrick_list_ranges_mcols
Load a NxN dimensional sub-distance _cis_ matrix into the Brick store.Brick_load_cis_matrix_till_distance
Load a NxN dimensional matrix into the Brick store from an mcool file.Brick_load_data_from_mcool
Identify compartments in the Hi-C dataBrick_load_data_from_sparse
Load a NxM dimensional matrix into the Brick store.Brick_load_matrix
Do TAD Calls with Local Score Differentiator on a Hi-C matrixBrick_local_score_differentiator
Creates a ranges object from provided vectors.Brick_make_ranges
Return the dimensions of a matrixBrick_matrix_dimensions
Check if a chromosome pair exists.Brick_matrix_exists
Return the filename of the loaded matrixBrick_matrix_filename
Check if a matrix has been loaded for a chromosome pair.Brick_matrix_isdone
Check if a matrix for a chromosome pair is sparse.Brick_matrix_issparse
Get the maximum loaded distance from the diagonal of any matrix.Brick_matrix_maxdist
Return the value range of the matrixBrick_matrix_minmax
Check if a normalisation exists in an mcool file.Brick_mcool_normalisation_exists
Check to see if the Brick contains a ranges with a certain name.Brick_rangekey_exists
Provides the overlapping position (within) from the bintable.Brick_return_region_position
Create the entire HDF5 structure and load the bintableBrick_vizart_plot_heatmap
Change the location of HDF files in the BrickContainer objectBrickContainer_change_experiment_name
Change the location of HDF files in the BrickContainer objectBrickContainer_change_output_directory
Get the path to HDF files present in the Brick container.BrickContainer_get_path_to_file
Return the descriptive name of the BrickContainerBrickContainer_list_chromosomes
Return the descriptive name of the BrickContainerBrickContainer_list_experiment_name
Get the list of HDF files present in the Brick container.BrickContainer_list_files
Return the output directory of the BrickContainerBrickContainer_list_output_directory
Return the descriptive name of the BrickContainerBrickContainer_list_resolutions
Remove links to all Hi-C matrices for a given resolution.BrickContainer_unlink_resolution
Create the entire HDF5 structure and load the bintableCreate_many_Bricks
Create the entire HDF5 structure and load the bintable from a mcool fileCreate_many_Bricks_from_mcool
A package for storing, accessing and plotting Hi-C dataHiCBricks
Create a BrickContainer object from a JSON fileload_BrickContainer