Package: idr2d 1.26.0

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]

idr2d_1.26.0.tar.gz
idr2d_1.26.0.zip(r-4.7-any)idr2d_1.26.0.zip(r-4.6-any)idr2d_1.26.0.zip(r-4.5-any)
idr2d_1.26.0.tgz(r-4.6-any)idr2d_1.26.0.tgz(r-4.5-any)
idr2d_1.26.0.tar.gz(r-4.7-any)idr2d_1.26.0.tar.gz(r-4.6-any)
idr2d_1.26.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
idr2d/json (API)

# Install 'idr2d' in R:
install.packages('idr2d', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • chiapet - Example Genomic Interaction Data Set
  • chipseq - Example Genomic Peak Data Set
  • hic - Example Hi-C data set

On BioConductor:idr2d-1.27.0(bioc 3.24)idr2d-1.26.0(bioc 3.23)

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

dna3dstructuregeneregulationpeakdetectionepigeneticsfunctionalgenomicsclassificationhic

4.48 score 8 scripts 384 downloads 23 exports 55 dependencies

Last updated from:22eae8a266 (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE177
linux-devel-x86_64OK328
source / vignettesOK253
linux-release-x86_64OK323
macos-release-arm64OK148
macos-oldrel-arm64OK155
windows-develOK249
windows-releaseOK262
windows-oldrelOK258
wasm-releaseOK130

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:askpassBiocGenericsclicpp11curldplyrfarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicRangesggplot2gluegtableherehttridrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMatrixmimeopensslpillarpkgconfigpngR6rappdirsRColorBrewerRcppRcppTOMLreticulaterlangrprojrootS4VectorsS7scalesSeqinfostringistringrsystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithr

Identify reproducible genomic interactions from replicate ChIA-PET experiments
Input data | Example data - replicate 1 | Example data - replicate 2 | Analysis | Results | Summary | Distribution of IDRs | Rank - IDR dependence | Value - IDR dependence | Additional information | References
Rendered fromidr2d.Rmdusingknitr::rmarkdown

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

Identify reproducible genomic peaks from replicate ChIP-seq experiments
Input data | Example data - replicate 1 | Example data - replicate 2 | Analysis | Results | Summary | Distribution of IDRs | Rank - IDR dependence | Value - IDR dependence | Additional information | References
Rendered fromidr1d.Rmdusingknitr::rmarkdown

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