Showing 7 of total 7 results (show query)
bioc
imcRtools:Methods for imaging mass cytometry data analysis
This R package supports the handling and analysis of imaging mass cytometry and other highly multiplexed imaging data. The main functionality includes reading in single-cell data after image segmentation and measurement, data formatting to perform channel spillover correction and a number of spatial analysis approaches. First, cell-cell interactions are detected via spatial graph construction; these graphs can be visualized with cells representing nodes and interactions representing edges. Furthermore, per cell, its direct neighbours are summarized to allow spatial clustering. Per image/grouping level, interactions between types of cells are counted, averaged and compared against random permutations. In that way, types of cells that interact more (attraction) or less (avoidance) frequently than expected by chance are detected.
Maintained by Daniel Schulz. Last updated 5 months ago.
immunooncologysinglecellspatialdataimportclusteringimcsingle-cell
24 stars 7.58 score 126 scripts
predictiveecology
LandR:Landscape Ecosystem Modelling in R
Utilities for 'LandR' suite of landscape simulation models. These models simulate forest vegetation dynamics based on LANDIS-II, and incorporate fire and insect disturbance, as well as other important ecological processes. Models are implemented as 'SpaDES' modules.
Maintained by Eliot J B McIntire. Last updated 4 days ago.
ecological-modellinglandscape-ecosystem-modellingspades
17 stars 6.09 score 12 scripts 4 dependentsbioc
SpaNorm:Spatially-aware normalisation for spatial transcriptomics data
This package implements the spatially aware library size normalisation algorithm, SpaNorm. SpaNorm normalises out library size effects while retaining biology through the modelling of smooth functions for each effect. Normalisation is performed in a gene- and cell-/spot- specific manner, yielding library size adjusted data.
Maintained by Dharmesh D. Bhuva. Last updated 5 months ago.
softwaregeneexpressiontranscriptomicsspatialcellbiology
9 stars 5.86 score 3 scriptsbioc
scider:Spatial cell-type inter-correlation by density in R
scider is a user-friendly R package providing functions to model the global density of cells in a slide of spatial transcriptomics data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. After modelling density, the package allows for serveral downstream analysis, including colocalization analysis, boundary detection analysis and differential density analysis.
Maintained by Yunshun Chen. Last updated 5 months ago.
3 stars 5.08 score 3 scripts
gianlucafilippa
phenopix:Process Digital Images of a Vegetation Cover
A collection of functions to process digital images, depict greenness index trajectories and extract relevant phenological stages.
Maintained by Gianluca Filippa. Last updated 2 months ago.
5 stars 2.52 score 66 scripts
ajpete
scalpel:Processes Calcium Imaging Data
Identifies the locations of neurons, and estimates their calcium concentrations over time using the SCALPEL method proposed in Petersen, Ashley; Simon, Noah; Witten, Daniela. SCALPEL: Extracting neurons from calcium imaging data. Ann. Appl. Stat. 12 (2018), no. 4, 2430--2456. <doi:10.1214/18-AOAS1159>. <https://projecteuclid.org/euclid.aoas/1542078051>.
Maintained by Ashley Petersen. Last updated 4 years ago.
2.20 score 32 scripts
ifpri
STATEROOM:SpaTiAl resulTs gEneRatOr fOr iMpact (STATEROOM)
Spatial results generator for IMPACT.
Maintained by Abhijeet Mishra. Last updated 2 years ago.
1.00 score