Package: Bioi 0.2.10

Bioi: Biological Image Analysis

Single linkage clustering and connected component analyses are often performed on biological images. 'Bioi' provides a set of functions for performing these tasks. This functionality is implemented in several key functions that can extend to from 1 to many dimensions. The single linkage clustering method implemented here can be used on n-dimensional data sets, while connected component analyses are limited to 3 or fewer dimensions.

Authors:Zachary Colburn

Bioi_0.2.10.tar.gz
Bioi_0.2.10.zip(r-4.7-x86_64)Bioi_0.2.10.zip(r-4.7-arm64)Bioi_0.2.10.zip(r-4.6-x86_64)Bioi_0.2.10.zip(r-4.6-arm64)Bioi_0.2.10.zip(r-4.5-x86_64)
Bioi_0.2.10.tgz(r-4.6-x86_64)Bioi_0.2.10.tgz(r-4.6-arm64)Bioi_0.2.10.tgz(r-4.5-x86_64)Bioi_0.2.10.tgz(r-4.5-arm64)
Bioi_0.2.10.tar.gz(r-4.7-arm64)Bioi_0.2.10.tar.gz(r-4.7-x86_64)Bioi_0.2.10.tar.gz(r-4.6-arm64)Bioi_0.2.10.tar.gz(r-4.6-x86_64)
Bioi_0.2.10.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Bioi/json (API)

# Install 'Bioi' in R:

install.packages('Bioi', repos = c('https://zcolburn.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/zcolburn/bioi/issues

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

biological-data-analysis biology cell cpp image-analysis microscopy cpp

3.70 score 9 scripts 402 downloads 6 exports 21 dependencies

Last updated from:31137ab2a3. Checks:4 NOTE, 11 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	NOTE	116
linux-devel-x86_64	NOTE	129
source / vignettes	OK	203
linux-release-arm64	OK	107
linux-release-x86_64	OK	129
macos-release-arm64	OK	139
macos-release-x86_64	OK	239
macos-oldrel-arm64	OK	110
macos-oldrel-x86_64	OK	377
windows-devel-arm64	NOTE	342
windows-devel-x86_64	NOTE	126
windows-release-arm64	OK	355
windows-release-x86_64	OK	92
windows-oldrel-x86_64	OK	98
wasm-release	OK	104

Exports:.perform_grouping .perform_partitioning euclidean_linker find_blobs find_min_dists identify_thresholded_objects

Dependencies:assertthat cli cpp11 dplyr generics glue igraph lattice lifecycle magrittr Matrix pillar pkgconfig R6 Rcpp rlang tibble tidyselect utf8 vctrs withr

Bioi

Determine the minimum separation distance between two sets of points | Single linkage clustering | Label connected components (i.e. find contiguous blobs)

Rendered fromBioi.Rmdusingknitr::rmarkdown

Last update: 2018-01-15
Started: 2017-12-31

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Return the group number for each localization.	.euclidean_linker_cpp
For all points in matrix 1, return the distance to and index of the nearest point in matrix 2.	.find_min_dists_cpp
Return the group number for each localization.	.perform_grouping
Return the group number for each localization.	.perform_partitioning
'Bioi' package	Bioi
Return the group number for each localization.	euclidean_linker
Assign all neighboring pixels the same group number.	find_blobs
For all points in matrix 1, return the distance to and index of the nearest point in matrix 2.	find_min_dists
Assign all neighboring pixels the same group number.	identify_thresholded_objects