R-universe search: cellbasedassays

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iSEE:Interactive SummarizedExperiment Explorer

Create an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. The interface supports transmission of selections between plots and tables, code tracking, interactive tours, interactive or programmatic initialization, preservation of app state, and extensibility to new panel types via S4 classes. Special attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results.

Maintained by Kevin Rue-Albrecht. Last updated 9 days ago.

cellbasedassays clustering dimensionreduction featureextraction geneexpression gui immunooncology shinyapps singlecell transcription transcriptomics visualization dimension-reduction feature-extraction gene-expression hacktoberfest human-cell-atlas shiny single-cell

10.0 match 225 stars 12.86 score 380 scripts 9 dependents

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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

10.0 match 58 stars 11.25 score 362 scripts 5 dependents

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destiny:Creates diffusion maps

Create and plot diffusion maps.

Maintained by Philipp Angerer. Last updated 4 months ago.

cellbiology cellbasedassays clustering software visualization diffusion-maps dimensionality-reduction cpp

10.0 match 81 stars 10.94 score 792 scripts

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UCell:Rank-based signature enrichment analysis for single-cell data

UCell is a package for evaluating gene signatures in single-cell datasets. UCell signature scores, based on the Mann-Whitney U statistic, are robust to dataset size and heterogeneity, and their calculation demands less computing time and memory than other available methods, enabling the processing of large datasets in a few minutes even on machines with limited computing power. UCell can be applied to any single-cell data matrix, and includes functions to directly interact with SingleCellExperiment and Seurat objects.

Maintained by Massimo Andreatta. Last updated 5 months ago.

singlecell genesetenrichment transcriptomics geneexpression cellbasedassays

10.0 match 143 stars 10.43 score 454 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

10.0 match 10.34 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 1 months ago.

immunooncology flowcytometry proteomics singlecell cellbasedassays cellbiology clustering featureextraction software

10.0 match 20 stars 9.98 score 225 scripts 5 dependents

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ChemmineR:Cheminformatics Toolkit for R

ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures.

Maintained by Thomas Girke. Last updated 5 months ago.

cheminformatics biomedicalinformatics pharmacogenetics pharmacogenomics microtitreplateassay cellbasedassays visualization infrastructure dataimport clustering proteomics metabolomics cpp

10.0 match 14 stars 9.42 score 253 scripts 12 dependents

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scp:Mass Spectrometry-Based Single-Cell Proteomics Data Analysis

Utility functions for manipulating, processing, and analyzing mass spectrometry-based single-cell proteomics data. The package is an extension to the 'QFeatures' package and relies on 'SingleCellExpirement' to enable single-cell proteomics analyses. The package offers the user the functionality to process quantitative table (as generated by MaxQuant, Proteome Discoverer, and more) into data tables ready for downstream analysis and data visualization.

Maintained by Christophe Vanderaa. Last updated 15 days ago.

geneexpression proteomics singlecell massspectrometry preprocessing cellbasedassays bioconductor mass-spectrometry single-cell software

10.0 match 25 stars 8.94 score 115 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

10.0 match 13 stars 8.24 score 195 scripts 1 dependents

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spicyR:Spatial analysis of in situ cytometry data

The spicyR package provides a framework for performing inference on changes in spatial relationships between pairs of cell types for cell-resolution spatial omics technologies. spicyR consists of three primary steps: (i) summarizing the degree of spatial localization between pairs of cell types for each image; (ii) modelling the variability in localization summary statistics as a function of cell counts and (iii) testing for changes in spatial localizations associated with a response variable.

Maintained by Ellis Patrick. Last updated 10 days ago.

singlecell cellbasedassays spatial

10.0 match 9 stars 8.02 score 57 scripts 1 dependents

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ChemmineOB:R interface to a subset of OpenBabel functionalities

ChemmineOB provides an R interface to a subset of cheminformatics functionalities implemented by the OpelBabel C++ project. OpenBabel is an open source cheminformatics toolbox that includes utilities for structure format interconversions, descriptor calculations, compound similarity searching and more. ChemineOB aims to make a subset of these utilities available from within R. For non-developers, ChemineOB is primarily intended to be used from ChemmineR as an add-on package rather than used directly.

Maintained by Thomas Girke. Last updated 5 months ago.

cheminformatics biomedicalinformatics pharmacogenetics pharmacogenomics microtitreplateassay cellbasedassays visualization infrastructure dataimport clustering proteomics metabolomics openbabel cpp

10.0 match 10 stars 7.87 score 77 scripts 1 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

10.0 match 7.71 score 468 scripts 10 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

10.0 match 7.44 score 231 scripts 12 dependents

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iSEEu:iSEE Universe

iSEEu (the iSEE universe) contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels, or modes allowing easy configuration of iSEE applications.

Maintained by Kevin Rue-Albrecht. Last updated 5 months ago.

immunooncology visualization gui dimensionreduction featureextraction clustering transcription geneexpression transcriptomics singlecell cellbasedassays hacktoberfest

10.0 match 9 stars 7.15 score 35 scripts 1 dependents

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GeomxTools:NanoString GeoMx Tools

Tools for NanoString Technologies GeoMx Technology. Package provides functions for reading in DCC and PKC files based on an ExpressionSet derived object. Normalization and QC functions are also included.

Maintained by Maddy Griswold. Last updated 5 months ago.

geneexpression transcription cellbasedassays dataimport transcriptomics proteomics mrnamicroarray proprietaryplatforms rnaseq sequencing experimentaldesign normalization spatial

10.0 match 7.11 score 239 scripts 3 dependents

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fmcsR:Mismatch Tolerant Maximum Common Substructure Searching

The fmcsR package introduces an efficient maximum common substructure (MCS) algorithms combined with a novel matching strategy that allows for atom and/or bond mismatches in the substructures shared among two small molecules. The resulting flexible MCSs (FMCSs) are often larger than strict MCSs, resulting in the identification of more common features in their source structures, as well as a higher sensitivity in finding compounds with weak structural similarities. The fmcsR package provides several utilities to use the FMCS algorithm for pairwise compound comparisons, structure similarity searching and clustering.

Maintained by Thomas Girke. Last updated 5 months ago.

cheminformatics biomedicalinformatics pharmacogenetics pharmacogenomics microtitreplateassay cellbasedassays visualization infrastructure dataimport clustering proteomics metabolomics cpp

10.0 match 5 stars 7.03 score 60 scripts 1 dependents

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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 2 months ago.

statisticalmethod cellbasedassays

10.0 match 20 stars 7.00 score 45 scripts

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MPRAnalyze:Statistical Analysis of MPRA data

MPRAnalyze provides statistical framework for the analysis of data generated by Massively Parallel Reporter Assays (MPRAs), used to directly measure enhancer activity. MPRAnalyze can be used for quantification of enhancer activity, classification of active enhancers and comparative analyses of enhancer activity between conditions. MPRAnalyze construct a nested pair of generalized linear models (GLMs) to relate the DNA and RNA observations, easily adjustable to various experimental designs and conditions, and provides a set of rigorous statistical testig schemes.

Maintained by Tal Ashuach. Last updated 5 months ago.

immunooncology software statisticalmethod sequencing geneexpression cellbiology cellbasedassays differentialexpression experimentaldesign classification

10.0 match 12 stars 6.86 score 30 scripts

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CellNOptR:Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

This package does optimisation of boolean logic networks of signalling pathways based on a previous knowledge network and a set of data upon perturbation of the nodes in the network.

Maintained by Attila Gabor. Last updated 5 months ago.

cellbasedassays cellbiology proteomics pathways network timecourse immunooncology

10.0 match 6.72 score 98 scripts 6 dependents

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bioassayR:Cross-target analysis of small molecule bioactivity

bioassayR is a computational tool that enables simultaneous analysis of thousands of bioassay experiments performed over a diverse set of compounds and biological targets. Unique features include support for large-scale cross-target analyses of both public and custom bioassays, generation of high throughput screening fingerprints (HTSFPs), and an optional preloaded database that provides access to a substantial portion of publicly available bioactivity data.

Maintained by Thomas Girke. Last updated 5 months ago.

immunooncology microtitreplateassay cellbasedassays visualization infrastructure dataimport bioinformatics proteomics metabolomics

10.0 match 5 stars 6.70 score 46 scripts

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lisaClust:lisaClust: Clustering of Local Indicators of Spatial Association

lisaClust provides a series of functions to identify and visualise regions of tissue where spatial associations between cell-types is similar. This package can be used to provide a high-level summary of cell-type colocalization in multiplexed imaging data that has been segmented at a single-cell resolution.

Maintained by Ellis Patrick. Last updated 4 months ago.

singlecell cellbasedassays spatial

10.0 match 3 stars 6.64 score 48 scripts

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NanoStringNCTools:NanoString nCounter Tools

Tools for NanoString Technologies nCounter Technology. Provides support for reading RCC files into an ExpressionSet derived object. Also includes methods for QC and normalizaztion of NanoString data.

Maintained by Maddy Griswold. Last updated 5 months ago.

geneexpression transcription cellbasedassays dataimport transcriptomics proteomics mrnamicroarray proprietaryplatforms rnaseq

10.0 match 6.35 score 94 scripts 4 dependents

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spatialHeatmap:spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions

The spatialHeatmap package offers the primary functionality for visualizing cell-, tissue- and organ-specific assay data in spatial anatomical images. Additionally, it provides extended functionalities for large-scale data mining routines and co-visualizing bulk and single-cell data. A description of the project is available here: https://spatialheatmap.org.

Maintained by Jianhai Zhang. Last updated 4 months ago.

spatial visualization microarray sequencing geneexpression datarepresentation network clustering graphandnetwork cellbasedassays atacseq dnaseq tissuemicroarray singlecell cellbiology genetarget

10.0 match 5 stars 6.26 score 12 scripts

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CNORode:ODE add-on to CellNOptR

Logic based ordinary differential equation (ODE) add-on to CellNOptR.

Maintained by Attila Gabor. Last updated 5 months ago.

immunooncology cellbasedassays cellbiology proteomics bioinformatics timecourse

10.0 match 6.05 score 37 scripts 1 dependents

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Dino:Normalization of Single-Cell mRNA Sequencing Data

Dino normalizes single-cell, mRNA sequencing data to correct for technical variation, particularly sequencing depth, prior to downstream analysis. The approach produces a matrix of corrected expression for which the dependency between sequencing depth and the full distribution of normalized expression; many existing methods aim to remove only the dependency between sequencing depth and the mean of the normalized expression. This is particuarly useful in the context of highly sparse datasets such as those produced by 10X genomics and other uninque molecular identifier (UMI) based microfluidics protocols for which the depth-dependent proportion of zeros in the raw expression data can otherwise present a challenge.

Maintained by Jared Brown. Last updated 5 months ago.

software normalization rnaseq singlecell sequencing geneexpression transcriptomics regression cellbasedassays

10.0 match 9 stars 6.02 score 13 scripts

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scFeatures:scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction

scFeatures constructs multi-view representations of single-cell and spatial data. scFeatures is a tool that generates multi-view representations of single-cell and spatial data through the construction of a total of 17 feature types. These features can then be used for a variety of analyses using other software in Biocondutor.

Maintained by Yue Cao. Last updated 5 months ago.

cellbasedassays singlecell spatial software transcriptomics

10.0 match 10 stars 5.95 score 15 scripts

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cicero:Predict cis-co-accessibility from single-cell chromatin accessibility data

Cicero computes putative cis-regulatory maps from single-cell chromatin accessibility data. It also extends monocle 2 for use in chromatin accessibility data.

Maintained by Hannah Pliner. Last updated 5 months ago.

sequencing clustering cellbasedassays immunooncology generegulation genetarget epigenetics atacseq singlecell

10.0 match 5.80 score 312 scripts

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rcellminer:rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines

The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP, http://dtp.nci.nih.gov/) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others (Reinhold, et al., 2012). The purpose of the CellMiner project (http://discover.nci.nih.gov/ cellminer) has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data.

Maintained by Augustin Luna. Last updated 5 months ago.

acgh cellbasedassays copynumbervariation geneexpression pharmacogenomics pharmacogenetics mirna cheminformatics visualization software systemsbiology

10.0 match 5.71 score 113 scripts

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CytoGLMM:Conditional Differential Analysis for Flow and Mass Cytometry Experiments

The CytoGLMM R package implements two multiple regression strategies: A bootstrapped generalized linear model (GLM) and a generalized linear mixed model (GLMM). Most current data analysis tools compare expressions across many computationally discovered cell types. CytoGLMM focuses on just one cell type. Our narrower field of application allows us to define a more specific statistical model with easier to control statistical guarantees. As a result, CytoGLMM finds differential proteins in flow and mass cytometry data while reducing biases arising from marker correlations and safeguarding against false discoveries induced by patient heterogeneity.

Maintained by Christof Seiler. Last updated 5 months ago.

flowcytometry proteomics singlecell cellbasedassays cellbiology immunooncology regression statisticalmethod software

10.0 match 2 stars 5.68 score 1 scripts 1 dependents

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eiR:Accelerated similarity searching of small molecules

The eiR package provides utilities for accelerated structure similarity searching of very large small molecule data sets using an embedding and indexing approach.

Maintained by Thomas Girke. Last updated 1 months ago.

cheminformatics biomedicalinformatics pharmacogenetics pharmacogenomics microtitreplateassay cellbasedassays visualization infrastructure dataimport clustering proteomics metabolomics

10.0 match 3 stars 5.51 score 12 scripts

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DepecheR:Determination of essential phenotypic elements of clusters in high-dimensional entities

The purpose of this package is to identify traits in a dataset that can separate groups. This is done on two levels. First, clustering is performed, using an implementation of sparse K-means. Secondly, the generated clusters are used to predict outcomes of groups of individuals based on their distribution of observations in the different clusters. As certain clusters with separating information will be identified, and these clusters are defined by a sparse number of variables, this method can reduce the complexity of data, to only emphasize the data that actually matters.

Maintained by Jakob Theorell. Last updated 5 months ago.

software cellbasedassays transcription differentialexpression datarepresentation immunooncology transcriptomics classification clustering dimensionreduction featureextraction flowcytometry rnaseq singlecell visualization cpp

10.0 match 5.18 score 15 scripts

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seahtrue:Seahtrue revives XF data for structured data analysis

Seahtrue organizes oxygen consumption and extracellular acidification analysis data from experiments performed on an XF analyzer into structured nested tibbles.This allows for detailed processing of raw data and advanced data visualization and statistics. Seahtrue introduces an open and reproducible way to analyze these XF experiments. It uses file paths to .xlsx files. These .xlsx files are supplied by the userand are generated by the user in the Wave software from Agilent from the assay result files (.asyr). The .xlsx file contains different sheets of important data for the experiment; 1. Assay Information - Details about how the experiment was set up. 2. Rate Data - Information about the OCR and ECAR rates. 3. Raw Data - The original raw data collected during the experiment. 4. Calibration Data - Data related to calibrating the instrument. Seahtrue focuses on getting the specific data needed for analysis. Once this data is extracted, it is prepared for calculations through preprocessing. To make sure everything is accurate, both the initial data and the preprocessed data go through thorough checks.

Maintained by Vincent de Boer. Last updated 5 months ago.

cellbasedassays functionalprediction datarepresentation dataimport cellbiology cheminformatics metabolomics microtitreplateassay visualization qualitycontrol batcheffect experimentaldesign preprocessing go

10.0 match 5.04 score 2 scripts

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CDI:Clustering Deviation Index (CDI)

Single-cell RNA-sequencing (scRNA-seq) is widely used to explore cellular variation. The analysis of scRNA-seq data often starts from clustering cells into subpopulations. This initial step has a high impact on downstream analyses, and hence it is important to be accurate. However, there have not been unsupervised metric designed for scRNA-seq to evaluate clustering performance. Hence, we propose clustering deviation index (CDI), an unsupervised metric based on the modeling of scRNA-seq UMI counts to evaluate clustering of cells.

Maintained by Jiyuan Fang. Last updated 5 months ago.

singlecell software clustering visualization sequencing rnaseq cellbasedassays

10.0 match 5 stars 5.00 score 4 scripts

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iSEEfier:Streamlining the creation of initial states for starting an iSEE instance

iSEEfier provides a set of functionality to quickly and intuitively create, inspect, and combine initial configuration objects. These can be conveniently passed in a straightforward manner to the function call to launch iSEE() with the specified configuration. This package currently works seamlessly with the sets of panels provided by the iSEE and iSEEu packages, but can be extended to accommodate the usage of any custom panel (e.g. from iSEEde, iSEEpathways, or any panel developed independently by the user).

Maintained by Najla Abassi. Last updated 5 months ago.

cellbasedassays clustering dimensionreduction featureextraction gui geneexpression immunooncology shinyapps singlecell software transcription transcriptomics visualization

10.0 match 4.90 score 2 scripts

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GRmetrics:Calculate growth-rate inhibition (GR) metrics

Functions for calculating and visualizing growth-rate inhibition (GR) metrics.

Maintained by Nicholas Clark. Last updated 5 months ago.

immunooncology cellbasedassays cellbiology software timecourse visualization

10.0 match 1 stars 4.83 score 17 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

10.0 match 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

10.0 match 4.72 score 11 scripts 2 dependents

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FuseSOM:A Correlation Based Multiview Self Organizing Maps Clustering For IMC Datasets

A correlation-based multiview self-organizing map for the characterization of cell types in highly multiplexed in situ imaging cytometry assays (`FuseSOM`) is a tool for unsupervised clustering. `FuseSOM` is robust and achieves high accuracy by combining a `Self Organizing Map` architecture and a `Multiview` integration of correlation based metrics. This allows FuseSOM to cluster highly multiplexed in situ imaging cytometry assays.

Maintained by Elijah Willie. Last updated 5 months ago.

singlecell cellbasedassays clustering spatial

10.0 match 1 stars 4.71 score 17 scripts

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RTCA:Open-source toolkit to analyse data from xCELLigence System (RTCA)

Import, analyze and visualize data from Roche(R) xCELLigence RTCA systems. The package imports real-time cell electrical impedance data into R. As an alternative to commercial software shipped along the system, the Bioconductor package RTCA provides several unique transformation (normalization) strategies and various visualization tools.

Maintained by Jitao David Zhang. Last updated 5 months ago.

immunooncology cellbasedassays infrastructure visualization timecourse

10.0 match 4.60 score 4 scripts

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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

10.0 match 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

10.0 match 4.48 score 8 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 4 months ago.

clustering flowcytometry singlecell cellbasedassays immunooncology gsl cpp

10.0 match 4.38 score 4 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

10.0 match 6 stars 4.38 score 7 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

10.0 match 4.30 score 2 scripts

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MICSQTL:MICSQTL (Multi-omic deconvolution, Integration and Cell-type-specific Quantitative Trait Loci)

Our pipeline, MICSQTL, utilizes scRNA-seq reference and bulk transcriptomes to estimate cellular composition in the matched bulk proteomes. The expression of genes and proteins at either bulk level or cell type level can be integrated by Angle-based Joint and Individual Variation Explained (AJIVE) framework. Meanwhile, MICSQTL can perform cell-type-specic quantitative trait loci (QTL) mapping to proteins or transcripts based on the input of bulk expression data and the estimated cellular composition per molecule type, without the need for single cell sequencing. We use matched transcriptome-proteome from human brain frontal cortex tissue samples to demonstrate the input and output of our tool.

Maintained by Qian Li. Last updated 5 months ago.

geneexpression genetics proteomics rnaseq sequencing singlecell software visualization cellbasedassays coverage

10.0 match 4.30 score 3 scripts

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SpatialOmicsOverlay:Spatial Overlay for Omic Data from Nanostring GeoMx Data

Tools for NanoString Technologies GeoMx Technology. Package to easily graph on top of an OME-TIFF image. Plotting annotations can range from tissue segment to gene expression.

Maintained by Maddy Griswold. Last updated 5 months ago.

geneexpression transcription cellbasedassays dataimport transcriptomics proteomics proprietaryplatforms rnaseq spatial datarepresentation visualization openjdk

10.0 match 4.30 score 8 scripts

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flowCyBar:Analyze flow cytometric data using gate information

A package to analyze flow cytometric data using gate information to follow population/community dynamics

Maintained by Joachim Schumann. Last updated 5 months ago.

immunooncology cellbasedassays clustering flowcytometry software visualization

10.0 match 4.15 score 1 scripts

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CFAssay:Statistical analysis for the Colony Formation Assay

The package provides functions for calculation of linear-quadratic cell survival curves and for ANOVA of experimental 2-way designs along with the colony formation assay.

Maintained by Herbert Braselmann. Last updated 5 months ago.

cellbasedassays cellbiology immunooncology regression survival

10.0 match 4.08 score 2 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

10.0 match 4.00 score 7 scripts

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netprioR:A model for network-based prioritisation of genes

A model for semi-supervised prioritisation of genes integrating network data, phenotypes and additional prior knowledge about TP and TN gene labels from the literature or experts.

Maintained by Fabian Schmich. Last updated 5 months ago.

immunooncology cellbasedassays preprocessing network

10.0 match 4.00 score 1 scripts

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flowGraph:Identifying differential cell populations in flow cytometry data accounting for marker frequency

Identifies maximal differential cell populations in flow cytometry data taking into account dependencies between cell populations; flowGraph calculates and plots SpecEnr abundance scores given cell population cell counts.

Maintained by Alice Yue. Last updated 5 months ago.

flowcytometry statisticalmethod immunooncology software cellbasedassays visualization

10.0 match 4.00 score 10 scripts

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sights:Statistics and dIagnostic Graphs for HTS

SIGHTS is a suite of normalization methods, statistical tests, and diagnostic graphical tools for high throughput screening (HTS) assays. HTS assays use microtitre plates to screen large libraries of compounds for their biological, chemical, or biochemical activity.

Maintained by Elika Garg. Last updated 5 months ago.

immunooncology cellbasedassays microtitreplateassay normalization multiplecomparison preprocessing qualitycontrol batcheffect visualization

10.0 match 4.00 score 9 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

10.0 match 4.00 score 8 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

10.0 match 3.92 score 21 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

10.0 match 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

10.0 match 3.78 score 1 scripts

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CNORdt:Add-on to CellNOptR: Discretized time treatments

This add-on to the package CellNOptR handles time-course data, as opposed to steady state data in CellNOptR. It scales the simulation step to allow comparison and model fitting for time-course data. Future versions will optimize delays and strengths for each edge.

Maintained by A. MacNamara. Last updated 5 months ago.

immunooncology cellbasedassays cellbiology proteomics timecourse

10.0 match 3.78 score 15 scripts

bioc

CNORfeeder:Integration of CellNOptR to add missing links

This package integrates literature-constrained and data-driven methods to infer signalling networks from perturbation experiments. It permits to extends a given network with links derived from the data via various inference methods and uses information on physical interactions of proteins to guide and validate the integration of links.

Maintained by Attila Gabor. Last updated 5 months ago.

cellbasedassays cellbiology proteomics networkinference

10.0 match 3.60 score 9 scripts

bioc

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

10.0 match 3.60 score 4 scripts

bioc

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

10.0 match 3.30 score 2 scripts

bioc

flowPlots:flowPlots: analysis plots and data class for gated flow cytometry data

Graphical displays with embedded statistical tests for gated ICS flow cytometry data, and a data class which stores "stacked" data and has methods for computing summary measures on stacked data, such as marginal and polyfunctional degree data.

Maintained by N. Hawkins. Last updated 5 months ago.

immunooncology flowcytometry cellbasedassays visualization datarepresentation

10.0 match 3.30 score 1 scripts

bioc

PANR:Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations

This package provides S4 classes and methods for inferring functional gene networks with edges encoding posterior beliefs of gene association types and nodes encoding perturbation effects.

Maintained by Xin Wang. Last updated 5 months ago.

immunooncology networkinference visualization graphandnetwork clustering cellbasedassays

10.0 match 3.30 score 2 scripts

bioc

synlet:Hits Selection for Synthetic Lethal RNAi Screen Data

Select hits from synthetic lethal RNAi screen data. For example, there are two identical celllines except one gene is knocked-down in one cellline. The interest is to find genes that lead to stronger lethal effect when they are knocked-down further by siRNA. Quality control and various visualisation tools are implemented. Four different algorithms could be used to pick up the interesting hits. This package is designed based on 384 wells plates, but may apply to other platforms with proper configuration.

Maintained by Chunxuan Shao. Last updated 5 months ago.

immunooncology cellbasedassays qualitycontrol preprocessing visualization featureextraction

10.0 match 3.30 score 2 scripts