GenePattern Modules


Click the Html or Pdf icons to view a module's documentation.

Modules in the repository can be installed on a local GenePattern server. Most of these modules are also installed on the public GenePattern server.

View by Category:

NameTypeAvailability
ApplyGatingML
Apply a Gating-ML file on an FCS data file (gate and/or transform list mode data)
Pdf  Version: 1
Flow Cytometry * Public Server Only
CompensateFCS
Compensates an FCS data file
Pdf  Version: 1
Flow Cytometry * Public Server Only
FCMFeatureExtraction
Calculation of features from clustered flow cytometry data.
Pdf  Version: 1
Flow Cytometry * Public Server Only
FCMSinglePanelQC
Single panel flow cytometry data quality control
Pdf  Version: 1
Flow Cytometry * Public Server Only
FCSNormalization
Per-channel basis normalization of flow cytometry data.
Pdf  Version: 1
Flow Cytometry * Public Server Only
FlowClustClassifyFCS
Classify flow cytometry data using the FlowClust algorithm.
Pdf  Version: 1
Flow Cytometry * Public Server Only
FlowFingerprinting
Takes a flow set and generates a description of the multivariate probability distribution function of its flow cytometry data in the form of a fingerprint
Pdf  Version: 1
Flow Cytometry * Public Server Only
FlowMeansCluster
Cluster flow cytometry data using the FlowMeans algorithm.
Pdf  Version: 1
Flow Cytometry * Public Server Only
FlowMergeCluster
Cluster flow cytometry data using FlowMerge.
Pdf  Version: 1
Flow Cytometry * Public Server Only
ImmPortCSV2TXT
Convert a .csv file to a .txt file that FLOCK can read
Html  Version: 1
Flow Cytometry * Public Server Only
ImmPortColSelection
Select a set of columns from a txt file
Html  Version: 1
Flow Cytometry * Public Server Only
ImmPortCrossSample
Applying an individual FLOCK result across another FCM sample (.txt) version 1 (1-round Kmeans)
Html  Version: 1
Flow Cytometry * Public Server Only
ImmPortFCSConvLogicleTrans
Logicle transformation of an fcs file to .txt file
Html  Version: 1
Flow Cytometry * Public Server Only
ImmPortFLOCK
Automated Gating with ImmPort FLOCK algorithm
Html  Version: 1
Flow Cytometry * Public Server Only
KMeansClassifyFCS
Find clusters in a flow cytometry file with k means clustering
Pdf  Version: 1
Flow Cytometry * Public Server Only
MClustClusterLabel
Model based labeling/matching of clusters (mate-clustering)
Pdf  Version: 1
Flow Cytometry * Public Server Only
MClustClusterLabelBIC
Bayesian information criterion (BIC) for model based labeling/matching of clusters; helps estimating the number of labels for MClustClusterLabel.
Pdf  Version: 1
Flow Cytometry * Public Server Only
PlateQAFCS
Look for consistency between wells of a single plate by computing summary statistics.
Pdf  Version: 1
Flow Cytometry * Public Server Only
SamSPECTRALClusterFCS
Cluster flow cytometry data using the SamSPECTRAL algorithm.
Pdf  Version: 1
Flow Cytometry * Public Server Only
SuggestNumberOfPopulationsFCS
The FlowClust module requires that you specify how many populations you are looking for. This module takes a data driven approach and attempts to discover how many populations are present in an FCS file
Pdf  Version: 1
Flow Cytometry * Public Server Only
AddFCSEventIndex
Adds indexes to events in a Flow Cytometry Standard (FCS) data file.
Pdf  Version: 2
Flow Cytometry Module Repository
AddFCSParameter
Add parameters and their values to a FCS data file
Pdf  Version: 2
Flow Cytometry Module Repository
AddNoiseToFCS
Add noise to specified parameters in an FCS data file.
Pdf  Version: 2
Flow Cytometry Module Repository
DeIdentifyFCS
DeIdentifyFCS an FCS data file; remove keywords from a list or matching a regular expression; useful to anonymize FCS data files and/or to remove specific (e.g., clinical) information
Pdf  Version: 1
Flow Cytometry Module Repository
ExtractFCSDataset
Extract one or more FCS datasets from an FCS data file
Pdf  Version: 2
Flow Cytometry Module Repository
ExtractFCSKeywords
Extracts keyword(s) value(s) from a Flow Cytometry Standard (FCS) file.
Pdf  Version: 2
Flow Cytometry Module Repository
ExtractFCSParameters
Extract specified parameters (dimensions) from an FCS data file.
Pdf  Version: 2
Flow Cytometry Module Repository
LogicleTransformFCS
Logicle transformation of (selected) parameters in a list mode FCS data file.
Pdf  Version: 1
Flow Cytometry Module Repository
MergeFCSDataFiles
Merge multiple FCS data files into a single FCS datasets; includes multimple subsampling options.
Pdf  Version: 1
Flow Cytometry Module Repository
PreviewFCS
Allows viewing of structural metadata, parameters, and descriptive statistics from a Flow Cytometry Standard (FCS) data file
Pdf  Version: 2
Flow Cytometry Module Repository
RemoveSaturatedFCSEvents
Remove saturated events from an FCS data file
Pdf  Version: 1
Flow Cytometry Module Repository
SetFCSKeywords
Sets keyword/value(s) in a Flow Cytometry Standard (FCS) file.
Pdf  Version: 2
Flow Cytometry Module Repository