Showing 33 of total 33 results (show query)
amices
mice:Multivariate Imputation by Chained Equations
Multiple imputation using Fully Conditional Specification (FCS) implemented by the MICE algorithm as described in Van Buuren and Groothuis-Oudshoorn (2011) <doi:10.18637/jss.v045.i03>. Each variable has its own imputation model. Built-in imputation models are provided for continuous data (predictive mean matching, normal), binary data (logistic regression), unordered categorical data (polytomous logistic regression) and ordered categorical data (proportional odds). MICE can also impute continuous two-level data (normal model, pan, second-level variables). Passive imputation can be used to maintain consistency between variables. Various diagnostic plots are available to inspect the quality of the imputations.
Maintained by Stef van Buuren. Last updated 5 days ago.
chained-equationsfcsimputationmicemissing-datamissing-valuesmultiple-imputationmultivariate-datacpp
11.5 match 462 stars 16.50 score 10k scripts 154 dependents
bioc
flowCore:flowCore: Basic structures for flow cytometry data
Provides S4 data structures and basic functions to deal with flow cytometry data.
Maintained by Mike Jiang. Last updated 5 months ago.
immunooncologyinfrastructureflowcytometrycellbasedassayscpp
17.9 match 10.34 score 1.7k scripts 59 dependentsbioc
tidytof:Analyze High-dimensional Cytometry Data Using Tidy Data Principles
This package implements an interactive, scientific analysis pipeline for high-dimensional cytometry data built using tidy data principles. It is specifically designed to play well with both the tidyverse and Bioconductor software ecosystems, with functionality for reading/writing data files, data cleaning, preprocessing, clustering, visualization, modeling, and other quality-of-life functions. tidytof implements a "grammar" of high-dimensional cytometry data analysis.
Maintained by Timothy Keyes. Last updated 5 months ago.
singlecellflowcytometrybioinformaticscytometrydata-sciencesingle-celltidyversecpp
9.4 match 19 stars 7.26 score 35 scriptsbioc
flowWorkspace:Infrastructure for representing and interacting with gated and ungated cytometry data sets.
This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.
Maintained by Greg Finak. Last updated 8 days ago.
immunooncologyflowcytometrydataimportpreprocessingdatarepresentationzlibopenblascpp
5.3 match 7.89 score 576 scripts 10 dependentsbioc
FlowSOM:Using self-organizing maps for visualization and interpretation of cytometry data
FlowSOM offers visualization options for cytometry data, by using Self-Organizing Map clustering and Minimal Spanning Trees.
Maintained by Sofie Van Gassen. Last updated 5 months ago.
cellbiologyflowcytometryclusteringvisualizationsoftwarecellbasedassays
5.4 match 7.71 score 468 scripts 10 dependentsbioc
MetaCyto:MetaCyto: A package for meta-analysis of cytometry data
This package provides functions for preprocessing, automated gating and meta-analysis of cytometry data. It also provides functions that facilitate the collection of cytometry data from the ImmPort database.
Maintained by Zicheng Hu. Last updated 5 months ago.
immunooncologycellbiologyflowcytometryclusteringstatisticalmethodsoftwarecellbasedassayspreprocessing
8.7 match 4.73 score 18 scriptsbioc
flowFP:Fingerprinting for Flow Cytometry
Fingerprint generation of flow cytometry data, used to facilitate the application of machine learning and datamining tools for flow cytometry.
Maintained by Herb Holyst. Last updated 5 months ago.
flowcytometrycellbasedassaysclusteringvisualization
8.0 match 4.72 score 11 scripts 2 dependentsbioc
CytoPipeline:Automation and visualization of flow cytometry data analysis pipelines
This package provides support for automation and visualization of flow cytometry data analysis pipelines. In the current state, the package focuses on the preprocessing and quality control part. The framework is based on two main S4 classes, i.e. CytoPipeline and CytoProcessingStep. The pipeline steps are linked to corresponding R functions - that are either provided in the CytoPipeline package itself, or exported from a third party package, or coded by the user her/himself. The processing steps need to be specified centrally and explicitly using either a json input file or through step by step creation of a CytoPipeline object with dedicated methods. After having run the pipeline, obtained results at all steps can be retrieved and visualized thanks to file caching (the running facility uses a BiocFileCache implementation). The package provides also specific visualization tools like pipeline workflow summary display, and 1D/2D comparison plots of obtained flowFrames at various steps of the pipeline.
Maintained by Philippe Hauchamps. Last updated 5 months ago.
flowcytometrypreprocessingqualitycontrolworkflowstepimmunooncologysoftwarevisualization
5.5 match 4 stars 6.78 score 18 scripts 2 dependents
nutriverse
dietry:Utilities for Calculating Dietary Intake Indicators for Food Security Assessments
Food security assessments utilise several dietary intake indicators as proxy measures for diet quality, diet sufficiency, and food availability either at individual or household level. Utilities for recoding and calculating these indicators support in establishing consistent and reliable results.
Maintained by Ernest Guevarra. Last updated 3 months ago.
10.3 match 2 stars 3.48 score 3 scripts
gitdemont
IFC:Tools for Imaging Flow Cytometry
Contains several tools to treat imaging flow cytometry data from 'ImageStream®' and 'FlowSight®' cytometers ('Amnis®' 'Cytek®'). Provides an easy and simple way to read and write .fcs, .rif, .cif and .daf files. Information such as masks, features, regions and populations set within these files can be retrieved for each single cell. In addition, raw data such as images stored can also be accessed. Users, may hopefully increase their productivity thanks to dedicated functions to extract, visualize, manipulate and export 'IFC' data. Toy data example can be installed through the 'IFCdata' package of approximately 32 MB, which is available in a 'drat' repository <https://gitdemont.github.io/IFCdata/>. See file 'COPYRIGHTS' and file 'AUTHORS' for a list of copyright holders and authors.
Maintained by Yohann Demont. Last updated 8 days ago.
cytometrycytometry-dataflowflow-cytometryflow-cytometry-analysisflow-cytometry-dataflow-cytometry-filesifcimageimaging-flow-cytometryimaging-flow-cytometry-datamicroscopycpp
6.5 match 4 stars 5.34 score 12 scripts
jwb133
smcfcs:Multiple Imputation of Covariates by Substantive Model Compatible Fully Conditional Specification
Implements multiple imputation of missing covariates by Substantive Model Compatible Fully Conditional Specification. This is a modification of the popular FCS/chained equations multiple imputation approach, and allows imputation of missing covariate values from models which are compatible with the user specified substantive model.
Maintained by Jonathan Bartlett. Last updated 14 hours ago.
3.7 match 11 stars 9.00 score 59 scripts 1 dependentsbioc
flowCHIC:Analyze flow cytometric data using histogram information
A package to analyze flow cytometric data of complex microbial communities based on histogram images
Maintained by Author: Joachim Schumann. Last updated 5 months ago.
immunooncologycellbasedassaysclusteringflowcytometrysoftwarevisualization
8.6 match 3.78 score 1 scriptsbioc
CATALYST:Cytometry dATa anALYSis Tools
CATALYST provides tools for preprocessing of and differential discovery in cytometry data such as FACS, CyTOF, and IMC. Preprocessing includes i) normalization using bead standards, ii) single-cell deconvolution, and iii) bead-based compensation. For differential discovery, the package provides a number of convenient functions for data processing (e.g., clustering, dimension reduction), as well as a suite of visualizations for exploratory data analysis and exploration of results from differential abundance (DA) and state (DS) analysis in order to identify differences in composition and expression profiles at the subpopulation-level, respectively.
Maintained by Helena L. Crowell. Last updated 4 months ago.
clusteringdataimportdifferentialexpressionexperimentaldesignflowcytometryimmunooncologymassspectrometrynormalizationpreprocessingsinglecellsoftwarestatisticalmethodvisualization
2.7 match 67 stars 11.06 score 362 scripts 2 dependentsbioc
diffcyt:Differential discovery in high-dimensional cytometry via high-resolution clustering
Statistical methods for differential discovery analyses in high-dimensional cytometry data (including flow cytometry, mass cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on a combination of high-resolution clustering and empirical Bayes moderated tests adapted from transcriptomics.
Maintained by Lukas M. Weber. Last updated 1 months ago.
immunooncologyflowcytometryproteomicssinglecellcellbasedassayscellbiologyclusteringfeatureextractionsoftware
2.3 match 20 stars 9.98 score 225 scripts 5 dependentsbioc
distinct:distinct: a method for differential analyses via hierarchical permutation tests
distinct is a statistical method to perform differential testing between two or more groups of distributions; differential testing is performed via hierarchical non-parametric permutation tests on the cumulative distribution functions (cdfs) of each sample. While most methods for differential expression target differences in the mean abundance between conditions, distinct, by comparing full cdfs, identifies, both, differential patterns involving changes in the mean, as well as more subtle variations that do not involve the mean (e.g., unimodal vs. bi-modal distributions with the same mean). distinct is a general and flexible tool: due to its fully non-parametric nature, which makes no assumptions on how the data was generated, it can be applied to a variety of datasets. It is particularly suitable to perform differential state analyses on single cell data (i.e., differential analyses within sub-populations of cells), such as single cell RNA sequencing (scRNA-seq) and high-dimensional flow or mass cytometry (HDCyto) data. To use distinct one needs data from two or more groups of samples (i.e., experimental conditions), with at least 2 samples (i.e., biological replicates) per group.
Maintained by Simone Tiberi. Last updated 5 months ago.
geneticsrnaseqsequencingdifferentialexpressiongeneexpressionmultiplecomparisonsoftwaretranscriptionstatisticalmethodvisualizationsinglecellflowcytometrygenetargetopenblascpp
3.4 match 11 stars 6.35 score 34 scripts 1 dependentsbioc
scDataviz:scDataviz: single cell dataviz and downstream analyses
In the single cell World, which includes flow cytometry, mass cytometry, single-cell RNA-seq (scRNA-seq), and others, there is a need to improve data visualisation and to bring analysis capabilities to researchers even from non-technical backgrounds. scDataviz attempts to fit into this space, while also catering for advanced users. Additonally, due to the way that scDataviz is designed, which is based on SingleCellExperiment, it has a 'plug and play' feel, and immediately lends itself as flexibile and compatibile with studies that go beyond scDataviz. Finally, the graphics in scDataviz are generated via the ggplot engine, which means that users can 'add on' features to these with ease.
Maintained by Kevin Blighe. Last updated 5 months ago.
singlecellimmunooncologyrnaseqgeneexpressiontranscriptionflowcytometrymassspectrometrydataimport
2.9 match 63 stars 6.30 score 16 scriptsbioc
flowClean:flowClean
A quality control tool for flow cytometry data based on compositional data analysis.
Maintained by Kipper Fletez-Brant. Last updated 5 months ago.
flowcytometryqualitycontrolimmunooncology
4.0 match 4.56 score 18 scriptsbioc
MAPFX:MAssively Parallel Flow cytometry Xplorer (MAPFX): A Toolbox for Analysing Data from the Massively-Parallel Cytometry Experiments
MAPFX is an end-to-end toolbox that pre-processes the raw data from MPC experiments (e.g., BioLegend's LEGENDScreen and BD Lyoplates assays), and further imputes the ‘missing’ infinity markers in the wells without those measurements. The pipeline starts by performing background correction on raw intensities to remove the noise from electronic baseline restoration and fluorescence compensation by adapting a normal-exponential convolution model. Unwanted technical variation, from sources such as well effects, is then removed using a log-normal model with plate, column, and row factors, after which infinity markers are imputed using the informative backbone markers as predictors. The completed dataset can then be used for clustering and other statistical analyses. Additionally, MAPFX can be used to normalise data from FFC assays as well.
Maintained by Hsiao-Chi Liao. Last updated 5 months ago.
softwareflowcytometrycellbasedassayssinglecellproteomicsclustering
3.5 match 1 stars 4.54 score
cwwhitney
ethnobotanyR:Calculate Quantitative Ethnobotany Indices
An implementation of the quantitative ethnobotany indices in R. The goal is to provide an easy-to-use platform for ethnobotanists to assess the cultural significance of plant species based on informant consensus. The package closely follows the paper by Tardio and Pardo-de-Santayana (2008). Tardio, J., and M. Pardo-de-Santayana, 2008. Cultural Importance Indices: A Comparative Analysis Based on the Useful Wild Plants of Southern Cantabria (Northern Spain) 1. Economic Botany, 62(1), 24-39. <doi:10.1007/s12231-007-9004-5>.
Maintained by Cory Whitney. Last updated 22 days ago.
ethnobotanyindicesquantitative-methods
3.3 match 9 stars 4.30 score 22 scriptsbioc
ncdfFlow:ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
Provides HDF5 storage based methods and functions for manipulation of flow cytometry data.
Maintained by Mike Jiang. Last updated 2 months ago.
immunooncologyflowcytometryzlibcpp
1.9 match 7.56 score 96 scripts 11 dependentsbioc
CytoML:A GatingML Interface for Cross Platform Cytometry Data Sharing
Uses platform-specific implemenations of the GatingML2.0 standard to exchange gated cytometry data with other software platforms.
Maintained by Mike Jiang. Last updated 8 days ago.
immunooncologyflowcytometrydataimportdatarepresentationzlibopenblaslibxml2cpp
1.7 match 30 stars 7.60 score 132 scripts
ustervbo
beadplexr:Analysis of Multiplex Cytometric Bead Assays
Reproducible and automated analysis of multiplex bead assays such as CBA (Morgan et al. 2004; <doi: 10.1016/j.clim.2003.11.017>), LEGENDplex (Yu et al. 2015; <doi: 10.1084/jem.20142318>), and MACSPlex (Miltenyi Biotec 2014; Application note: Data acquisition and analysis without the MACSQuant analyzer; <https://www.miltenyibiotec.com/upload/assets/IM0021608.PDF>). The package provides functions for streamlined reading of fcs files, and identification of bead clusters and analyte expression. The package eases the calculation of standard curves and the subsequent calculation of the analyte concentration.
Maintained by Ulrik Stervbo. Last updated 2 years ago.
2.5 match 5.07 score 39 scriptsbioc
EnrichmentBrowser:Seamless navigation through combined results of set-based and network-based enrichment analysis
The EnrichmentBrowser package implements essential functionality for the enrichment analysis of gene expression data. The analysis combines the advantages of set-based and network-based enrichment analysis in order to derive high-confidence gene sets and biological pathways that are differentially regulated in the expression data under investigation. Besides, the package facilitates the visualization and exploration of such sets and pathways.
Maintained by Ludwig Geistlinger. Last updated 5 months ago.
immunooncologymicroarrayrnaseqgeneexpressiondifferentialexpressionpathwaysgraphandnetworknetworkgenesetenrichmentnetworkenrichmentvisualizationreportwriting
1.2 match 20 stars 9.37 score 164 scripts 3 dependentsbioc
flowAI:Automatic and interactive quality control for flow cytometry data
The package is able to perform an automatic or interactive quality control on FCS data acquired using flow cytometry instruments. By evaluating three different properties: 1) flow rate, 2) signal acquisition, 3) dynamic range, the quality control enables the detection and removal of anomalies.
Maintained by Gianni Monaco. Last updated 5 months ago.
flowcytometryqualitycontrolbiomedicalinformaticsimmunooncology
1.7 match 5.67 score 86 scripts 3 dependentsbioc
flowTime:Annotation and analysis of biological dynamical systems using flow cytometry
This package facilitates analysis of both timecourse and steady state flow cytometry experiments. This package was originially developed for quantifying the function of gene regulatory networks in yeast (strain W303) expressing fluorescent reporter proteins using BD Accuri C6 and SORP cytometers. However, the functions are for the most part general and may be adapted for analysis of other organisms using other flow cytometers. Functions in this package facilitate the annotation of flow cytometry data with experimental metadata, as often required for publication and general ease-of-reuse. Functions for creating, saving and loading gate sets are also included. In the past, we have typically generated summary statistics for each flowset for each timepoint and then annotated and analyzed these summary statistics. This method loses a great deal of the power that comes from the large amounts of individual cell data generated in flow cytometry, by essentially collapsing this data into a bulk measurement after subsetting. In addition to these summary functions, this package also contains functions to facilitate annotation and analysis of steady-state or time-lapse data utilizing all of the data collected from the thousands of individual cells in each sample.
Maintained by R. Clay Wright. Last updated 5 months ago.
flowcytometrytimecoursevisualizationdataimportcellbasedassaysimmunooncology
1.8 match 4.48 score 8 scriptsbioc
Sconify:A toolkit for performing KNN-based statistics for flow and mass cytometry data
This package does k-nearest neighbor based statistics and visualizations with flow and mass cytometery data. This gives tSNE maps"fold change" functionality and provides a data quality metric by assessing manifold overlap between fcs files expected to be the same. Other applications using this package include imputation, marker redundancy, and testing the relative information loss of lower dimension embeddings compared to the original manifold.
Maintained by Tyler J Burns. Last updated 5 months ago.
immunooncologysinglecellflowcytometrysoftwaremultiplecomparisonvisualization
1.7 match 4.74 score 11 scriptsbioc
CytoDx:Robust prediction of clinical outcomes using cytometry data without cell gating
This package provides functions that predict clinical outcomes using single cell data (such as flow cytometry data, RNA single cell sequencing data) without the requirement of cell gating or clustering.
Maintained by Zicheng Hu. Last updated 5 months ago.
immunooncologycellbiologyflowcytometrystatisticalmethodsoftwarecellbasedassaysregressionclassificationsurvival
1.8 match 4.00 score 8 scriptsbioc
tidyFlowCore:tidyFlowCore: Bringing flowCore to the tidyverse
tidyFlowCore bridges the gap between flow cytometry analysis using the flowCore Bioconductor package and the tidy data principles advocated by the tidyverse. It provides a suite of dplyr-, ggplot2-, and tidyr-like verbs specifically designed for working with flowFrame and flowSet objects as if they were tibbles; however, your data remain flowCore data structures under this layer of abstraction. tidyFlowCore enables intuitive and streamlined analysis workflows that can leverage both the Bioconductor and tidyverse ecosystems for cytometry data.
Maintained by Timothy Keyes. Last updated 5 months ago.
singlecellflowcytometryinfrastructure
1.6 match 1 stars 4.30 score 7 scripts
cran
CytobankAPI:Cytobank API Wrapper for R
Tools to interface with Cytobank's API via R, organized by endpoints that represent various areas of Cytobank functionality. Learn more about Cytobank at <https://www.beckman.com/flow-cytometry/software>.
Maintained by Stu Blair. Last updated 2 years ago.
2.0 match 3.00 scorebioc
infinityFlow:Augmenting Massively Parallel Cytometry Experiments Using Multivariate Non-Linear Regressions
Pipeline to analyze and merge data files produced by BioLegend's LEGENDScreen or BD Human Cell Surface Marker Screening Panel (BD Lyoplates).
Maintained by Etienne Becht. Last updated 5 months ago.
softwareflowcytometrycellbasedassayssinglecellproteomics
1.6 match 3.60 score 4 scriptsbioc
flowGate:Interactive Cytometry Gating in R
flowGate adds an interactive Shiny app to allow manual GUI-based gating of flow cytometry data in R. Using flowGate, you can draw 1D and 2D span/rectangle gates, quadrant gates, and polygon gates on flow cytometry data by interactively drawing the gates on a plot of your data, rather than by specifying gate coordinates. This package is especially geared toward wet-lab cytometerists looking to take advantage of R for cytometry analysis, without necessarily having a lot of R experience.
Maintained by Andrew Wight. Last updated 5 months ago.
softwareworkflowstepflowcytometrypreprocessingimmunooncologydataimport
1.2 match 4.00 score 3 scriptsbioc
flowPloidy:Analyze flow cytometer data to determine sample ploidy
Determine sample ploidy via flow cytometry histogram analysis. Reads Flow Cytometry Standard (FCS) files via the flowCore bioconductor package, and provides functions for determining the DNA ploidy of samples based on internal standards.
Maintained by Tyler Smith. Last updated 5 months ago.
flowcytometryguiregressionvisualizationbioconductorevolutionflow-cytometrypolyploidy
0.5 match 5 stars 6.26 score 5 scripts
rorynolan
detrendr:Detrend Images
Detrend fluorescence microscopy image series for fluorescence fluctuation and correlation spectroscopy ('FCS' and 'FFS') analysis. This package contains functionality published in a 2016 paper <doi:10.1093/bioinformatics/btx434> but it has been extended since then with the Robin Hood algorithm and thus contains unpublished work.
Maintained by Rory Nolan. Last updated 2 months ago.
0.5 match 3 stars 6.08 score 25 scripts 1 dependents