Package: idr2d 1.21.0

Konstantin Krismer

idr2d: Irreproducible Discovery Rate for Genomic Interactions Data

A tool to measure reproducibility between genomic experiments that produce two-dimensional peaks (interactions between peaks), such as ChIA-PET, HiChIP, and HiC. idr2d is an extension of the original idr package, which is intended for (one-dimensional) ChIP-seq peaks.

Authors:Konstantin Krismer [aut, cre, cph], David Gifford [ths, cph]

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idr2d.pdf |idr2d.html✨
idr2d/json (API)
NEWS

# Install 'idr2d' in R:
install.packages('idr2d', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • chiapet - Example Genomic Interaction Data Set
  • chipseq - Example Genomic Peak Data Set
  • hic - Example Hi-C data set

On BioConductor:idr2d-1.21.0(bioc 3.21)idr2d-1.20.0(bioc 3.20)

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

dna3dstructuregeneregulationpeakdetectionepigeneticsfunctionalgenomicsclassificationhic

4.30 score 6 scripts 148 downloads 23 exports 61 dependencies

Last updated 25 days agofrom:43c8e8a346. Checks:OK: 4 WARNING: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winWARNINGOct 31 2024
R-4.5-linuxOKOct 31 2024
R-4.4-winWARNINGOct 31 2024
R-4.4-macOKOct 31 2024
R-4.3-winWARNINGOct 31 2024
R-4.3-macOKOct 31 2024

Exports:calculate_midpoint_distance1dcalculate_midpoint_distance2dcalculate_relative_overlap1dcalculate_relative_overlap2ddetermine_anchor_overlapdraw_hic_contact_mapdraw_idr_distribution_histogramdraw_rank_idr_scatterplotdraw_value_idr_scatterplotestablish_bijectionestablish_bijection1destablish_bijection2destablish_overlap1destablish_overlap2destimate_idrestimate_idr1destimate_idr2destimate_idr2d_hicparse_hic_pro_matrixparse_juicer_matrixpreprocessremove_nonstandard_chromosomes1dremove_nonstandard_chromosomes2d

Dependencies:askpassBiocGenericsclicolorspacecurldplyrfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtableherehttridrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeopensslpillarpkgconfigpngR6rappdirsRColorBrewerRcppRcppTOMLreticulaterlangrprojrootS4VectorsscalesstringistringrsystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

Identify reproducible genomic interactions from replicate ChIA-PET experiments

Konstantin Krismer

Rendered fromidr2d.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2020-03-28
Started: 2018-10-24

Identify reproducible genomic peaks from replicate ChIP-seq experiments

Konstantin Krismer

Rendered fromidr1d.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2020-03-28
Started: 2019-03-19

Readme and manuals

Help Manual

Help pageTopics
Distance between Midpoints of two Peakscalculate_midpoint_distance1d
Distance between Anchor Midpoints of two Interactionscalculate_midpoint_distance2d
Relative Anchor Overlap of two Peakscalculate_relative_overlap1d
Relative Anchor Overlap of two Interactionscalculate_relative_overlap2d
Example Genomic Interaction Data Setchiapet
Example Genomic Peak Data Setchipseq
Identifies Overlapping Anchorsdetermine_anchor_overlap
Create Hi-C contact mapdraw_hic_contact_map
Create histogram of IDR valuesdraw_idr_distribution_histogram
Create scatterplot of IDR valuesdraw_rank_idr_scatterplot
Create scatterplot of IDR valuesdraw_value_idr_scatterplot
Finds One-to-One Correspondence between Peaks or interactions from Replicate 1 and 2establish_bijection
Finds One-to-One Correspondence between Peaks from Replicate 1 and 2establish_bijection1d
Finds One-to-One Correspondence between Interactions from Replicate 1 and 2establish_bijection2d
Establish m:n Mapping Between Peaks from Replicate 1 and 2establish_overlap1d
Establish m:n mapping between interactions from replicate 1 and 2establish_overlap2d
Estimates IDR for Genomic Peaks or Genomic Interactionsestimate_idr
Estimates IDR for Genomic Peak Dataestimate_idr1d
Estimates IDR for Genomic Interaction Dataestimate_idr2d
Estimates IDR for Genomic Interactions measured by Hi-C experimentsestimate_idr2d_hic
Example Hi-C data sethic
Parse .matrix and .bed files from HiC-Pro for IDR2D analysisparse_hic_pro_matrix
Parse .hic files from Juicer for IDR2D analysisparse_juicer_matrix
Prepares Data for IDR Analysispreprocess
Removes Peaks on Non-standard Chromosomesremove_nonstandard_chromosomes1d
Removes Interactions on Non-standard Chromosomesremove_nonstandard_chromosomes2d