SHIFTX
Calculates the diamagnetic 1H, 13C and 15N chemical shifts of both backbone and sidechain atoms in proteins.
SPARTA / Shifts Predicted from Analogy in Residue type and Torsion Angle
A database system for empirical prediction of backbone chemical shifts (N, HN, HA, CA, CB, CO) using a combination of backbone phi, psi torsion angles and sidechain chi1 angles from a given protein with known PDB coordinates.
SPARTA+
Employs a well-trained neural network algorithm to make rapid chemical shift prediction on the basis of known structure.
CamShift
A method for the rapid and accurate prediction of NMR chemical shifts from protein structures. The calculations performed by CamShift are based on an approximate expression of the chemical shifts in terms of polynomial functions of interatomic distances. Since these functions are very fast to compute and readily differentiable, the CamShift approach can be utilized in standard protein structure calculation protocols.
SHIFTCALC
This package calculates shifts for all 1H and for Ca and Cb shifts.
CheShift
Allows protein structure validation based on a quantum mechanics database of 13Cα chemical shifts. CheShift is a physics-based validation tool that permits users to determine the existence of local flaws in protein models. The software displays the differences between observed and predicted 13Cα chemical shifts by using a four-color code mapped onto a 3D protein model. A standalone version consisting of a PyMOL plugin is also available.
CS23D
A web server for rapidly generating accurate 3D protein structures using only assigned NMR chemical shifts as input.
cleverSuite
Predicts secondary structure properties, solubility, chaperone requirements and RNA-binding abilities.
Ionwinze
Tool to pick out ion signals that discriminate two groups of samples (e.g. diseased/healthy, resistant/susceptible) by quasi-datapoint-wise comparison using univariate statistic procedures.
FAIR / Find All Internal Repeats
A web server which has been deployed to identify the internal sequence repeats in protein as well as DNA sequences. FAIR has been tested with a protein sequence of more than 35000 residues available in the genome database. Also, the proposed server accepts many sequences at a time.
SCLAP
Investigates chloroplast proteins to forecast potential subchloroplast location. SCLAP intends to assist researchers in annotating existing and new plant genomes. It provides a platform able to perform either a single protein from a raw sequence or a batch submission from a file including several sequences in FASTA format. This software can not be used to qualify a protein as chloroplast or not.
Genomon ITDetector
Detects somatic internal tandem duplications (ITDs) from cancer genome sequencing data. Genomon ITDectector performs genome-wide identification of ITDs in the target tumor sample and filters out uncertain candidates to remove false positives because of the mis-alignments brought by the redundancy of the genome. This software is specifically designed for performing sensitive and genome-wide detection of somatic ITDs spanning several tens to several hundreds of base pairs.
BBT / BioBloom tools
Enables creation of filters for a given reference and then categorization of sequences. BBT is a Bloom filter implementation that includes heuristics to control false positives and increase speed. The software was designed for pre-processing and quality check (QC) applications like contamination detection, but it can be suitable for other purposes.
subSeq
Performs subsampling sequencing reads with binomial sampling. After constructing subsamples and performing an analysis on each, subSeq calculates and visualizes summary metrics about each sequencing depth. It reports metrics representing (i) the power to detect differential expression or abundance, (ii) the accuracy of effect size estimation and (iii) the estimated rate of false discoveries relative to the full experiment.
VirVarSeq
Allows variant calling at the codon level. VirVarSeq is a low frequency virus variant detection pipeline that identifies true variants at the codon level within a viral population using Illumina sequencing. Q-cpileup, an approach for variant calling at the codon level, that reduces the number of false-positive findings by exploiting the Quality scores (Qs) of the nucleotides generated by sequencing, is imbedded in the pipeline.
matplotlib
Produces for researchers publication-quality figures in a variety of hardcopy formats and interactive environments across platforms. Matplotlib is conceptually divided into three parts: (1) the pylab interface user to create plots with code quite similar to MATLAB; (2) the frontend or API is the set of classes that do the heavy lifting, creating and managing figures, text, lines, plots; and (3) the backends are device-dependent drawing devices that transform the frontend representation to hardcopy or a display device.
Inkscape
An open-source vector graphics editor similar to Adobe Illustrator, Corel Draw, Freehand, or Xara X.
TikZ and PGF
TeX packages for creating graphics programmatically. TikZ is build on top of PGF and allows you to create sophisticated graphics in a rather intuitive and easy manner. TikZ offers all the advantages of the “TEX-approach to typesetting” for graphics: quick creation of simple graphics, precise positioning, the use of macros, often superior typography. PGF is a TeX macro package for generating graphics. It is platform- and format-independent and works together with the most important TeX backend drivers, including pdftex and dvips.
GIMP / GNU Image Manipulation Program
Provides top-notch color management features to ensure high-fidelity color reproduction across digital and printed media. GIMP is a freely distributed program for such tasks as photo retouching, image composition and image authoring. It provides extensibility through integration with many programming languages including Scheme, Python, Perl, and more, and results is a high level of customization as demonstrated by the large number of scripts and plug-ins created by the GIMP community.
ImageMagick
A software suite to create, edit, compose, or convert bitmap images from the command line.
D3.js
Allows to manipulate documents based on data. D3.js is a library that combines visualization components and a data-driven approach to Document Object Model (DOM) manipulation. User can bind arbitrary data to a DOM and apply data-driven transformations to the document.
Adobe Illustrator
Create vector art and illustrations using advanced, precise drawing and typography tools.
CorelDraw
A software tool for designing graphics and layouts, edit photos, and create websites. With advanced support for Windows 10, multi-monitor viewing and 4K displays, the suite lets first-time users, graphics pros, small business owners and design enthusiasts deliver professional results with speed and confidence. Discover high-caliber and intuitive tools within your graphic design software to create logos, brochures, web graphics, social media ads or any original project.
jointseg
This package implements functions to quickly segment multivariate signals into piecewise constant profiles and a framework to generate realistic copy-number profiles.
PSCBS
Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome.
UbPred
A random forest-based predictor of potential ubiquitination sites in proteins.
UbiProber
Designed for large-scale predictions of both general and species-specific ubiquitylation sites.
UbiPred
An informative physicochemical property mining algorithm for mining informative physicochemical properties from protein sequences to build an SVM-based prediction system. UbiPred can predict ubiquitylation sites accompanied with a prediction score each to help biologists in identifying promising sites for experimental verification.
hCKSAAP_UbSite
A human-specific ubiquitination site predictor through the integration of multiple complementary classifiers. Firstly, a Support Vector Machine (SVM) classier was constructed based on the composition of k-spaced amino acid pairs (CKSAAP) encoding, which has been utilized in our previous yeast ubiquitination site predictor. To further exploit the pattern and properties of the ubiquitination sites and their flanking residues, three additional SVM classifiers were constructed using the binary amino acid encoding, the AAindex physicochemical property encoding and the protein aggregation propensity encoding, respectively. Through an integration that relied on logistic regression, the resulting predictor termed hCKSAAP_UbSite achieved an area under ROC curve (AUC) of 0.770 in 5-fold cross-validation test on a class-balanced training dataset.
DDI / Drug-Drug Interactions
Retrieves drug-drug interactions (DDIs) from biomedical text. DDI employs a method that combines feature sets and partitions datasets into subsets based on their syntactic properties. It maps each candidate DDI pair into a syntactic container before generating features. This tool utilizes various natural language processing (NLP) approaches and a support vector machine (SVM) method.
INDI
Deduces novel drug-drug interactions (DDIs). INDI supports pharmacokinetic and pharmacodynamic DDIs. It enables the recommendation of the type of action to take upon administration of the two drugs and the inference of the cytochrome P450 (CYP) isoforms involved when the interaction is CYP-related. This tool does not consider the method of administration of the drug. It can be used for the improvement of patient treatment.
Drug Interactions Checker
Explains what the interaction is, how it occurs, the level of significance (major, moderate, or minor) and usually a suggested course of action. Drug Interactions Checker is an informational resource designed to assist licensed healthcare practitioners in caring for their patients and provide consumers with drug specific information. This web app can also display any interactions between chosen drug(s) and food, beverages, or a medical condition.
DynDom
A program that determines protein domains, hinge axes and amino acid residues involved in the hinge bending.
ProSTRIP
Finds similar structural repeats in a three-dimensional protein structure. ProSTRIP uses the protein backbone dihedral angles (computed using the four consecutive Cα atoms) for repeat detection. Further, the computed angles are translated into alpha characters for quick scanning. ProSTRIP uses a dynamic programming method to identify the internal sequence repeats. In addition to the detection of ungapped repeat stretch, the method has been designed with an additional feature of finding high scoring segment pairs (HSPs). An internet computing server is also created by implementing this method and enables graphical visualization of the results.
REPPER / REPeats and their PERiodicities
Detects and analyzes regions with short gapless repeats in protein sequences or alignments. REPPER is a web server that implements programs using a sliding window, so as to show the boundaries of periodic regions and allow the detection of multiple regions with different periodicities in the same protein. User can take a multiple sequence alignment as input, and also calculate a profile for a given single input sequence using PSI-BLAST with two iterations and an E-value cutoff of 0.001.
CENSOR
A software tool which screens query sequences against a reference collection of repeats and "censors" (masks) homologous portions with masking symbols, as well as generating a report classifying all found repeats.
CutProtFam-Pred
An on-line tool that allows one to query sequences from proteomes or translated transcriptomes, for the accurate detection and classification of putative structural cuticular proteins.
jvenn
A plug-in for the jQuery Javascript library. Jvenn hanldes up to six classes venn diagram and is easily integrable within web sites. It allows to display Edwards-Venn diagram and to provide the data from three different ways (lists/intersection counts/count lists). It provides statistic charts based on input data and exports the venn diagram to PNG and SVG, and exports lists to CSV. jvenn is based upon the venny tool.
VENNTURE
Allows simultaneous analysis of multiple large and complex pharmacological datasets. VENNTURE provides an interface for Edwards Venn diagram generation. The software facilitates the analysis of two to six sets of any length of dataset. It can be useful in the analysis of complex datasets in pharmacology, genomics, and bioinformatics research fields. Applied to complex sets of signaling data, VENNTURE can assist in the elucidation of the subtle effects that environmental perturbations can exert upon dose-dependent ligand actions.
Pangloss Venn diagram generator
Generates little Venn diagram representing the intersections of the lists. Pangloss Venn diagram generator needs four lists as inputs. The software then provides what they share in common.
VENNY
Assists users in comparing lists. Venny provides an interactive application with Venn's diagrams, a figure that shows all possible logical relations between a finite collection of different sets. It permits to compare 2, 3 or 4 lists of data. It also offers an offline version that consists on a single standard html file. Finally, this method allows basic customization of user’s diagrams (line weight, font size and style).
DrawVenn
Generates area-proportional 2-Venn diagrams. DrawVenn processes by using circles and area-proportional 3-Venn diagrams using rectangles.
BioVenn
Allows users to compare and visualize biological lists using Venn diagrams. BioVenn is a web application that generates circular area-proportional Venn diagrams from lists of biological identifiers. The software supports a wide range of identifiers from the most used biological databases (Affymetrix, COG, Ensembl, EntrezGene, Gene Ontology, InterPro, IPI, KEGG Pathway, KOG, PhyloPat [and RefSeq).
GeneVenn
Creates Venn diagrams from two or three gene lists. GeneVenn is a web application that generates Venn diagrams with hyperlinks, on each area on the diagram, showing the related gene list. Each gene name has linked to the related information in NCBI’s Entrez Nucleotide database. Users can modify every element of the generated diagram, including font, color and title.
VennMaster
Provides an alternative visualization approach with area-proportional Euler diagrams. VennMaster was integrated into the GoMiner software. That integration provides a seamless interface for user, and eliminates the overhead of performing file operations and managing external files. This application is implemented as a platform-independent open source Java application. It shows set relationships with semi-quantitative size information in a single diagram to support biological hypothesis formulation.
VennDiagram
Allows generation of highly customizable, high-resolution Venn diagrams with up to four sets and Euler diagrams of two or three sets. VennDiagram allows drawing Euler diagrams using circles and/or ellipses with two or three sets and generation of high resolution TIFF files that are standard in publications. The software can assist the promotion of the usage of automatically generated Venn diagrams within computational pipelines.
CanvasXpress
Enables creation of visualizations. CanvasXpress is a standalone JavaScript library for reproducible research with complete tracking of data and end-user modifications, which supports a large number of visualizations to display scientific and non-scientific data. The software also includes a standalone unobtrusive data table and a filtering widget to allow data exploration. It allows to sort, group, transpose, transform or dynamically cluster data.
ClaRNA
A method for computational classification of contacts in RNA 3D structures.
RNAView
Generates 2-dimensional displays of RNA/DNA secondary structures with tertiary interactions.
Mc-Annotate
Extracts and manipulates structural information, to simplify further structural analyses and searches, and to objectively represent structural knowledge. Mc-Annotate allows one to classify the nucleotide conformations and base-base interactions, and to detect marginal regions that could indicate interactions with other molecules, or new sites that are responsible for structure and/or function. Mc-Annotate also made possible the creation of databases of nucleotide conformations and base-base interactions, extracted from all available DNA and RNA 3-D structures, which were indexed using the symbolic information.
Kotai Antibody Builder
A web app for tertiary structural modeling of antibody variable regions. Kotai Antibody Builder constructs three-dimensional (3D) structures of antibody variable domains from sequence using canonical rules, new H3-rules and evolutionary information. This web app is a fully automated version of the semi-automated pipeline used successfully in the Second Antibody Modeling Assessment (AMA-II).
PIGS
A web server for the automatic modeling of immunoglobulin variable domains based on the canonical structure method. PIGS has a user-friendly and flexible interface, that allows the user to choose templates (for the frameworks and the loops) and modeling strategies in an automatic or manual fashion. Its final output is a complete three-dimensional model of the target antibody that can be downloaded or displayed on-line. The server is freely accessible to academic users, with no restriction on the number of submitted sequences.
ArrayMining
Provides access to multiple algorithms for tasks in statistical microarray analysis. ArrayMining consists of six main modules for microarray analysis: Cross-Study Normalization, Gene selection, Class Discovery, Class Assignment, Network Analysis, and Gene Set Analysis. The software allows users to analyze arbitrary DNA-chip data and other high-dimensional data sets. Depending on the chosen module and algorithm, the data can be forwarded to further analysis modules and is interlinked with annotation data from external web-tools and data bases.
EnrichNet
Enables a direct molecular interpretation of how a user-defined set of genes/proteins is related to a gene/protein set of known function. EnrichNet is an integrative enrichment analysis method. It combines a novel graph-based statistic, developed to exploit information from the molecular network structure connecting two gene/protein sets, with a new interactive visualization of network sub-structures.
GSAASeqSP
A toolset for genome-wide gene set association analysis of sequence count data. This toolset offers a variety of statistical procedures via combinations of multiple gene-level and gene set-level statistics, each having their own strengths under different sample and experimental conditions. These methods can be employed independently, or results generated from multiple or all methods can be integrated to determine more robust profiles of significantly altered biological pathways.
SUPPA
Allows to analyze differential splicing. SUPPA measures differential splicing between conditions by exploiting the variability between biological replicates to determine the uncertainty in the proportion spliced-in (PSI) values. The software is also able to analyze multiple conditions by computing the pairwise differential splicing between conditions, and can detect groups of events with similar splicing patterns across conditions using density-based clustering.
Pegasus
A pipeline for the annotation and prediction of biologically functional gene fusion candidates. Pegasus provides a common interface for various gene fusion detection tools, reconstruction of novel fusion proteins, reading-frame-aware annotation of preserved/lost functional domains, and data-driven classification of oncogenic potential. Pegasus dramatically streamlines the search for oncogenic gene fusions, bridging the gap between raw RNA-Seq data and a final, tractable list of candidates for experimental validation.
SimMet
A robust high throughput informatics tool for qualitative and quantitative analysis of mass spectrometry metabolite data. SimMet® supports peak detection, peak picking, retention time alignment and differential analysis of LC-MS data across multiple biological samples. It enables you to run metabolite identification studies using MS and MS/MS data in batch mode.
SimGlycan
Predicts structure of glycans from the MS/MS and multi-stage mass spectrometry (MSn) data. Furthermore, comprehensive support for resolving glycopeptides using LC-MS/MS glycopeptide data facilitates glycosylation studies.
ProteoIQ
A comprehensive suite to validate and quantify proteins by combining results from popular mass spectrometry platforms and database search engines. With dynamic extracted ion chromatogram plots, the ability to view every MS spectra at any time point and the ability to manually select a peak area, ProteoIQ® provides the ultimate level of control. ProteoIQ® provides a completely customizable interface to support any form of biological annotation. You can easily compare protein quantitative results in relation to biological pathways, protein localization, protein function, or even compare to transcript abundance. Every protein identification in ProteoIQ® can be linked to any external or internal knowledge database. Custom links are provided to GenBank, UniProt, IPI, and SwissProt databases or even an in-house LIMS.
OpenCyto
Enables automated, datadriven gating of high-dimensional flow cytometry (FCM) data sets. OpenCyto is a collection of well-integrated open-source R/BioConductor packages: ncdfFlow, flowCore, flowViz, flowWorkspace, and openCyto. The software aims to meet the challenges of ease of use, interpretability, scalability, collaboration, comparative analysis, reproducibility and robustness, while allowing analysts to integrate domain-specific knowledge into the analysis pipeline. It supports importing gates from external software.
flowBeads
Extends flowCore to provide functionality specific to bead data. One of the goals of flowBeads is to automate analysis of bead data for the purpose of normalisation.
flowBin
A package based on a parameterization-free method for combining multitube FCM data into a higher-dimensional form suitable for deep profiling and discovery. FlowBin allocates cells to bins defined by the common markers across tubes in a multitube experiment, then computes aggregate expression for each bin within each tube, to create a matrix of expression of all markers assayed in each tube. It is designed to accept multiple FCM assays from the same multitube assay and combine these into a complete matrix of measurements for all the markers. To this end, flowBin consists of four stages: (i) normalization, (ii) binning, (iii) bin matching across tubes and (iv) expression measurement. Compared with NNs merging of tubes, flowBin produces cleaner data, with far fewer false double-positive marker combinations.
flowCL
Performs semantic labelling of cell populations based on their surface markers and applied it to labelling of the Federation of Clinical Immunology Societies Human Immunology Project Consortium lyoplate populations as a use case. flowCL enables researchers to unambiguously label their cell populations based on their immunophenotype using the CL and allows for unambiguous and reproducible identification of standardized cell types. It decomposes a query such as ‘CD4+CD8−’ (as provided in the conventional format used by immunologists) into its individual markers (CD4, CD8) and translates their relative abundance into a relation used in the CL, such as + for has plasma membrane part. As the CL development proceeds, flowCL automatically remains up-to-date with the latest scientific knowledge.
flowClust
A package dedicated to FCM gating analysis, addressing the increasing demand for software capable of processing and analyzing the voluminous amount of FCM data efficiently via an objective, reproducible and automated means. flowClust implements a robust model-based clustering approach based on multivariate t mixture models with the Box-Cox transformation. It provides the functionality to identify cell populations whilst simultaneously handling the commonly encountered issues of outlier identification and data transformation. flowClust offers various tools to summarize and visualize a wealth of features of the clustering results. To ensure its convenience of use, it has been adapted for the FCM data format, and integrated with existing Bioconductor packages dedicated to FCM analysis. flowClust contributes to the cytometry community by offering an efficient, automated analysis platform which facilitates the active, ongoing technological advancement.
flowCore
A data management system for flow cytometry data analysis. flowCore allows to handle flow cytometry high content screening data and encourages open development of tools for their coherent analysis. A key component of this package is having suitable data structures that support the application of similar operations to a collection of samples or a clinical cohort. Flowcore constitutes a shared and extensible research platform that enables collaboration between bioinformaticians, statisticians, biologists and clinicians.
flowCyBar
A package to analyze flow cytometric data using gate information to follow population/community dynamics.
flowFlowJo
Provides a way to extract data from one such commercial package, FlowJo, into the publicly accessible analysis platform R/Bioconductor. flowflowJo can produce R data structures with either summary statistics or fully flowCore compliant objects representing the various gates, compensation matrices, and other related information embedded in FlowJo sessions. Its goal is to make it easy to use compensation and gating information that has been produced using FlowJo. The flowFlowJo package provides the ability to work with both the raw data and the gating information in a powerful analysis environment that makes full use of the existing open source community efforts. Additional functionality is gained by the ability of the user to effectively run all of the compensation and gating functions described by the workspace(s) and automatically retrieve all of the relevant summary statistics into a concise data structure.
flowFP
A package for the analysis of flow cytometry data. flowFP provides tools to transform raw flow cytometry data into a form suitable for direct input into conventional statistical analysis and empirical modeling software tools. The approach of flowFP is to generate a description of the multivariate probability distribution function of flow cytometry data in the form of a “fingerprint.” As such, it is independent of a presumptive functional form for the distribution, in contrast with model-based methods such as Gaussian Mixture Modeling. The broad aim of the package is to directly transform raw FC list-mode data into a representation suitable for direct input to other statistical analysis and empirical modeling tools. Thus, it is useful to think of flowFP as an intermediate step between the acquisition of high-throughput FC data on the one hand, and empirical modeling, machine learning, and knowledge discovery on the other.
flowMap
Quantifies the similarity of cell populations across multiple flow cytometry samples using a nonparametric multivariate statistical test. flowMap is able to map cell populations of different size, shape, and proportion across multiple flow cytometry samples. The algorithm can be incorporate in any flow cytometry work flow that requires accurate quantification of similarity between cell populations.
flowFit
Performs quantitative analysis of cell proliferation in tracking dye-based experiments. flowFit, distributed as an R Bioconductor library, is based on a mathematical model that takes into account the height of each peak, the size and position of the parental population (labeled but not proliferating) and the estimated distance between the brightness of a cell and the brightness of its daughter (in which the dye is assumed to undergo a 2-fold dilution). Although the algorithm does not make any inference on cell types, rates of cell divisions or rates of cell death, it deconvolutes the actual collected data into a set of peaks, whereby each peak corresponds to a subpopulation of cells that have divided N times.
flowMatch
A package based on a hierarchical algorithm to first match the corresponding clusters across samples for producing robust meta-clusters, and to then construct a high-dimensional template as a collection of meta-clusters for each class of samples. The flowMatch algorithm is able to construct representative templates from the samples before and after stimulation, and to match corresponding meta-clusters across templates. The templates of the pre-stimulation and post-stimulation data corresponding to memory and naive T cell populations clearly show, at the level of the meta-clusters, the overall phosphorylation shift due to the stimulation. Using flowMatch, the meta-clusters across samples can be matched to assess overall differences among the samples of various phenotypes or time-points.
flowMeans
A package based on a time-efficient and accurate method for automated identification of cell populations in flow cytometry (FCM) data based on K-means clustering. Unlike traditional K-means, flowMeans can identify concave cell populations by modelling a single population with multiple clusters. It uses a change point detection algorithm to determine the number of sub-populations, enabling the method to be used in high throughput FCM data analysis pipelines. Our approach compares favourably to manual analysis by human experts and current state-of-the-art automated gating algorithms. flowMeans addresses all the issues that prevented the application of K-means to FCM data in the past. This package is a powerful tool for identification of cell populations as part of high throughput and accurate FCM data analysis.
flowPeaks
A fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.
flowMerge
A framework for the identification of cell subpopulations in flow cytometry data based on merging mixture components using the flowClust methodology. flowMerge is based on a cluster merging algorithm which improves model fit and provides a better estimate of the number of distinct cell subpopulations than either Gaussian mixture models or flowClust, especially for complicated flow cytometry data distributions. It allows the automated selection of the number of distinct cell subpopulations and enables to identify cases where the algorithm fails, thus making it suitable for application in a high throughput FCM analysis pipeline. flowMerge provides a good compromise between the flowClustBIC and flowClustICL solutions by combining the good model fitting characteristics of BIC-based model selection with a more modest estimate of the true number of clusters, a characteristic of the ICL-based model selection.
flowPhyto
An R package that performs aggregate statistics on virtually unlimited collections of raw flow cytometry files and provides a memory efficient, parallelized solution for analyzing high-throughput flow cytometric data.
MALDIVision
A comprehensive bioinformatics tool for MALDI tissue imaging, facilitates data processing, visualization and analysis of spatial distribution of individual ions across the sampled locations on a tissue section. The program accepts imaging mass spectrometric data in standard file formats. MALDIVision generates an ion intensity map for any m/z in the analysis range, enabling simultaneous imaging of many compounds. Users can view images in 2-D and in 3-D.
flowPlots
A package which offers 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.
flowQB
Evaluates backgrounds and statistical photoelectron (Spe) scales on fluorescence cytometers. flowQB is an automated analysis method that allows users to calculate detector efficiency, optical background and intrinsic CV of the beads. An alternative method, included in the flowQB package, re-evaluates the weights after initial fitting and refits until the results reach convergence. This software was applied to a series of instruments using both LED signals and multilevel, multidye bead sets.
flowStats
Methods and functionality to analyse flow data that is beyond the basic infrastructure provided by the flowCore package.
flowTrans
A package that provides profile maximum likelihood estimation of parameters for flow cytometry data transformations. Parameter-optimized transformations improve visualization, reduce variability in the location of discovered cell populations across samples, and decrease the misclassification (mis-gating) of individual events when compared to default-parameter counterparts.
flowType
A package based on a computational approach that automatically reveals all possible cell subsets. By using flowType, from tens of thousands of subsets, those that correlate strongly with clinical outcome are selected and grouped. Within each group, markers that have minimal relevance to the biological outcome are removed, thereby distilling the complex dataset into the simplest, most clinically relevant subsets. This allows complex information from PFC studies to be translated into clinical or resource-poor settings, where multiparametric analysis is less feasible. In particular, this computational approach holds significant potential for: (i) detailed exploratory analysis of the immune system (using a high number of markers to parse the cell populations); (ii) analysis of large cohorts of subjects (e.g. clinical studies and vaccine/drug trials); and (iii) screening studies to identify appropriate marker panels for further clinical investigation.
flowUtils
A package that provides utilities for flow cytometry data.
flowViz
A package that provides graphical diagnostics and quality assessment applications. flowViz adapts principles of Trellis graphics to FCM data. It provides useful visualizations that can aid automated analysis of flow cytometry data.
flowWorkspace
A package that makes manually gated data accessible to BioConductor’s computational flow tools by importing pre–processed and gated data from the widely used manual gating tool, FlowJo. flowWorkspace makes manually gated data from large, arbitrarily complex FCM studies accessible in the R environment. It imports compensation matrices, data transformations, manual gates, and FCS files from analyses described in FlowJo workspaces, and reproduces them using the BioConductor flow toolset, thus making manually gated data accessible to the computational flow community. The tool has methods implemented for visualizing, summarizing, extracting and exporting population statistics for gated cell populations. Importantly, it can handle large FCM data sets through support of NetCDF via the ncdfFlow package. flowWorkspace can also be used to export data to the LabKey tool, allowing one to use R as the engine for flow data analysis with a LabKey front end and data repository.
ncdfFlow
Provides netCDF storage based methods and functions for manipulation of flow cytometry data.
QUALIFIER
Takes advantage of the manual gates to perform an extensive series of statistical quality assessment checks on the gated cell sub–populations while taking into account the structure of the data and the study design to monitor the consistency of population statistics across staining panels, subject, aliquots, channels, or other experimental variables. QUAliFiER implements SVG–based interactive visualization methods, allowing investigators to examine quality assessment results across different views of the data, and has a flexible interface allowing users to tailor quality checks and outlier detection routines to suit their data analysis needs. The QUAliFiER tool objectively, efficiently, and reproducibly identifies outlier samples in an automated manner by monitoring cell population statistics from gated or ungated flow data conditioned on experiment–level metadata.
FLAME / FLow analysis with Automated Multivariate Estimation
Uses finite mixture model clustering techniques with novel algorithms and models to define and characterize discrete populations in flow cytometric data. A distinguishing feature of FLAME is its use of skewt distributions, which was motivated by the observation that biologically meaningful data clusters are often skew and heavy-tailed. FLAME includes a metaclustering step during which cell populations are matched across samples.
FlowAnd
A flow cytometric tool for systematic and efficient analysis of large multidimensional datasets.
FlowJo
A flow cytometry data analysis software.. FlowJo contains a list of loaded samples (experimental data), statistics, gates, and other analyses, as well as tabular and graphical layouts. FlowJo provides features and tools for the creation of histogram and other plot overlays, cell cycle analysis, calcium flux analysis, proliferation analysis, quantitation, cluster identification and backgating display.
WinList
Offers a platform dedicated to cytometry analysis. WinList is an application provindingg a wide range of features including: (i) the production of ratio parameters, equations, alerts as well as reusable report templates and individual histograms; (ii) multiple analysis dealing with rare-event or leukemia-lymphomaanalysis; (iii) the highlighting of events and possible relationships of markers.
Cytometry
Designed to help you find fluorescent reagents, kits, and protocols for cell biology–related flow cytometry applications.
GenoSIGHT
An imaging system package relying on a closed-loop control algorithm to adapt the collection of a series of time-lapse images to optimize the measurement of gene expression data in individual cells. GenoSIGHT allows users to define their own functions to analyze cell properties like fluorescence, growth, shape, or intracellular distribution of proteins to any criteria defined by the user. GenoSIGHT is capable of detecting that cells are not behaving as expected and notify the operator in real-time so that the experiment can be restarted immediately.
TACTICS
A modular MATLAB(R) Toolbox for time-lapse image analysis.
CellTracer
An integrated graphical user interface written in MATLAB that implements methods for automating cell segmentation/lineage reconstruction. The automated analysis iteratively combines a set of extended morphological methods for segmentation, and uses a neighborhood-based scoring method for frame-to-frame lineage linking.
RchyOptimyx / cellular hieraRCHY OPTIMization
Constructs cellular hierarchies by combining automated gating with dynamic programming and graph theory to provide the best gating strategies to identify a target population to a desired level of purity or correlation with a clinical outcome, using the simplest possible marker panels. RchyOptimyx can assess and graphically present the trade-offs between marker choice and population specificity in high-dimensional flow or mass cytometry datasets.
SamSPECTRAL
Identifies overlapping populations that are generally hard to identify by manual gating that uses sequential two dimensional visualizations of the data, based on a multidimensional clustering approach. SamSPECTRAL demonstrates significant advantages in proper identification of populations with non-elliptical shapes, low density populations close to dense ones, minor subpopulations of a major population and rare populations.
SPADE / Spanning tree Progression of Density normalized Events
Facilitates the analysis of cellular heterogeneity, the identification of cell types, and comparison of functional markers in response to perturbations, based on a versatile method. SPADE helps to organize high-dimensional cytometry data in an unsupervised manner, and to investigate natural and pathogenic cellular heterogeneity for biological insight. The SPADE algorithm consists of four components: (i) density-dependent downsampling, (ii) clustering, (iii) linking clusters with a minimum spanning tree, and (iv) upsampling to restore all cells in the final result. This modularized process allows more efficient sub-algorithms to replace the current components. In this sense, SPADE can be viewed as a framework for cytometric data analysis and visualization that has the capacity to be evolved and adapted.
COMPASS
A statistical framework that enables unbiased analysis of antigen-specific T-cell subsets. COMPASS uses a Bayesian hierarchical framework to model all observed cell-subsets and select the most likely to be antigen-specific while regularizing the small cell counts that often arise in multi-parameter space. The model provides a posterior probability of specificity for each cell subset and each sample, which can be used to profile a subject's immune response to external stimuli such as infection or vaccination.
plateCore
Creates methods and data structures for processing large, plate-based FCM data sets by taking advantage of the functionality in flowCore and flowViz. plateCore makes it easier to integrate textual descriptions of plate layouts and also to perform automated gating based on nonparametric analysis of negative control wells.