Showing 11 of total 11 results (show query)
bioc
pRoloc:A unifying bioinformatics framework for spatial proteomics
The pRoloc package implements machine learning and visualisation methods for the analysis and interogation of quantitiative mass spectrometry data to reliably infer protein sub-cellular localisation.
Maintained by Lisa Breckels. Last updated 3 days ago.
immunooncologyproteomicsmassspectrometryclassificationclusteringqualitycontrolbioconductorproteomics-dataspatial-proteomicsvisualisationopenblascpp
15 stars 10.31 score 101 scripts 2 dependentsbioc
splatter:Simple Simulation of Single-cell RNA Sequencing Data
Splatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented. Parameters can be estimated from real data and functions are provided for comparing real and simulated datasets.
Maintained by Luke Zappia. Last updated 4 months ago.
singlecellrnaseqtranscriptomicsgeneexpressionsequencingsoftwareimmunooncologybioconductorbioinformaticsscrna-seqsimulation
224 stars 9.92 score 424 scripts 1 dependents
sizespectrum
mizer:Dynamic Multi-Species Size Spectrum Modelling
A set of classes and methods to set up and run multi-species, trait based and community size spectrum ecological models, focused on the marine environment.
Maintained by Gustav Delius. Last updated 2 months ago.
ecosystem-modelfish-population-dynamicsfisheriesfisheries-managementmarine-ecosystempopulation-dynamicssimulationsize-structurespecies-interactionstransport-equationcpp
39 stars 9.41 score 207 scriptsbioc
SpatialFeatureExperiment:Integrating SpatialExperiment with Simple Features in sf
A new S4 class integrating Simple Features with the R package sf to bring geospatial data analysis methods based on vector data to spatial transcriptomics. Also implements management of spatial neighborhood graphs and geometric operations. This pakage builds upon SpatialExperiment and SingleCellExperiment, hence methods for these parent classes can still be used.
Maintained by Lambda Moses. Last updated 2 months ago.
datarepresentationtranscriptomicsspatial
49 stars 9.40 score 322 scripts 1 dependents
r-forge
fPortfolio:Rmetrics - Portfolio Selection and Optimization
A collection of functions to optimize portfolios and to analyze them from different points of view.
Maintained by Stefan Theussl. Last updated 10 days ago.
1 stars 6.65 score 179 scripts 2 dependentsbioc
xCell2:A Tool for Generic Cell Type Enrichment Analysis
xCell2 provides methods for cell type enrichment analysis using cell type signatures. It includes three main functions - 1. xCell2Train for training custom references objects from bulk or single-cell RNA-seq datasets. 2. xCell2Analysis for conducting the cell type enrichment analysis using the custom reference. 3. xCell2GetLineage for identifying dependencies between different cell types using ontology.
Maintained by Almog Angel. Last updated 11 days ago.
geneexpressiontranscriptomicsmicroarrayrnaseqsinglecelldifferentialexpressionimmunooncologygenesetenrichment
7 stars 6.24 score 15 scriptsbioc
NPARC:Non-parametric analysis of response curves for thermal proteome profiling experiments
Perform non-parametric analysis of response curves as described by Childs, Bach, Franken et al. (2019): Non-parametric analysis of thermal proteome profiles reveals novel drug-binding proteins.
Maintained by Nils Kurzawa. Last updated 5 months ago.
5.35 score 37 scripts
magnusdv
pedmut:Mutation Models for Pedigree Likelihood Computations
A collection of functions for modelling mutations in pedigrees with marker data, as used e.g. in likelihood computations with microsatellite data. Implemented models include equal, proportional and stepwise models, as well as random models for experimental work, and custom models allowing the user to apply any valid mutation matrix. Allele lumping is done following the lumpability criteria of Kemeny and Snell (1976), ISBN:0387901922.
Maintained by Magnus Dehli Vigeland. Last updated 2 days ago.
2 stars 4.76 score 5 scripts 19 dependentsbioc
flowBeads:flowBeads: Analysis of flow bead data
This package extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalisation.
Maintained by Nikolas Pontikos. Last updated 5 months ago.
immunooncologyinfrastructureflowcytometrycellbasedassays
4.00 score 7 scripts
jamescbell
gestate:Generalised Survival Trial Assessment Tool Environment
Provides tools to assist planning and monitoring of time-to-event trials under complicated censoring assumptions and/or non-proportional hazards. There are three main components: The first is analytic calculation of predicted time-to-event trial properties, providing estimates of expected hazard ratio, event numbers and power under different analysis methods. The second is simulation, allowing stochastic estimation of these same properties. Thirdly, it provides parametric event prediction using blinded trial data, including creation of prediction intervals. Methods are based upon numerical integration and a flexible object-orientated structure for defining event, censoring and recruitment distributions (Curves).
Maintained by James Bell. Last updated 2 years ago.
2 stars 2.60 score 8 scripts
jmcurran
tfer:Forensic Glass Transfer Probabilities
Statistical interpretation of forensic glass transfer (Simulation of the probability distribution of recovered glass fragments).
Maintained by James Curran. Last updated 5 years ago.
1.15 score 14 scripts