eiR

Accelerated similarity searching of small molecules

eiR

Accelerated similarity searching of small molecules

girke-lab/eiR-release

Accelerated similarity searching of small molecules

girke-lab/eiR

Accelerated similarity searching of small molecules

saezlab/CNORdt

Add-on to CellNOptR: Discretized time treatments

CNORdt

Add-on to CellNOptR: Discretized time treatments

rprops/Phenoflow_package

Advanced analysis of microbial flow cytometry data

netprioR

A model for network-based prioritisation of genes

cbg-ethz/netprioR

A model for network-based prioritisation of genes

cellHTS2

Analysis of cell-based screens - revised version of cellHTS

coRNAi

Analysis of co-knock-down RNAi data

LBMC/criblejurkat

Analysis of FACS data for the Jurkat crible project

imageHTS

Analysis of high-throughput microscopy-based screens

flowCyBar

Analyze flow cytometric data using gate information

flowCHIC

Analyze flow cytometric data using histogram information

flowTime

Annotation and analysis of biological dynamical systems using flow cytometry

wrightrc/flowTime

Annotation and analysis of biological dynamical systems using flow cytometry

OperaMate

An R package of Data Importing, Processing and Analysis for Opera High Content Screening System

JhuangLab/flowSpy

A Toolkit for Flow And Mass Cytometry Data

flowSpy

A Toolkit for Flow And Mass Cytometry Data

JhuangLab/CytoTree

A Toolkit for Flow And Mass Cytometry Data

saezlab/BraDiPluS

BraDiPluS - Braille Display Plugs Data Analysis

uc-bd2k/GRmetrics_old

Calculate growth-rate inhibition (GR) metrics

uc-bd2k/GRmetrics

Calculate growth-rate inhibition (GR) metrics

GRmetrics

Calculate growth-rate inhibition (GR) metrics

girke-lab/ChemmineR-git-svn-bridge

Cheminformatics Toolkit for R

girke-lab/ChemmineR-release

Cheminformatics Toolkit for R

ChemmineR

Cheminformatics Toolkit for R

girke-lab/ChemmineR

Cheminformatics Toolkit for R

flowBin

Combining multitube flow cytometry data by binning

destiny

Creates diffusion maps

theislab/destiny

Creates diffusion maps

bioassayR

Cross-target analysis of small molecule bioactivity

TylerBackman/bioassayR

Cross-target analysis of small molecule bioactivity

prada

Data analysis for cell-based functional assays

DepecheR

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

Theorell/DepecheR

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

lmweber/diffcyt

Differential discovery in high-dimensional cytometry via high-resolution clustering

diffcyt

Differential discovery in high-dimensional cytometry via high-resolution clustering

YosefLab/LineagePulse

Differential expression analysis and model fitting for single-cell RNA-seq data

LineagePulse

Differential expression analysis and model fitting for single-cell RNA-seq data

ImpulseDE2

Differential expression analysis of longitudinal count data sets

YosefLab/ImpulseDE2

Differential expression analysis of longitudinal count data sets

DavidQuigley/HTDoseResponseCurve

Dose Response Curve Evaluation from Incucyte and Other High-Throughput Platforms

RNAinteract

Estimate Pairwise Interactions from multidimensional features

flowFit

Estimate proliferation in cell-tracking dye studies

flowFP

Fingerprinting for Flow Cytometry

SamGG/cellGrowth

Fitting cell population growth models

cellGrowth

Fitting cell population growth models

flowBeads

flowBeads: Analysis of flow bead data

pontikos/flowBeads

flowBeads: Analysis of flow bead data

RGLab/flowCore

flowCore: Basic structures for flow cytometry data

flowCore

flowCore: Basic structures for flow cytometry data

flowPlots

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

HTSanalyzeR

Gene set over-representation, enrichment and network analyses for high-throughput screens

cbg-ethz/gespeR

Gene-Specific Phenotype EstimatoR

gespeR

Gene-Specific Phenotype EstimatoR

synlet

Hits Selection for Synthetic Lethal RNAi Screen Data

immunoClust

immunoClust - Automated Pipeline for Population Detection in Flow Cytometry

mitoODE

Implementation of the differential equation model described in "Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay"

oneillkza/ContiBAIT

Improves Early Build Genome Assemblies using Strand-Seq Data

contiBAIT

Improves Early Build Genome Assemblies using Strand-Seq Data

saezlab/CellNOpt-Feeder

Integration of CellNOptR to add missing links

CNORfeeder

Integration of CellNOptR to add missing links

saezlab/CNORfeeder

Integration of CellNOptR to add missing links

iSEE

Interactive SummarizedExperiment Explorer

csoneson/SEE

Interactive SummarizedExperiment Explorer

iSEE/iSEE

Interactive SummarizedExperiment Explorer

csoneson/iSEE

Interactive SummarizedExperiment Explorer

iSEEu

iSEE Universe

csoneson/iSEEu

iSEE Universe

iSEE/iSEEu

iSEE Universe

theislab/kBET

k-nearest neighbour batch effect test

MetaCyto

MetaCyto: A package for meta-analysis of cytometry data

hzc363/MetaCyto

MetaCyto: A package for meta-analysis of cytometry data

fmcsR

Mismatch Tolerant Maximum Common Substructure Searching

girke-lab/fmcsR-release

Mismatch Tolerant Maximum Common Substructure Searching

girke-lab/fmcsR

Mismatch Tolerant Maximum Common Substructure Searching

MIMOSA

Mixture Models for Single-Cell Assays

RGLab/MIMOSA

Mixture Models for Single-Cell Assays

bhklab/mCI

Modified Concordance Index

bhklab/wCI

Modified Concordance Index

CNORode

ODE add-on to CellNOptR

RTCA

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

DragonDuck/MaxContrastProjection

Perform a maximum contrast projection of 3D images along the z-dimension into 2D

MaxContrastProjection

Perform a maximum contrast projection of 3D images along the z-dimension into 2D

phenoDist

Phenotypic distance measures

CMET-UGent/MicroRaman

Phenotyping of microbial Raman spectroscopy data

PANR

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

cole-trapnell-lab/cicero

Precict cis-co-accessibility from single-cell chromatin accessibility data

cicero

Precict cis-co-accessibility from single-cell chromatin accessibility data

cole-trapnell-lab/cicero-release

Precict cis-co-accessibility from single-cell chromatin accessibility data

jmeskas/flowCut

Precise and Accurate Automated Removal of Outlier Events and Flagging of Files Based on Time Versus Fluorescence Analysis

RGLab/cytoqc

Quality control and standardization of cytometry data

flowQ

Quality control for flow cytometry

QUALIFIER

Quality Control of Gated Flow Cytometry Experiments

RGLab/cytoCore

R bindings for cytolib c++ library

cannin/rcellminer

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

CBIIT/rcellminer

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

rcellminer

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

girke-lab/ChemmineOB

R interface to a subset of OpenBabel functionalities

ChemmineOB

R interface to a subset of OpenBabel functionalities

hzc363/CytoDx

Robust prediction of clinical outcomes using cytometry data without cell gating

CytoDx

Robust prediction of clinical outcomes using cytometry data without cell gating

ellispatrick/SegmentedCellExperiment

S4 Class for segmented spatial 'omics data

Rchemcpp

Similarity measures for chemical compounds

C3BI-pasteur-fr/UTechSCB-SCHNAPPs

Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data

spicyR

Spatial analysis of in situ cytometry data

ellispatrick/spicyR

Spatial analysis of in situ cytometry data

staRank

Stability Ranking

CFAssay

Statistical analysis for the Colony Formation Assay

ZytoHMGU/CFAssay

Statistical analysis for the Colony Formation Assay

cbg-ethz/knockout

Statistical Analysis of High-Throughput Genetic Perturbation Screens

cbg-ethz/perturbatr

Statistical Analysis of High-Throughput Genetic Perturbation Screens

cbg-ethz/knockdown

Statistical Analysis of High-Throughput Genetic Perturbation Screens

dirmeier/knockout

Statistical Analysis of High-Throughput Genetic Perturbation Screens

perturbatr

Statistical Analysis of High-Throughput Genetic Perturbation Screens

RNAither

Statistical analysis of high-throughput RNAi screens

YosefLab/MPRAnalyze

Statistical Analysis of MPRA data

MPRAnalyze

Statistical Analysis of MPRA data

flowStats

Statistical methods for the analysis of flow cytometry data

RGLab/flowStats

Statistical methods for the analysis of flow cytometry data

plateCore

Statistical tools and data structures for plate-based flow cytometry

eg-r/sights

Statistics and dIagnostic Graphs for HTS

sights

Statistics and dIagnostic Graphs for HTS

jtheorell/flowSpecs

Tools for processing of high-dimensional cytometry data

flowSpecs

Tools for processing of high-dimensional cytometry data

saezlab/CellNOptR

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

CellNOptR

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

cokelaer/CellNOptR

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

SofieVG/FlowSOM

Using self-organizing maps for visualization and interpretation of cytometry data

FlowSOM

Using self-organizing maps for visualization and interpretation of cytometry data

saeyslab/FlowSOM

Using self-organizing maps for visualization and interpretation of cytometry data

jspidlen/flowUtils

Utilities for flow cytometry

flowUtils

Utilities for flow cytometry

flowVS

Variance stabilization in flow cytometry (and microarrays)

flowViz

Visualization for flow cytometry

ggcyto

Visualize Cytometry data with ggplot

RGLab/ggcyto

Visualize Cytometry data with ggplot

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