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IFC (version 0.1.2)

Tools for Imaging Flow Cytometry

Description

Contains several tools to treat imaging flow cytometry data from 'ImageStream' and 'FlowSight' cytometers ('Amnis', part of 'Luminex'). Provides an easy and simple way to read and write .fcs, .rif, .cif and .daf files. Information such as masks, features, regions and populations set within these files can be retrieved for each single cell. In addition, raw data such as images stored can also be accessed. Users, may hopefully increase their productivity thanks to dedicated functions to extract, visualize, manipulate and export 'IFC' data. Toy data example can be installed through the 'IFCdata' package of approximately 32 MB, which is available in a 'drat' repository . See file 'COPYRIGHTS' and file 'AUTHORS' for a list of copyright holders and authors.

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Version

Install

install.packages('IFC')

Monthly Downloads

283

Version

0.1.2

License

GPL-3

Maintainer

Yohann Demont

Last Published

October 13th, 2021

Functions in IFC (0.1.2)

Gallery Display

RIF/CIF File Writer

Graphical and Statistic Report Generation

FCS File Reader

RIF/CIF File Reader

base_axis_constr

Axis Constructor

IFC Mask Coercion

base_hist_constr

Histogram Constructor for 'base' Plot

DAF File Reader

IFC Graph Adjustment

Spatial Offsets Image Correction

buildPopulation

IFC Population Coercion

Tools for Imaging Flow Cytometry

Batch File Writer

Input Parameters Assertive Tool

RIF/CIF File Conversion to TIFF

IFC_object Decompression

Apply Transformation

DAF File Writer

IFC Files Checksum

IFC Graph Coercion

Assert that Certain Conditions are Met

Image Field Directory Builder

IFC Region Coercion

cpp_getoffsets_noid

IFC_offsets Computation without Id Determination

RIF/CIF File Checksum

IFD Tags Extraction

Ellipse Boundaries to Coordinates

DAF File Checksum

applyGatingStrategy

Apply Gating Strategy

`IFC_data` Object Check

IFC_object Extraction

IFC Statistics Coercion

Checksum for RIF/CIF

IFD Fast Tags Extraction

data_rm_regions

Remove Region from an IFC_data Object

Matrix Cleanser

cpp_int64_to_uint64

Int64 to Uint64 64bits Conversion

cpp_smoothLinLog

Smooth LinLog Transformation with Rcpp

DAF File Writer

escape_entities

XML Entities Protection

Batch Generation of Graphical and Statistic Report

Matrix Normalization

Matrix HSV to RGB Conversion

convert_to_baseplot

IFC Graph Conversion to 'base' Plot

File Path Placeholders Formatting

RIF/CIF Image Field Directories Extraction

cpp_pnt_in_gate

XML Node List Expansion

getImagesValues

RIF/CIF Image Values Extraction

fromXML2_gating

GatingML Conversion from XML2

IFC File Information Extraction

cpp_inv_smoothLinLog

Inverse Smooth LinLog Transformation with Rcpp

Luminance Computation

Numeric to String Formatting

Next Component Prediction

CreateGraphReport

Graph Report Generation

IFC_pops Levels Dependency Determination

popsGetObjectsIds

IFC_pops Object Numbers

redefine_masks_mask

IFC_masks Mask Redefinition

IFC_data Redefinition

popsRetrieveGraph

Graph Retrieval from Graphical IFC_pops

IFC_pops Population Level Ordering

Object Cleanser

String Decomposition with Operators

Object Colorizer

data_add_features

Add Feature to IFC_data Object

Lattice Histogram Panel Contructor

ExtractImages_toMatrix

Shorcut for Batch Images Extraction to Matrices/Arrays

IFC_images XML Conversion

ExtractMasks_toMatrix

Shorcut for Batch Masks Extraction to Matrices/Arrays

String Decomposition with Placeholders

First Letter Only Capitalization

Image Text Incrustation

Ellipsoid Polygon Constructor

cpp_uint64_to_int64

Uint64 to Int64 64bits Conversion

cpp_uint32_to_raw

Uint32 to Raw Conversion

Image Scale Bar Incrustation

Lattice Key Panel Contructor

popsGetSiblings2

IFC_pops Sibling Population from Same Region Identification

2D Binned Kernel Density Estimation

Colors for Smooth Density Plots

Progress Bar Terminator

IFC_masks XML Conversion

Feature Default Name Computation

Statistics Extraction

List to XML Conversion

FCS File Writer

ExportToGallery

cpp_computeGamma

Gamma Computation

FCS File Parser

IFC_pops Network Display

Character Color Check and RGB Conversion

Random Name Generator

Smooth Asinh Transformation

Equal Sized Matrix to Matrix Writer According to Mask

Smooth LinLog Transformation

Matrix Cropping

Matrix to Matrix Writer According to Mask with Offsets

data_rm_features

Remove Features from an IFC_data Object

ASSIST Database Extraction

Remove Population from an IFC_data Object

RIF/CIF File Image Field Directories Offsets Extraction

Aborted Batch Files Retrieval

inv_smoothAsinh

Inverse Smooth Asinh Transformation

Scale Constructor for IFC Graphs Plotting

ExtractImages_toBase64

Shorcut for Batch Images Extraction to Base64

inv_smoothLinLog

Inverse Smooth LinLog Transformation

Histogram y-Axis Limits Constructor

toXML2_spillover_gs

Spillover GatingML Conversion

IFC_object Decompression to RAW

Progress Bar Initializer

ExtractImages_toFile

Shorcut for Batch Images Extraction to Files

Image Field Directory Full Tag Retrieval

Matrix Resizing

File Extension Retrieval

IFC_stats XML Conversion

Hexadecimal to Integer Color Conversion

Histogram Constructor

R/IDEAS Color Palette Mapping

Object File Export

Automatic Parameters Detection for IFC Graphs

Object Extraction

Plot and Stats Computation for IFC Graph

IFC Files Generic Writer

Image Field Directory Writer

Histogram Smooth Constructor

Image Gamma Modification

RIF/CIF File Merging

popsGetSiblings

IFC_pops Sibling Population Identification

Parse Transformation Information

popsGetSiblings1

IFC_pops Sibling Population from Same Base Identification

Object Resizing

IFC_masks Redefinition

IFC_pops Computation

IFC Files Generic Reader

RIF/CIF Image Order Test

redefine_masks_image

IFC_masks Image Redefinition

objectTransform

Object Transformation

Raw Images to Base64 Encoding

Text to Image Conversion

IFC_images Raw Conversion

IFC_features Raw Conversion

redefine_features_def

IFC_features_def Redefinition

IFC_pops Checker for Object Membership to Populations

Name Protection

List to XML Node Conversion

XML Node to List Conversion

IFC Feature Coercion

redefine_features_def_feat

IFC_features_def Feature Redefinition

Integer to Hexadecimal Color Conversion

Image Gamma Computation

File Extenstion Removal

IFC_data Channel Swap

toXML2_boolpop_gs

Boolean Population GatingML Conversion to XML2

RIF/CIF File Subsetting

redefine_features_def_msk_img

IFC_features_def Mask or Image Redefinition

cpp_base64_encode

Raw to Base64 Conversion

Special Character Replacement

Progress Bar Updater

Input Identification

toXML2_features

IFC_features XML Conversion

toXML2_features_def

IFC_features_def XML Conversion

toXML2_graphpop_gs

Graphical Population GatingML Conversion to XML2

File Path Decomposition

cpp_getoffsets_wid

IFC_offsets Computation with Object Identification

writeGatingStrategy

Gating Strategy File Writer

IFC_pops XML Conversion

Histogram Type Constructor

IFC_data Default Naming

IFC_regions XML Conversion

cpp_int32_to_uint32

Int32 to Uint32 32bits Conversion

Matrix Transformation

Object Extraction Parameters Definition

data_add_regions

Add Region to IFC_data Object

Add Population to IFC_data Object

Copy Populations from One File to Another File

cpp_uint32_to_int32

Uint32 to Int32 32bits Conversion

objectNormalize

Object Intensity Normalization

popsGetAffiliation

IFC_pops Affiliation Finder

GatingML File Reader

IFC_stats Computation

readGatingStrategy

Gating Strategy File Reader

IFC_offset Subsetting

IFC_graphs XML Conversion

toXML2_graphs_gs

IFC_graphs GatingML Conversion

tryReportFileCreation

Report File Creation

String Truncation

Boolean Expression Validation

Histogram Val Constructor

Graphical and Statistic Report Display