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IFC (version 0.1.7)

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

0.1.7

License

GPL-3

Maintainer

Yohann Demont

Last Published

October 5th, 2022

Functions in IFC (0.1.7)

CreateGraphReport

Graph Report Generation

Gallery Display

FCS File Writer

RIF/CIF File Writer

ExtractImages_toMatrix

Shorcut for Batch Images Extraction to Matrices/Arrays

Graphical and Statistic Report Generation

ExtractImages_toFile

Shorcut for Batch Images Extraction to Files

ExtractMasks_toMatrix

Shorcut for Batch Masks Extraction to Matrices/Arrays

FCS_merge_sample

FCS Object Samples Merging

FCS_merge_dataset

FCS Object Data Sets Merging

FCS Object Converter

FCS File Reader

DAF File Reader

RIF/CIF File Conversion to TIFF

Image Scale Bar Incrustation

Tools for Imaging Flow Cytometry

Statistical Report Generation

ExtractImages_toBase64

Shorcut for Batch Images Extraction to Base64

RIF/CIF File Reader

Automatic Parameters Detection for IFC Graphs

IFC Graph Adjustment

Image Text Incrustation

Assert that Certain Conditions are Met

IFC Feature Coercion

IFC Graph Coercion

base_hist_constr

Histogram Constructor for 'base' Plot

base_axis_constr

Axis Constructor

Apply Transformation

applyGatingStrategy

Apply Gating Strategy

Raw Images to Base64 Encoding

IFC Region Coercion

Input Parameters Assertive Tool

Image Field Directory Builder

DAF File Checksum

Integer to Hexadecimal Color Conversion

Spatial Offsets Image Correction

2D Binned Kernel Density Estimation

IFC Image Coercion

buildPopulation

IFC Population Coercion

Raw Vectors Collapse

IFC_object Decompression

IFC Statistics Coercion

IFC Mask Coercion

Character Color Check and RGB Conversion

convert_spillover

Spillover Converter

Image Gamma Computation

`IFC_data` Object Check

cpp_fast_cbind_DF_L

Fast Dataframe and List Column Binding

cpp_fast_cbind_DF_M

Fast Dataframe and Matrix Column Binding

cpp_as_nativeRaster

Image to Native Raster Conversion

Draw Shape to Image

IFC Files Checksum

cpp_computeGamma

Gamma Computation

Matrix Cleanser

User's Coordinates to Pixels Conversion

Checksum for RIF/CIF

Matrix HSV to RGB Conversion

Matrix Cropping

cpp_fast_cbind_M_M

Matrix and Matrix Column Binding

cpp_coord_to_px

Coordinates to Pixels

cpp_base64_encode

Raw to Base64 Conversion

RIF/CIF File Checksum

cpp_fast_factor

Fast Factorize Vector

cpp_fast_rowAny

Use Rcpp to Apply Any on Matrix Rows

cpp_fast_sample

Use Rcpp for Sampling

cpp_fast_cbind_M_DF

Fast Matrix and Dataframe Column Binding

cpp_fast_cbind_L_DF

Fast List and Dataframe Column Binding

Ellipse Boundaries to Coordinates

IFD Tags Extraction

cpp_get_bytes_order

Get Bytes Order

cpp_fast_cbind_DF_DF

Dataframe and Dataframe Column Binding

IFD Fast Tags Extraction

data_add_features

Add Feature to IFC_data Object

data_add_graphs

Add Graphs to IFC_data Object

IFC_object Extraction

Matrix to Matrix Writer According to Mask with Offsets

cpp_int32_to_uint32

Int32 to Uint32 32bits Conversion

cpp_inv_smoothLinLog

Inverse Smooth LinLog Transformation with Rcpp

Equal Sized Matrix to Matrix Writer According to Mask

IFC_object Decompression to RAW

cpp_int64_to_uint64

Int64 to Uint64 64bits Conversion

cpp_uint32_to_raw

Uint32 to Raw Conversion

cpp_v_int64_to_uint64

Vectorize Int64 to Uint64 64bits Conversion

cpp_uint32_to_int32

Uint32 to Int32 32bits Conversion

Data Frame Merge Groups with Rcpp

cpp_fast_listAny

Use Rcpp to Apply Any on List members

cpp_getoffsets_noid

IFC_offsets Computation without Id Determination

cpp_getoffsets_wid

IFC_offsets Computation with Object Identification

Use Rcpp for Range

cpp_replace_non_finite

Non Finite Values Replacement

Matrix Resizing

data_rm_regions

Remove Region from an IFC_data Object

AST File Writer

XML Node List Expansion

Sequence of Strings Matching

cpp_v_int32_to_uint32

Vectorize Int32 to Uint32 32bits Conversion

cpp_uint64_to_int64

Uint64 to Int64 64bits Conversion

data_rm_features

Remove Features from an IFC_data Object

data_add_regions

Add Region to IFC_data Object

List IFC features

Feature Default Name Computation

ASSIST Database Extraction

Alternative Names Generator

Matrix Normalization

cpp_pnt_in_gate

Luminance Computation

IFC File Information Extraction

Aborted Batch Files Retrieval

Histogram y-Axis Limits Constructor

getFeaturesValues

Features Values Extraction

Statistics Extraction

DAF File Writer

escape_entities

XML Entities Protection

Colors for Smooth Density Plots

File Extension Retrieval

Progress Bar Terminator

inv_smoothLinLog

Inverse Smooth LinLog Transformation

Image Field Directory Full Tag Retrieval

Image Gamma Modification

get_coordmap_raw

Device Raw Coordinates

cpp_smoothLinLog

Smooth LinLog Transformation with Rcpp

Groups Combination

objectTransform

Object Transformation

Report Layout Extraction

Remove Graph from an IFC_data Object

Object Cleanser

String Sequence Replacement

Object Resizing

Matrix Transformation

RIF/CIF File Merging

get_coordmap_adjusted

Device Adjusted Coordinates

R/IDEAS Color Palette Mapping

Object File Export

Histogram Constructor

Object Colorizer

Lattice Key Panel Contructor

Lattice Histogram Panel Contructor

Remove Population from an IFC_data Object

`IFC_plot` Conversion to 'raster' Plot

Scale Constructor for IFC Graphs Plotting

Progress Bar Initializer

IFC_pops Checker for Object Membership to Populations

Combine by Columns

Statistics Report Template Extraction

popsGetObjectsIds

IFC_pops Object Numbers

Object Extraction

FCS File Parser

popsGetSiblings

IFC_pops Sibling Population Identification

Add Population to IFC_data Object

data_add_pop_sample

Population Sampling

Smooth LinLog Transformation

IFC_pops Network Display

Special Character Replacement

GatingML File Reader

readGatingStrategy

Gating Strategy File Reader

`IFC_plot` Statistics Extraction

IFC Files Generic Reader

RIF/CIF File Image Field Directories Offsets Extraction

Parse Transformation Information

Next Component Prediction

popsGetAffiliation

IFC_pops Affiliation Finder

Object Extraction Parameters Definition

`IFC_plot` Conversion to 'base' Plot

File Path Placeholders Formatting

`IFC_plot` Conversion to 'lattice' Plot

objectNormalize

Object Intensity Normalization

Hexadecimal to Integer Color Conversion

Name Protection

popsGetSiblings1

IFC_pops Sibling Population from Same Base Identification

IFC_images XML Conversion

redefine_masks_mask

IFC_masks Mask Redefinition

popsGetSiblings2

IFC_pops Sibling Population from Same Region Identification

IFC_regions XML Conversion

Random Name Generator

IFC_pops XML Conversion

IFC_masks XML Conversion

Populations Renaming

File Extension Removal

Numeric to String Formatting

Plot and Stats Computation for IFC Graph

popsRetrieveGraph

Graph Retrieval from Graphical IFC_pops

IFC_pops Levels Dependency Determination

redefine_features_def

IFC_features_def Redefinition

IFC_features_def Definition Splitting

File Path Decomposition

fromXML2_gating

GatingML Conversion from XML2

RIF/CIF Image Field Directories Extraction

Progress Bar Updater

IFC_pops Population Level Ordering

Statistics Extraction from Populations

toXML2_boolpop_gs

Boolean Population GatingML Conversion to XML2

Text to Image Conversion

Histogram Type Constructor

IFC_data Redefinition

RIF/CIF Image Order Test

IFC_offset Subsetting

RIF/CIF File Subsetting

toXML2_features_def

IFC_features_def XML Conversion

XML Node to List Conversion

toXML2_graphpop_gs

Graphical Population GatingML Conversion to XML2

IFC_stats XML Conversion

IFC_data Default Naming

toXML2_spillover_gs

Spillover GatingML Conversion

toXML2_features

IFC_features XML Conversion

Input Identification

List to XML Node Conversion

List to XML Conversion

Feature Values Computation

Histogram Smooth Constructor

getImagesValues

RIF/CIF Image Values Extraction

FCS Name Parser

inv_smoothAsinh

Inverse Smooth Asinh Transformation

IFC_pops Computation

writeGatingStrategy

Gating Strategy File Writer

IFC_graphs XML Conversion

redefine_masks_image

IFC_masks Image Redefinition

Copy Populations from One File to Another File

IFC_masks Redefinition

String Truncation

Smooth Asinh Transformation

IFC_features Raw Conversion

redefine_features_def_feat

IFC_features_def Feature Redefinition

IFC_images Raw Conversion

IFC Files Generic Writer

Image Field Directory Writer

toXML2_graphs_gs

IFC_graphs GatingML Conversion

tryReportFileCreation

Report File Creation

redefine_features_def_msk_img

IFC_features_def Mask or Image Redefinition

Histogram Val Constructor

String Decomposition with Placeholders

String Decomposition with Operators

Boolean Expression Validation

Ellipsoid Polygon Constructor

First Letter Only Capitalization

BatchStatsReport

Batch Generation of Statistic Report

Batch File Writer

Batch Generation of Graphical and Statistic Report

DAF File Writer

Graphical and Statistic Report Display

ExportToGallery