R-universe search: needs:cytolib

bioc

ggcyto:Visualize Cytometry data with ggplot

With the dedicated fortify method implemented for flowSet, ncdfFlowSet and GatingSet classes, both raw and gated flow cytometry data can be plotted directly with ggplot. ggcyto wrapper and some customed layers also make it easy to add gates and population statistics to the plot.

Maintained by Mike Jiang. Last updated 5 months ago.

immunooncology flowcytometry cellbasedassays infrastructure visualization

58 stars 11.25 score 362 scripts 5 dependents

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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.

clustering dataimport differentialexpression experimentaldesign flowcytometry immunooncology massspectrometry normalization preprocessing singlecell software statisticalmethod visualization

67 stars 10.99 score 362 scripts 2 dependents

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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.

immunooncology infrastructure flowcytometry cellbasedassays cpp

10.17 score 1.7k scripts 59 dependents

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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 2 months ago.

immunooncology flowcytometry proteomics singlecell cellbasedassays cellbiology clustering featureextraction software

20 stars 9.98 score 225 scripts 5 dependents

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cmapR:CMap Tools in R

The Connectivity Map (CMap) is a massive resource of perturbational gene expression profiles built by researchers at the Broad Institute and funded by the NIH Library of Integrated Network-Based Cellular Signatures (LINCS) program. Please visit https://clue.io for more information. The cmapR package implements methods to parse, manipulate, and write common CMap data objects, such as annotated matrices and collections of gene sets.

Maintained by Ted Natoli. Last updated 5 months ago.

dataimport datarepresentation geneexpression bioconductor bioinformatics cmap

90 stars 8.86 score 298 scripts

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flowStats:Statistical methods for the analysis of flow cytometry data

Methods and functionality to analyse flow data that is beyond the basic infrastructure provided by the flowCore package.

Maintained by Greg Finak. Last updated 5 months ago.

immunooncology flowcytometry cellbasedassays

14 stars 8.27 score 195 scripts 1 dependents

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openCyto:Hierarchical Gating Pipeline for flow cytometry data

This package is designed to facilitate the automated gating methods in sequential way to mimic the manual gating strategy.

Maintained by Mike Jiang. Last updated 6 days ago.

immunooncology flowcytometry dataimport preprocessing datarepresentation cpp

8.02 score 404 scripts 1 dependents

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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 26 days ago.

immunooncology flowcytometry dataimport preprocessing datarepresentation zlib openblas cpp

7.89 score 576 scripts 10 dependents

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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.

cellbiology flowcytometry clustering visualization software cellbasedassays

7.71 score 468 scripts 10 dependents

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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 26 days ago.

immunooncology flowcytometry dataimport datarepresentation zlib openblas libxml2 cpp

30 stars 7.60 score 132 scripts

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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 3 months ago.

immunooncology flowcytometry zlib cpp

7.56 score 96 scripts 11 dependents

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flowViz:Visualization for flow cytometry

Provides visualization tools for flow cytometry data.

Maintained by Mike Jiang. Last updated 5 months ago.

immunooncology infrastructure flowcytometry cellbasedassays visualization

7.44 score 231 scripts 12 dependents

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PeacoQC:Peak-based selection of high quality cytometry data

This is a package that includes pre-processing and quality control functions that can remove margin events, compensate and transform the data and that will use PeacoQCSignalStability for quality control. This last function will first detect peaks in each channel of the flowframe. It will remove anomalies based on the IsolationTree function and the MAD outlier detection method. This package can be used for both flow- and mass cytometry data.

Maintained by Annelies Emmaneel. Last updated 5 months ago.

flowcytometry qualitycontrol preprocessing peakdetection

16 stars 7.38 score 28 scripts 3 dependents

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flowClust:Clustering for Flow Cytometry

Robust model-based clustering using a t-mixture model with Box-Cox transformation. Note: users should have GSL installed. Windows users: 'consult the README file available in the inst directory of the source distribution for necessary configuration instructions'.

Maintained by Greg Finak. Last updated 5 months ago.

immunooncology clustering visualization flowcytometry

7.31 score 83 scripts 6 dependents

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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.

singlecell flowcytometry bioinformatics cytometry data-science single-cell tidyverse cpp

18 stars 7.24 score 35 scripts

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treeclimbR:An algorithm to find optimal signal levels in a tree

The arrangement of hypotheses in a hierarchical structure appears in many research fields and often indicates different resolutions at which data can be viewed. This raises the question of which resolution level the signal should best be interpreted on. treeclimbR provides a flexible method to select optimal resolution levels (potentially different levels in different parts of the tree), rather than cutting the tree at an arbitrary level. treeclimbR uses a tuning parameter to generate candidate resolutions and from these selects the optimal one.

Maintained by Charlotte Soneson. Last updated 3 months ago.

statisticalmethod cellbasedassays

20 stars 6.86 score 45 scripts

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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.

flowcytometry preprocessing qualitycontrol workflowstep immunooncology software visualization

4 stars 6.71 score 18 scripts 2 dependents

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Statial:A package to identify changes in cell state relative to spatial associations

Statial is a suite of functions for identifying changes in cell state. The functionality provided by Statial provides robust quantification of cell type localisation which are invariant to changes in tissue structure. In addition to this Statial uncovers changes in marker expression associated with varying levels of localisation. These features can be used to explore how the structure and function of different cell types may be altered by the agents they are surrounded with.

Maintained by Farhan Ameen. Last updated 5 months ago.

singlecell spatial classification single-cell

5 stars 6.49 score 23 scripts

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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.

singlecell immunooncology rnaseq geneexpression transcription flowcytometry massspectrometry dataimport

63 stars 6.30 score 16 scripts

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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.

flowcytometry gui regression visualization bioconductor evolution flow-cytometry polyploidy

5 stars 6.26 score 5 scripts

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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.

flowcytometry qualitycontrol biomedicalinformatics immunooncology

5.67 score 86 scripts 3 dependents

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cydar:Using Mass Cytometry for Differential Abundance Analyses

Identifies differentially abundant populations between samples and groups in mass cytometry data. Provides methods for counting cells into hyperspheres, controlling the spatial false discovery rate, and visualizing changes in abundance in the high-dimensional marker space.

Maintained by Aaron Lun. Last updated 5 months ago.

immunooncology flowcytometry multiplecomparison proteomics singlecell cpp

5.64 score 48 scripts

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flowMeans:Non-parametric Flow Cytometry Data Gating

Identifies cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection. Note: R 2.11.0 or newer is required.

Maintained by Nima Aghaeepour. Last updated 5 months ago.

immunooncology flowcytometry cellbiology clustering

5.64 score 36 scripts 2 dependents

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scifer:Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences

Have you ever index sorted cells in a 96 or 384-well plate and then sequenced using Sanger sequencing? If so, you probably had some struggles to either check the electropherogram of each cell sequenced manually, or when you tried to identify which cell was sorted where after sequencing the plate. Scifer was developed to solve this issue by performing basic quality control of Sanger sequences and merging flow cytometry data from probed single-cell sorted B cells with sequencing data. scifer can export summary tables, 'fasta' files, electropherograms for visual inspection, and generate reports.

Maintained by Rodrigo Arcoverde Cerveira. Last updated 4 months ago.

preprocessing qualitycontrol sangerseq sequencing software flowcytometry singlecell

5 stars 5.54 score 9 scripts

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CytoMDS:Low Dimensions projection of cytometry samples

This package implements a low dimensional visualization of a set of cytometry samples, in order to visually assess the 'distances' between them. This, in turn, can greatly help the user to identify quality issues like batch effects or outlier samples, and/or check the presence of potential sample clusters that might align with the exeprimental design. The CytoMDS algorithm combines, on the one hand, the concept of Earth Mover's Distance (EMD), a.k.a. Wasserstein metric and, on the other hand, the Multi Dimensional Scaling (MDS) algorithm for the low dimensional projection. Also, the package provides some diagnostic tools for both checking the quality of the MDS projection, as well as tools to help with the interpretation of the axes of the projection.

Maintained by Philippe Hauchamps. Last updated 2 months ago.

flowcytometry qualitycontrol dimensionreduction multidimensionalscaling software visualization

1 stars 5.23 score 2 scripts

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flowDensity:Sequential Flow Cytometry Data Gating

This package provides tools for automated sequential gating analogous to the manual gating strategy based on the density of the data.

Maintained by Mehrnoush Malek. Last updated 5 months ago.

bioinformatics flowcytometry cellbiology clustering cancer flowcytdata datarepresentation stemcell densitygating

5.17 score 83 scripts 3 dependents

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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.

immunooncology singlecell flowcytometry software multiplecomparison visualization

4.74 score 11 scripts

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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.

immunooncology cellbiology flowcytometry clustering statisticalmethod software cellbasedassays preprocessing

4.73 score 18 scripts

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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.

flowcytometry cellbasedassays clustering visualization

4.72 score 11 scripts 2 dependents

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CytoPipelineGUI:GUI's for visualization of flow cytometry data analysis pipelines

This package is the companion of the `CytoPipeline` package. It provides GUI's (shiny apps) for the visualization of flow cytometry data analysis pipelines that are run with `CytoPipeline`. Two shiny applications are provided, i.e. an interactive flow frame assessment and comparison tool and an interactive scale transformations visualization and adjustment tool.

Maintained by Philippe Hauchamps. Last updated 5 months ago.

flowcytometry preprocessing qualitycontrol workflowstep immunooncology software visualization gui shinyapps

4.70 score 2 scripts

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ddPCRclust:Clustering algorithm for ddPCR data

The ddPCRclust algorithm can automatically quantify the CPDs of non-orthogonal ddPCR reactions with up to four targets. In order to determine the correct droplet count for each target, it is crucial to both identify all clusters and label them correctly based on their position. For more information on what data can be analyzed and how a template needs to be formatted, please check the vignette.

Maintained by Benedikt G. Brink. Last updated 5 months ago.

ddpcr clustering biological-data-analysis

4 stars 4.60 score 4 scripts

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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.

flowcytometry qualitycontrol immunooncology

4.56 score 18 scripts

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flowMerge:Cluster Merging for Flow Cytometry Data

Merging of mixture components for model-based automated gating of flow cytometry data using the flowClust framework. Note: users should have a working copy of flowClust 2.0 installed.

Maintained by Greg Finak. Last updated 5 months ago.

immunooncology clustering flowcytometry

4.56 score 6 scripts 1 dependents

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treekoR:Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations

treekoR is a novel framework that aims to utilise the hierarchical nature of single cell cytometry data to find robust and interpretable associations between cell subsets and patient clinical end points. These associations are aimed to recapitulate the nested proportions prevalent in workflows inovlving manual gating, which are often overlooked in workflows using automatic clustering to identify cell populations. We developed treekoR to: Derive a hierarchical tree structure of cell clusters; quantify a cell types as a proportion relative to all cells in a sample (%total), and, as the proportion relative to a parent population (%parent); perform significance testing using the calculated proportions; and provide an interactive html visualisation to help highlight key results.

Maintained by Adam Chan. Last updated 5 months ago.

clustering differentialexpression flowcytometry immunooncology massspectrometry singlecell software statisticalmethod visualization

4.56 score 12 scripts 1 dependents

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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.

software flowcytometry cellbasedassays singlecell proteomics clustering

1 stars 4.54 score

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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.

flowcytometry timecourse visualization dataimport cellbasedassays immunooncology

4.48 score 8 scripts

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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.

singlecell flowcytometry infrastructure

2 stars 4.48 score 7 scripts

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immunoClust:immunoClust - Automated Pipeline for Population Detection in Flow Cytometry

immunoClust is a model based clustering approach for Flow Cytometry samples. The cell-events of single Flow Cytometry samples are modelled by a mixture of multinominal normal- or t-distributions. The cell-event clusters of several samples are modelled by a mixture of multinominal normal-distributions aiming stable co-clusters across these samples.

Maintained by Till Soerensen. Last updated 13 days ago.

clustering flowcytometry singlecell cellbasedassays immunooncology gsl cpp

4.41 score 4 scripts

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flowTrans:Parameter Optimization for Flow Cytometry Data Transformation

Profile maximum likelihood estimation of parameters for flow cytometry data transformations.

Maintained by Greg Finak. Last updated 5 months ago.

immunooncology flowcytometry

4.40 score 21 scripts

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flowSpecs:Tools for processing of high-dimensional cytometry data

This package is intended to fill the role of conventional cytometry pre-processing software, for spectral decomposition, transformation, visualization and cleanup, and to aid further downstream analyses, such as with DepecheR, by enabling transformation of flowFrames and flowSets to dataframes. Functions for flowCore-compliant automatic 1D-gating/filtering are in the pipe line. The package name has been chosen both as it will deal with spectral cytometry and as it will hopefully give the user a nice pair of spectacles through which to view their data.

Maintained by Jakob Theorell. Last updated 5 months ago.

software cellbasedassays datarepresentation immunooncology flowcytometry singlecell visualization normalization dataimport

6 stars 4.38 score 7 scripts

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cytofQC:Labels normalized cells for CyTOF data and assigns probabilities for each label

cytofQC is a package for initial cleaning of CyTOF data. It uses a semi-supervised approach for labeling cells with their most likely data type (bead, doublet, debris, dead) and the probability that they belong to each label type. This package does not remove data from the dataset, but provides labels and information to aid the data user in cleaning their data. Our algorithm is able to distinguish between doublets and large cells.

Maintained by Jill Lundell. Last updated 5 months ago.

software singlecell annotation

2 stars 4.30 score 3 scripts

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censcyt:Differential abundance analysis with a right censored covariate in high-dimensional cytometry

Methods for differential abundance analysis in high-dimensional cytometry data when a covariate is subject to right censoring (e.g. survival time) based on multiple imputation and generalized linear mixed models.

Maintained by Reto Gerber. Last updated 5 months ago.

immunooncology flowcytometry proteomics singlecell cellbasedassays cellbiology clustering featureextraction software survival

4.30 score 2 scripts

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spillR:Spillover Compensation in Mass Cytometry Data

Channel interference in mass cytometry can cause spillover and may result in miscounting of protein markers. We develop a nonparametric finite mixture model and use the mixture components to estimate the probability of spillover. We implement our method using expectation-maximization to fit the mixture model.

Maintained by Marco Guazzini. Last updated 5 months ago.

flowcytometry immunooncology massspectrometry preprocessing singlecell software statisticalmethod visualization regression

4.30 score 3 scripts

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cyanoFilter:Phytoplankton Population Identification using Cell Pigmentation and/or Complexity

An approach to filter out and/or identify phytoplankton cells from all particles measured via flow cytometry pigment and cell complexity information. It does this using a sequence of one-dimensional gates on pre-defined channels measuring certain pigmentation and complexity. The package is especially tuned for cyanobacteria, but will work fine for phytoplankton communities where there is at least one cell characteristic that differentiates every phytoplankton in the community.

Maintained by Oluwafemi Olusoji. Last updated 5 months ago.

flowcytometry clustering onechannel

4.30 score 4 scripts

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cytoMEM:Marker Enrichment Modeling (MEM)

MEM, Marker Enrichment Modeling, automatically generates and displays quantitative labels for cell populations that have been identified from single-cell data. The input for MEM is a dataset that has pre-clustered or pre-gated populations with cells in rows and features in columns. Labels convey a list of measured features and the features' levels of relative enrichment on each population. MEM can be applied to a wide variety of data types and can compare between MEM labels from flow cytometry, mass cytometry, single cell RNA-seq, and spectral flow cytometry using RMSD.

Maintained by Jonathan Irish. Last updated 5 months ago.

proteomics systemsbiology classification flowcytometry datarepresentation dataimport cellbiology singlecell clustering

4.18 score 15 scripts

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CyTOFpower:Power analysis for CyTOF experiments

This package is a tool to predict the power of CyTOF experiments in the context of differential state analyses. The package provides a shiny app with two options to predict the power of an experiment: i. generation of in-sicilico CyTOF data, using users input ii. browsing in a grid of parameters for which the power was already precomputed.

Maintained by Anne-Maud Ferreira. Last updated 17 days ago.

flowcytometry singlecell cellbiology statisticalmethod software

4.18 score 2 scripts

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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.

immunooncology cellbiology flowcytometry statisticalmethod software cellbasedassays regression classification survival

4.00 score 8 scripts

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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.

software workflowstep flowcytometry preprocessing immunooncology dataimport

4.00 score 3 scripts

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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.

immunooncology infrastructure flowcytometry cellbasedassays

4.00 score 7 scripts

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flowCut:Automated Removal of Outlier Events and Flagging of Files Based on Time Versus Fluorescence Analysis

Common techinical complications such as clogging can result in spurious events and fluorescence intensity shifting, flowCut is designed to detect and remove technical artifacts from your data by removing segments that show statistical differences from other segments.

Maintained by Justin Meskas. Last updated 5 months ago.

flowcytometry preprocessing qualitycontrol cellbasedassays

3.92 score 21 scripts

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CONFESS:Cell OrderiNg by FluorEScence Signal

Single Cell Fluidigm Spot Detector.

Maintained by Diana LOW. Last updated 5 months ago.

immunooncology geneexpression dataimport cellbiology clustering rnaseq qualitycontrol visualization timecourse regression classification

3.90 score 2 scripts

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flowMatch:Matching and meta-clustering in flow cytometry

Matching cell populations and building meta-clusters and templates from a collection of FC samples.

Maintained by Ariful Azad. Last updated 5 months ago.

immunooncology clustering flowcytometry cpp

3.90 score 1 scripts

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flowVS:Variance stabilization in flow cytometry (and microarrays)

Per-channel variance stabilization from a collection of flow cytometry samples by Bertlett test for homogeneity of variances. The approach is applicable to microarrays data as well.

Maintained by Ariful Azad. Last updated 5 months ago.

immunooncology flowcytometry cellbasedassays microarray

3.82 score 11 scripts

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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.

immunooncology cellbasedassays clustering flowcytometry software visualization

3.78 score 1 scripts

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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.

software flowcytometry cellbasedassays singlecell proteomics

3.60 score 4 scripts

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flowBin:Combining multitube flow cytometry data by binning

Software to combine flow cytometry data that has been multiplexed into multiple tubes with common markers between them, by establishing common bins across tubes in terms of the common markers, then determining expression within each tube for each bin in terms of the tube-specific markers.

Maintained by Kieran ONeill. Last updated 5 months ago.

immunooncology cellbasedassays flowcytometry

3.30 score 2 scripts

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GateFinder:Projection-based Gating Strategy Optimization for Flow and Mass Cytometry

Given a vector of cluster memberships for a cell population, identifies a sequence of gates (polygon filters on 2D scatter plots) for isolation of that cell type.

Maintained by Nima Aghaeepour. Last updated 5 months ago.

immunooncology flowcytometry cellbiology clustering

3.30 score 7 scripts

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