Package: ijAnalysis 0.0.4

ijAnalysis: Miscellaneous tools for image analysis tasks

A miscellaneous toolbox for various image analysis tasks. Initially contains tools for downstream analysis of my ImageJ plugin Puncta Tracker and hence the ij name. Part of the y3628 analysis suite.

Authors:Ye Yuan [aut, cre]

ijAnalysis_0.0.4.tar.gz
ijAnalysis_0.0.4.zip(r-4.5)ijAnalysis_0.0.4.zip(r-4.4)ijAnalysis_0.0.4.zip(r-4.3)
ijAnalysis_0.0.4.tgz(r-4.5-any)ijAnalysis_0.0.4.tgz(r-4.4-any)ijAnalysis_0.0.4.tgz(r-4.3-any)
ijAnalysis_0.0.4.tar.gz(r-4.5-noble)ijAnalysis_0.0.4.tar.gz(r-4.4-noble)
ijAnalysis_0.0.4.tgz(r-4.4-emscripten)ijAnalysis_0.0.4.tgz(r-4.3-emscripten)
ijAnalysis.pdf |ijAnalysis.html✨
ijAnalysis/json (API)

# Install 'ijAnalysis' in R:
install.packages('ijAnalysis', repos = c('https://yeyuan98.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/yeyuan98/ijanalysis/issues

On CRAN:

Conda:

2.85 score 1 scripts 21 exports 61 dependencies

Last updated 27 days agofrom:836b5a86a9. Checks:8 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 13 2025
R-4.5-winOKFeb 13 2025
R-4.5-macOKFeb 13 2025
R-4.5-linuxOKFeb 13 2025
R-4.4-winOKFeb 13 2025
R-4.4-macOKFeb 13 2025
R-4.3-winOKFeb 13 2025
R-4.3-macOKFeb 13 2025

Exports:actogram_loadFromMetadataactogram_plotctcf_plotctcf_read_csvij_nnd.computeij_RoiPointsSaverjtk.initjtkdistjtkgetjtkxnlsGroupperiodogram_loadClocklabplot_ggsaverfish_countrfish_read_dotsrfish_read_samplesspotInRoi_addMetaspotInRoi_as.data.frame.df.nndspotInRoi_nnd.sortspotInRoi_read_csvspotInRoi_selectNCT

Dependencies:behavrbitbit64cellrangerclicliprcolorspacecpp11crayondamrdata.tabledplyrfansifarvergenericsggethoggplot2gluegtableherehmsisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppRcppTOMLreadrreadxlrematchreticulaterlangrprojrootscalesstringistringrtibbletidyselecttzdbutf8vctrsviridisLitevroomwithry3628

spotInRoi

Rendered fromspotInRoi.Rmdusingknitr::rmarkdownon Feb 13 2025.

Last update: 2024-09-10
Started: 2024-08-29

Readme and manuals

Help Manual

Help pageTopics
Parse spot array JSON data to metaRcrd..parse_meta
Get index for spotInRoi nuclear/full-cell data subsetting..selectNCT.index
Load behavior activity data from metadataactogram_loadFromMetadata
Plotting actogramactogram_plot
Load behavior metadatabehavior_loadMetadata
Standardized plotting of CTCF datactcf_plot
Read CTCF results tablectcf_read_csv
Compute NND metrics for a pair of spot sets.ij_nnd.compute
Initialize an ImageJ ROI point set saver functionij_RoiPointsSaver
JTK Cycle V3.1 Adaptation 'jtk.init'jtk.init
JTK Cycle V3.1 Adaptation 'jtkdist'jtkdist
JTK Cycle V3.1 Adaptationjtkget
JTK Cycle V3.1 Adaptation 'jtkstat'jtkstat
JTK Cycle V3.1 Adaptation 'jtkx'jtkx
'nls()' fitting of multiple groupsnlsGroup
Order permutation for a NND result recordnnd.order
Load Clocklab periodogram batch export tableperiodogram_loadClocklab
Simple wrapper of ggsave for saving plots.plot_ggsave
Boxplot with data points, viridis_d color filledplot.boxPoint
Count number of dots per cellrfish_count
Read dots table from snakemake pipeline outputrfish_read_dots
Read samples table from snakemake pipeline outputrfish_read_samples
Add metadata column to spotInRoi dataspotInRoi_addMeta
Expand NND results as data frame entriesspotInRoi_as.data.frame.df.nnd
Join spotInRoi data with metadata columnsspotInRoi_joinMeta
Sort spotInRoi data based on NND resultsspotInRoi_nnd.sort
Read data for spotInRoi analysis of the Puncta Tracker ImageJ plugin.spotInRoi_read_csv
Predefined subsetting of spotInRoi nuclear/full-cell data.spotInRoi_selectNCT
Simple subset of 'behavr::behavr' behavior tablessubset_behavr