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Bioinformatics tools
Cox UM-MDR / Cox Unified Model based Multifactor Dimensionality Reduction method
Identifies gene-gene interactions associated with the survival phenotype. Cox UM-MDR is an approach that combines Cox-multifactor dimensionality reduction method (MDR) with the key procedure of unified model based multifactor dimensionality reduction method (UM-MDR). This software is robust to the censoring fraction. It was applied to a real dataset of Korean leukemia patients.
Surv-MDR / Survival Multifactor Dimensionality Reduction method
Detects and characterizes epistatic interactions in the context of survival analysis. Surv-MDR is an extension of the multifactor dimensionality reduction (MDR) algorithm that handles survival data by modifying MDR’s constructive induction algorithm to use the log-rank test. This software uses a non-parametric approach to determine the high or low risk group for genotype combinations. It is able to handle complex, nonlinear relationships between survival time and single nucleotide polymorphism (SNP) effects.
AFT-MDR / Accelerated Failure Time Multifactor Dimensionality Reduction method
Enables detection of gene-gene interactions with the survival time. AFT-MDR consists of an extension of the multifactor dimensionality reduction (MDR) method to the accelerated failure time (AFT) model. This software’ power is sensitive to the censoring fraction. It was used to analyze a real data for leukemia Korean patients.
ENVELOPE / EvolutioN of Viral populations modELd by stOchastic ProcEss
Performs simulation of the phenotypic model. ENVELOPE is a cross-platform application to provide a graphical interface for inputting data, visualizing graphics in real time, and exporting the output data. The software allows users to choose among five types of fitness distributions: deterministic, Poisson, geometric, binomial, or power law.
PHAT / Pathogen-Host Analysis Tool
Processes and analyzes next-generation sequencing (NGS) data. PHAT provides quality control (QC) reporting on sequence files, alignment of sequence files against reference files, single-nucleotide polymorphism (SNP) prediction, linear and circular alignment viewing. This tool permits the detection of relationships between pathogens and host organisms.
Simulates growth of the shoot apical meristem (SAM) of Arabidopsis thaliana. ScePlantCells simulates combined growth of the L1, L2, and deeper L3 layers of the SAM where individual cells are represented as collections of nodes representing subcellular components of cells. In the future, this tool wiil intend to combine this mechanical sub-model with a dynamic signaling model.
EVEE-Tools / EVolutionary Estimates of Expression Tools
Analyzes expression evolution across species. EVEE-Tools allows user to generate an expression matrix based on RSEM, to calculate expression divergence across species, to find the evolutionary mean and variance of each gene, to score gene expression levels for outlier expression, and to identify differential expression across a tree. This tool can also interpreting expression data in disease.
Post-processes haplotypes estimated by SHAPEIT. duoHMM corrects phasing errors to make them consistent with a pedigree structure and detects recombination errors and subtle genotyping errors. It incorporates pedigree information into the haplotype estimates in a post-hoc manner. This method incorporates the pedigree information in a cohort to increase the accuracy of haplotypes inferred.
Allows the combination of multiple genotype imputations. Ped_Pop is a general method able to impute rare and common variants by gathering both family and population-based imputation methods. It can compare the variance of the three genotype posterior probabilities between one family-based and one population-based. It aims to exploit identity by descent (IBD) and linkage disequilibrium (LD) information.
Aims to predict single cell perturbation response. scGen is a model combining variational autoencoders and latent space vector arithmetics that assists users with high-dimensional single-cell gene expression data. This model learns cell type and species specific response implying that it captures features that distinguish responding from non-responding genes and cells.
CDSeq / Complete Deconvolution Sequencing
Provides a deconvolution method using RNA-seq data. CDSeq is a computational approach that can estimate both sample-specific proportions of each cell type and cell-type-specific gene expression profiles simultaneously, using bulk RNA-Seq data only. This program leans on the latent Dirichlet allocation (LDA) model with the aim of improving the efficiency of the partial deconvolution method.
CSsam / Cell type-Specific Significance Analysis of Microarrays
Analyses differential gene expression for each cell type and relative cell-type frequencies. CSsam works on biological samples from microarray data. This tool addresses the extensive loss of biological signal in microarray datasets when analyzing complex tissue samples that vary in cellular composition. It localizes the identified differential expression to a particular cellular context, which allows hypothesis formulation for follow-up experiments, and is usable with microarray analysis of any heterogeneous tissue and to other types of molecular measurements.
m-pCMF / modified Probabilistic Count Matrix Factorization
Allows users to perform single-cell RNA-seq analysis. m-pCMF is a program that permits batch index annotations, enabling correction of batch effects if batch annotations are available. This tool is able to capture other gene-specific dispersion sources besides the count depth variation between cell. It can be employed for robust dimensionality reduction in modern data sets.
ZINBayes / Bayesian Zero-Inflated Negative binomial factorization
Provides a probabilistic model for single-cell RNA-seq (scRNA-seq) data. ZINBayes is a Bayesian zero-inflated negative binomial factorization application. It allows sparse mapping, which assists users in interpreting the most relevant genes for which latent component and, therefore, for which cell type. This method do not need full batch of data to perform inference.
Prevents the corruption of scientific data by Excel. Opentsv supports opening TSV and CSV files without automatic conversions, with or without installation. This tool also assist in the the use of separators.
Assists in selecting DNA substitution models using the PAUP* program. MrModeltest is an application that performs hierarchical likelihood ratio tests. It also calculates approximate Akaike information criterion (AIC) values of the nucleotide substitution models. This method is a modified version of the Modeltest software.
CcpNmr / Collaborative Computational Project for NMR
Analyses from scratch nuclear magnetic resonance (NMR) data, including liquid- and solid-state ones. CcpNmr consists in a suite of programs, developed around a unified code base, with dedicated functions such as assignment, NMR structure calculations, NMR-based screening or NMR-based metabolomics. This tool inspired on the Sparky and ANSIG programs implements a module named AnalysisAssign, which specifically targets the inspection, analysis and assignment of NMR spectral data.
Offers a platform to handle crystal structures. KPLOT is a software providing features for: (i) working simultaneously with two structures and comparing them by using the visualization function; (ii) computing multiple metrics such as torsion angles; (iii) performing analysis including space group determination; (iv) searching for 'cell candidates' and (v) drawing structures and generating plots.
Allows module discovery based on heterogeneous data. ReMoDiscovery correlates regulatory programs with regulators and corresponding motifs to a set of co-expressed genes provided by ChIP-chip data, motif information and gene expression microarray profiles. It predicts putative seed modules (genes, regulators and corresponding motifs) and then optimizes the gene content of the modules, indicating whether the seed modules' regulatory program is active in the microarray data.
SProCoP / Statistical Process Control in Proteomics
Identifies changes in a proteomics experiment by controlling liquid chromatogray tandem mass spectra (LC MS/MS) data. SProCoP assesses both chromatographic and mass spectrometric performance. It allows the computation of five metrics: (i) targeted peak areas reported by Skyline; (ii) mass measurement accuracy for high resolving power instruments of targeted peptides; (iii) full width at half maximum of targeted peptides; (iv) peak asymmetry of targeted peptides and (v) retention time of targeted peptides.
Allows the monitoring of system performance in liquid chromatography tandem mass spectra (LC MS/MS)-based proteomic experiments. AutoQC provides features such as (i) an automation of the the statistical process control in proteomics (SProCoP) data pipeline; (ii) longitudinal data storage and tracking; and (iii) a possible integration into the Panorama data management system.
Furnishes a methodology for trisomy prediction in non-invasive prenatal testing (NIPT). NIPTeR permits users to perform NIPT analysis for research and diagnostics. More specifically, it processes by computing chromosomal fractions which are used for trisomy prediction. These fractions are based on read counts of the different chromosomes, which are divided into bins to allow the correction of the reading count.
SIFT / Sequence Independent Filtering Tools
Serves for ordering putative models of protein structures and filtering out non-native structure with non-physical packing to enhance protein folding simulations and protein structure prediction. SIFT is made for being used in the context of a large number of putative models, to improve the convergence of folding simulation methods such as Rosetta. Moreover, it can be used for de novo simulations and alignment based models.
SCORPPION / Sequence-based identifiCation Of stRuctural units and Protein-Protein InteractiONs
Allows users to perform sequence-based identification of structural units and protein-protein interactions. SCORPPION is a web application that requires a gene Entrez IDs or names, protein IDs from UniProt or PDB, or protein sequences.
Allows the simulation of large-scale rhythmic data. Simphony is an R package able to mimic experiments in which the abundances of rhythmic and non-rhythmic features are measured at multiple time points. This application includes adjustable parameters for specifying experimental design and modeling rhythms, including the ability to sample from Gaussian and negative binomial distributions.
Annotates lists of genetic variants with quantitative trait loci (QTLs) data. Qtlizer is a platform that is able to process a wide range of published datasets and databases such as GEUVADIS, Scan DB or pGWAS. Users can query the data through a web-based application or a REST API. It can be used for release eQTL datasets, and, more generally, to study possible genetic effects on gene expression. This application is part of the GENEHOPPER project.
Performs kernel density based estimation of observed mass shifts and allows detection of poorly resolved mass deltas. DeltaMass can map observed mass shifts to known modifications from public databases such as UniMod, and augments it with additionally generated possible chemical changes to the molecule. It includes a graphical interface for visual interrogation of the data and identification of potentially interesting mass shifts or unusual artifacts for subsequent analysis.
Aims to scan RNA sequences and extracts structural motifs which have evidence of being ordered by evolution to form a stable structure. ScanFold provides a set of scripts that focuses on single RNA sequences analysis and divides the prediction process into a scanning step, a model building step, and an analysis step where homology data or experimental results can be considered.
Provides a toolbox for genomic analyses on BAM files. BamBam is a package of more than 10 applications intending to assist users in usual tasks including phylogeny inference or differential expression analysis. It includes features to: (i) quantify reads mapped to each gene in a genome; (ii) detect single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) or (iii) summarize read coverage of sequences or regions.
Ontology Recommender
Assists users in annotating or representing data. Ontology Recommender is a web service that uses textual metadata or a set of keywords to describe a domain of interest and to suggest appropriate ontologies. It is able to evaluate individual ontologies and different ontology sets in order to maximize input coverage. This system can be customized to specific user needs.
Allows users to score protein-protein docking model. iScore furnishes solution for categorizing protein-protein interfaces using a support vector machine approach on graph kernels. This program includes two binaries that (1) train a model using a training set and (2) use this model to determine the near-native character of unknown conformations.
BiOSS / Biomedical Ontology Selection System
Allows biomedical ontologies selection. BiOSS determines which ontologies are the most adapted to the description of datasets of interest. It allows users to retrieve information among more than 200 biomedical ontologies. It produces two types of outputs: one which classifies candidate ontologies according to the aggregated score obtained from the evaluation process and a combined one which gathers several ontologies that can be used together to provide a better coverage of the domain.
Permits to connect miRNAs to biological function by comparing miRNA and gene array expression data. miRConnect is able to identify activities of miRNAs that are relevant to primary cancers. This tool was used from data sets from the NCI60 cells and three human primary cancers cells OvCa, GBM and KIRC.
SAMBA / Small Animal Multivariate Brain Analysis
Proposes a voxel-based analysis (VBA) pipeline for multi-modal preclinical imaging from small animals. SAMBA provides an eight-steps software that generates unbiased affine and diffeomorphic targets, study-specific atlases, statistical maps and regional labels. This application intends to improve the rapidity of preclinical VBA leaning on the Advanced Normalization Tools package (ANTs).
DOCKS / Design Of Compact K-mer Set for hash functions
Produces compact sets of k-mers that hit all L-long sequences. DOCKS is a program able to calculate small universal hitting set (UHSs). This application intends to assist users with tasks that employs minimizers. It includes two variations algorithms: DOCKSany and DOCKSanyX which aim to extend the computation range of k and L values. This tool can be used in multiple analysis such as space efficient data structures or large-scale sequence analysis.
MSP / Minimum Substring Partitioning
Exploits a minimum substring partitioning technique to allow the building of de Bruijn graphs. MSP is a three-steps algorithm that (i) first, partitions the k-mers in DNA sequences; (ii) maps the detected k-mer and attribute a unique integer ID and an ID replacement table for each partition; (iii) lastly, merges all the tables to generate a unique ID replacement table and consructs a global de Bruijn graph from it.
Predicts protein shape strings. NMRDSP is an extension of DSP based on nuclear magnetic resonance (NMR) chemical shifts (CSs) and structural profiles obtained from sequence data. For each NMR CS data, it checks the availability of the data, and normalizes and alphabetizes the NMR CSs. DSP is then performed to generate the shape string profiles.
Allows users to perform the prediction of protein shape string and its profile. DSP leans on a knowledge-driven sequence alignment coupled to a sequence structure profile method. This platform proposes services for predicting and analyzing protein backbone conformation in shape string space. It can be run as a desktop application or through a web server.
Investigates annotations of homologous sequences to produce functional annotations. FunCUT is an application that classifies proteins into families and subfamilies, based on the use of a clustering algorithm. This application is a four-steps process that: (i) runs sequence searches; (ii) analyzes the local alignments and the assignments to alignment categories; (iii) selects the functional annotations that have to be transferred and lastly; (iv) attributes the functional annotations to their corresponding alignment categories.
Offers a platform to collect data about a planned experiment. EpiC displays annotation on a protein of interest, compiles data linked to it to allow the exploration and checking of the validity of information that have been gathered. This software can generate a graphical representation of the physicochemical properties analyses and antigenicity prediction, which can be useful in designing antibody-based experiments.
Offers a platform to perform electropharyngeogram (EPG) analysis. AutoEPG is a program allowing users to automate the annotation and statistical analysis of whole EPG traces. This software can process large volumes of data and is able to extract statistical features such as the duration of each individual waveform/pump, the instantaneous pump rate or the number of P-spikes per pump. It can be used for discovering and characterizing neurogenic or myogenic drugs.
SDAR / Serial Data Analysis and Regression
Offers a platform for the graphical analysis of two-dimensional data. SDAR provides features for: (i) data import; (ii) the creation of multiple graph types; (iii) the transformation of data series; (iv) analysis; (v) curve fitting with more than 10 functions including exponential or Michaelis-Menten curves and (vi) a toolbox allowing users to format the analyzed data. This software is part of the PCSB project.
ACDP / Automated Circular Dichroism data Processing
Processes protein circular dichroism (CD) spectra. ACDP applies baseline correction, converts raw CD into units of mean residue ellipticity, wavelength monitoring and graphical inspection and then deconvolves secondary structure using three different algorithms. This application does not need data reformatting to analyze these spectra, because of the use of a neural network approach, variable selection or linear combination of prototype spectra.
Assists users in handling of structural and biophysical problems. PCSB is a package that has several applications, such as peptide parameter calculation, automatization of circular dichroism (CD) data processing or fluorescence data processing, alignement of three-dimensional structures, calculation of rotation axes, searching of anomalous scattering factors, symmetry operations or calculation of the Matthews coefficient.
Creates publication-quality figures. cDraw is an interactive chemical drawing application allowing the production of InChI and InChI Key from structures. Its configuration was made to be compatible with multiple systems including those of the American Chemical Society (ACS) or the Royal Society of Chemistry (RSC). Users can manipulate figures in a wide range of formats including PDF, SVG or CDML.
Allows the investigation of multiple data sets including replicates of discrete bivariate data. DRfit computes means and standard errors to detect replicate data points from a defined matrix layout as well as outliers within sets of replicate data points. Data can be customized, allowing users to subtract background, normalize and/or scale the studied data. It lastly generates modifiable fits and the corresponding plots.
Offers a graphical interface allowing the customization of an included script for R. jBar is a platform that starts from a pre-configured spreadsheet and offers a set of features for the parametrization of a given R pipeline through the software interface. The application permits the computation means and standard errors/deviations for replicates of numerical data collected in dependence of two variables and produce a final result as a bar graph.
Estimates scattering of biological macromolecules from atomic coordinates. MolScat is an application able to compute the theoretical scattering intensities from atomic models and that can be run as a command-line software or as from a graphic user interface. It aims to shorten the computation time of these analysis. This program is part of the Program Collection for Structural Biology and Biophysical Chemistry (PCSB).
SAFIR / Small-Angle scattering data FItting with Rigid bodies
Fits small-angle scattering data with rigid body objects. SAFIR is a program allowing users to model oligomeric structures of biological macromolecules. It includes features to superpose and shape atomic models, assess theorical scatter data as well as to visualize individual protein monomers or oligomeric structures as rigid bodies. This program is part of the Program Collection for Structural Biology and Biophysical Chemistry (PCSB).
Allows users to construct protein structure models. PdbCompAA confronts two sequences: an amino acid sequence of a model and a reference sequence and leads a residue-by-residue comparison to highlight possible sequence mismatches. It can also be used in file validation. This software can be run through a graphic user interface or though a command-line terminal. It is part of the PCSB project.
Computes peptide and or protein parameters from a given sequence. Peptides is an application intending to furnish information related to number of residues, molecular mass and formula, molar extinction coefficient, volume, pI, amino acid content or pH-charge correlation. This program includes a graphic user interface to facilitate investigation of sequences of interest.
Handles secondary structure-based sequence alignments. SBAL is an application intending to ease the visualization of secondary structure assignments on a multiple sequence alignment, in multiple formats including files from ClustalW. This program provides a graphical user interface dedicated to the creation of structure-based sequence alignments, that can be further modified by the user through the same interface.
BBrowser / BioTuring Browser
Proposes a set of methods for both RNA-seq and single-cell RNA-seq analysis. BBrowser supplies interactive visualizations as well as multiple analytics such as quality control, enrichment analysis, sub-clustering or differential expression. The platform includes a set of precomputed datasets encompassing research studies and sequencing samples or allows users to submit their own data.
Performs quantitative trait loci (QTL) searches in two and three dimensions. This approach consists of a global optimization algorithm that was used to find point in search space with minimal value of objective function. This software can be coupled with any objective function routine fulfilling given specifications. It opens the possibility to detect triplets of interacting QTL by the use of simultaneous search .
Restores statistical regularity to likelihood ratio tests for positive selection by the incorporation of likelihood modification. codeml_modl is a software based on the codeml software which allows the estimation of w under different models as well as the possibility to quantify and test a model of interest. This alternative program can be used with the nested models M1a/M2a.
Offers a method to estimate the quality of somatic copy number calls. CNValidator is an application intending: (i) to validate a single copy-number algorithm, (ii) to compare two or more algorithms; (iii) to compare sets of algorithm parameters or (iv) to evaluate the union of segments called by all of the tested algorithms. It has to be used in cases where multiple samples came from the same individual.
Offers a method to predict transcription factors (TFs) binding profiles across cell types. Anchor is a feature-enriched method proposing an approach that aims at avoiding overfitting to the training data, including in unseen cell type. This program takes both the inter-dependencies between neighboring nucleotide positions and nonlinear interactions between TF motifs into account.
Allows users to perform sequence-based protein-protein interaction (PPI) prediction tasks. Lasagna is an end-to-end framework based on a residual recurrent convolutional neural network (RCNN), which provides an automatic multi-granular feature selection mechanism. This program intends to represent the mutual influence of protein pairs leaning on the analysis of primary sequences.
Aims to facilitate comprehensive neoantigen characterization. pVACtools is an in-silico sequence analysis method that consists of several tools for neoantigen prediction from somatic alterations (pVACseq and pVACfuse), prioritization and selection using a graphical web-based interface (pVACviz), and determining the optimal order of neoantigen candidates in a DNA vector-based vaccine(pVACvector).
CRUP / Condition-specific Regulatory Units Prediction
Furnishes a workflow for regulatory units prediction. CRUP is composed of three modules: (i) CRUP-EP, to forecast active enhancers; (ii) CRUP-ED, to attribute the enhancers to dynamic conditions and (iii) CRUP-ET, to generate differential regulatory units. It can be used for the identification of candidate enhancer regions that act dynamically in different disease states or to link enhancers to differentially expressed target genes.
Offers a method to remove errors and duplicates by the generation of consensus reads. Gencore is an application that aims to reduce false positive calling rates. It clusters read pairs by their mapping positions and unique molecular identifiers (UMIs) and then generates a consensus read for each cluster. This program can be used to determine low-frequency somatic mutations from cancer sequencing data.
DR-SIP / Distance Restraints- and Cyclic Symmetry-Imposed Packing
Allows users to forecast quaternary structures of homo-oligomeric transmembrane proteins (HoTPs). DR-SIP is composed of four modules including two docking protocols: (i) one for quaternary structures prediction, and (ii) one for predicting soluble proteins, as well as two filters: (iii) one for easing quaternary structure determination for soluble proteins and (iv) one to ease those of transmembrane proteins. It also provides a function allowing advanced users to import modules and functions in customized docking protocols.
Allows users to perform expression quantitative trait locus (eQTL) analysis on both single-cell and transcriptomic parallel sequencing data. SCeQTL is an R package intending to assist users in discovering potential regulatory relationships at single-cell level. This program can also be applied to detect association of gene expression with other grouping factors such as cell lineages.
SuSiE / Sum of Single Effects
Selects variables in multiple regression models. SuSiE is a package with the aim of improving features of the single effect regression (SER) model. This program can be applied in cases involving highly correlated variables. It is able to identify sets including relevant variable and to prioritize them inside of those sets. This approach can be used in various sparse regression applications, such as change point detection.
Generates and runs workflows on any set of samples and operations resulting from high throughput sequencing (HTS) analysis. NeatSeq-Flow is an application that can be run as a command-line or as a graphic user interface. This program can be used locally on a single computer or cluster and is able to automatically determines and manages the location of intermediate and final files.
Identifies breakpoints and report inserted mobile genetic elements (MGEs). iMGEins is a four-steps method able to: (i) exploit sequencing reads of individual genomes to determine novel MGE insertions; (ii) detect novel MGEs inserted differently to the individual genomes; (iii) consider sequence homology to annotate MGEs; or (iv) locate the chimeric points in assembled genomes.
TriPOINT / Triangulation of Perturbation Origins and Identification of Non-Coding Targets
Determines both most relevant genes for a phenotype and their non-coding regulators. TriPOINT is a pathway analysis application aiming at detecting genes perturbed in pathways and non-coding regulatory elements regulating them. This program combines multiple functionalities such as the use of pathway graphs, a visualization platform and approaches derived from the QuIN software for the incorporation of chromatin interactions.
CLC Genome Finishing Module
Assists users in finishing small genomes. CLC Genome Finishing is an additional function to the CLC Genomics Workbench which focuses on ease genome assembly. It includes more than 10 individuals tools including feature import, correct and assemble PacBio reads, create amplicons or primers as well as a function to search sequencing data by name, annotations or sequences.
CAPRG / Contigs Assembly Pipeline using Reference Genome
Allows the assemblage of long sequence reads. CAPRG is a method built around a overlap-layout consensus (OLC) strategy that constructs sequence clusters for sequence assembly by exploiting a reference genome. It proposes a three-steps approach that: (i) aligns the input sequences with a genome of reference; (ii) hosts the results in a repository; (iii) and lastly, assembles the reads. This application is able to work with non-model organisms.
CAnD / Chromosomal Ancestry Differences
Determines chromosomes that incorporate genomic regions with different proportional ancestry that are relevant compared to the rest of the genome. CAnD is an application intending to detect differences in genetic contributions from the underlying ancestral populations to chromosomes. It does not require knowledge about the studied population and can consider correlated ancestries among chromosomes within individuals.
DSDTWnano / Direct Subsequence Dynamic Time Warping for nanopore
Enables the direct subsequence searching and exact mapping in nanopore raw signals. DSDTWnano is based on the idea of subsequence-extended dynamic time warping and directly operate on the raw signals. This tool can serve as a standard criterion for performing genome-to-signal mapping studies. This program, for instance, can be used for detecting single nucleotide polymorphism (SNP) under a low coverage on Escherichia coli.
cwSDTWnano / continuous wavelet Subsequence Dynamic Time Warping for nanopore
Enables direct subsequence searching and exact mapping in nanopore raw signals. cwSDTWnano consists of an accelerated version of the DSDTWnano algorithm that reduces the execution time by utilizing the concept of seed and adopting the strategy of multi-scale analysis. It includes several techniques to accelerate the subsequence similarity search on nanopore raw signals: seeding, pre-filtering, and multi-scale search based on continuous wavelet transform (CWT).
Enables computer-automated identification of potential protein and nucleic acid (RNA or DNA) targets of a small molecule. INVDOCK searches a protein and nucleic acid 3-D structure database to detect the protein, RNA or DNA molecule that the small molecule (such as a drug, newly designed drug candidate, natural product or other chemical compound) can bind to. The software was able to predict the known therapeutic targets of a group of nine known drugs.
Graph Genome Suite
Provides population genomics tools. Graph Genome Suite contains tools for analysis of whole genome sequencing data provided on the Seven Bridges Platform. It consists of: (1) a ‘Graph Genome Reference’ data structure, (2) a ’Graph Genome Aligner’ for mapping sample reads considering many alternate haplotypes for each locus and thus reducing reference bias, and (3) a ‘Graph-Genome-Assisted Variant Caller’, enabling integrated calling of both small and common population structural variants.
Performs automated microscopy using the ImageXpress Pico system. CellReporterXpress is an automated image acquisition and analysis software that provides an interface enabling quantitative analysis on images acquired from automated microscopy. It permits distributed analysis of images for increased throughput. This program is suitable for scaling microscopy imaging with slides or microplates. It can be simultaneously used by researchers through a browser-based remote access.
Assists users in performing image analysis in 2-dimension (2D) or 3-dimension (3D). MetaXpress includes a module 3D dedicated to analyze spheroids, microtissues, cells in a 3D matrix, and small organisms. It contains a module for high-throughput quantification of 3D structures with volume, intensity, and distance measurements. Additionally, its interface simplifies management and organization of images, experimental information, and data analysis.
SoftMax Pro GxP
Provides a microplate reader conformable to 21 CFR Part 11. SoftMax Pro GxP is a validation system intending to facilitate the management of information related to microplates. It includes features that allows changes’ tracking and document management with the aim of supplying data with the maximum of integrity as possible. This program also integrates an export feature, compatible with a laboratory information management system (LIMS) or a scientific data management system (SDMS).
SoftMax Pro
Provides an application dedicated to microplate data acquisition and analysis. SoftMax Pro allows the performing of data, which can be originated from an external microplate, by using pre-configured protocols. It also furnishes more than 20 options for curve fit and automatic calculations of relative potency. Besides, it includes multiple export options towards notebooks or laboratory information management system (LIMS).
Allows users to generate a phylogenetic tree with horizontal gene transfer. HGT-Gen embeds features for converting an operational taxonomic unit or a clade from one place to another in a given phylogenetic tree. It also contains an algorithm permitting researchers to calculate the relative evolutionary time in order to normalize it for each lineage.
Proposes a module able to monitor features for laboratory-scale protein purification through the NGC Chromatography System. ChromLab Software is an application including functions for: (i) real-time monitoring of proteins, peptides, nucleic acids, and chromophores, (ii) settings of instrument; (iii) chromatogram comparison, and (iv) peak analysis. It also includes templates for common chromatography methods as well as for multistep tandem chromatography.
Precision Melt Analysis
Processes high resolution melt (HRM) analysis on genotype samples. Precision Melt Analysis is an application that permits users to characterize samples by considering sequence length, GC content as well as DNA sequence complementarity. It can be used for various analysis such as the scanning of new gene variants or the the determination of insertions or deletions. This program can be used with multiple real-time polymerase chain reaction (PCR) detection systems, including CFX Connect or CFX384.
Microplate Manager
Permits users to perform colorimetric and turbidimetric analyses, as well as report analysis for raw data, absorbance, limit, matrix, normalization, and curve fit. Microplate Manager is a program designed for reading the plate, generating an array of values, and performing data analysis. It supplies exact data with template design flexibility along with guides for designating plate wells, mapping dilutions, and multiple sample series.
Bio-Plex Data Pro
Assists researchers in observing multiplex data and understanding biological system. Bio-Plex Data Pro consists of a database application aiming to organize large volumes of multiplex data. This application is able to label samples with all biologically relevant information for data set comparisons. Additionally, this program offers the possibility to automate calculations with conservative statistics, select subgroups, and visualize results.
NASE / Nucleic Acid Search Engine
Offers a database search engine for RNA with a focus on high-resolution mass spectrometry (MS) data. NASE is an open-source software that reports oligonucleotide-spectrum matches with statistically meaningful false discovery rate (FDR) scores. It can support arbitrary modifications as well as salt adducts. This tool can also be downloaded as part of the OpenMS software.
Compute pI/Mw tool
Predicts protein isoelectric point (pI) and molecular weight (Mw). Compute pI/Mw tool is a web server that computes, given a list of UniProt Knowledgebase (Swiss-Prot or TrEMBL) entries or user entered sequences, the theoretical pI (isoelectric point) and Mw (molecular weight). This software can be useful to know the approximate region of a 2-D gel where a protein may be found.
Provides spatial and non-spatial cross-validation and boostrap methods. Sperrorest is an R package that contains several functions for spatial and non-spatial partitioning and resampling and a main function that performs error estimation based on prediction models implemented in other R packages. The software also allows users to perform cross-validation at the level of aggregated objects and includes functions for summarizing and plotting resampling schemes and for calculating and summarizing a variety of error measures.
AMBIORE / Applications for MCMC Bayesian Inference Of Rates in Evolution
Assesses rates in evolution starting from a sequence alignment and a tree topology relating the species. AMBIORE is a based on a model able to include context effects that are allowed to depend on sequence position and lineage. It aims to assist users in investigating complex models of the mutation and substitution process, and, extensively, to molecular evolution trends.
Enables analysis of the embryo growth and the sexualization thermal reaction norms. embryogrowth is an R package that implements a methodology for extracting the thermal reaction norm for the embryo growth rate directly from a time series of incubation temperatures recorded within natural nests. It can be used for any egg-laying species.
BAS / Bayesian Adaptive Sampling
Contributes to give a fast code to implementing Bayesian Model Averaging and Model Selection in R. BAS uses three main algoritms for sampling from the space of potential models: a deterministic algorithm for efficient enumeration, adaptive sampling without replacement algorithm for modest problems, and a MCMC algorithm that utilizes swapping to escape from local modes with standard Metropolis-Hastings proposals.
Serves for exploring a variety of biological questions concerning protein and coding sequence evolution. CodeAxe consists of a model of coding sequence evolution that incorporates context-dependent mutation rates and asymmetric exchange-dependent selection on amino acid substitutions. It permits users to estimate mutation and to select parameters from genome-wide coding sequence alignments by likelihood-based phylogenetic analysis.
Proposes an assortment of statistical methods related to biosciences. BIOMStat provides features including: (i) basic analysis such as permutation tests, logistic and isotonic regression; (ii) approaches allowing the investigation of variance; (iii) sample and effect size estimator; (iv) modules for nonparametric and descriptive statistics encompassing Komolgorov-Smirnov test or Kendal’s rank correlation tau.
Allows users to collect 3D landmarks and curves. StereoMorph is a program able to perform automated detection of checkerboard corners, camera calibration, and calibration accuracy assessment. This program embeds features for image processing, direct linear transformation (DLT) calibration, image digitization, and landmark and curve reconstruction.
Serves for digitizing landmarks and outlines for geometric morphometric analyses. TpsDIG permits computation of areas of enclosed regions, perimeters, and linear distances. This program contains image enhancement operations, scale factors, and image brightness profile.
Brings symmetry and asymmetry in geometric data. Sage calculates covariance matrix correlations between symmetric and asymmetric components of variation. It assists researchers in saving symmetrized datasets, residuals from symmetric component, and shape configurations representing each component of variation.
Enables matrix correlations for landmark data. Mace calculates significance of matrix correlations from permuting rows and columns of covariance matrices, maintaining the pairing of X,Y coordinates. This tool is able to perform significance tests including computation of repeatability, and bootstrap estimates of correlation statistics. It can transform covariance matrices into an "isotropic" version, in which all elements except for the diagonal are zero and all elements in diagonals are equal.
Aims to convert curves in semi-landmarks. SemiThinner allows saving of only semi-landmarks, landmarks only, or both landmarks and semi-landmarks. This application permits users to reduce the number of points to a specified number in all specimens.
Assists users with comparison via correlation analyses of matrices of distances among specimens or groups. Coriandis provides a set of analytical tools that aims to study associations among multivariate datasets such as shapes. It includes a graphical interface to determine which options users can apply for performing the analysis and which types of results can be produced.
Assists users in testing a priori models of morphological integration and modularity on multivariate data. Mint is an application that includes a module to carry out a variant of partial least squares (PLS) analysis on which a partition or putative module is regressed against the full set of traits. It also permits users to load individually created or edited models.
Assists users with the estimation and visualization of local deformations derived from landmark data. Lory is an application that uses shape information contained in landmarks to estimate, via interpolation, local deformations. It also provides a variety of useful visualizations (deformation grids, parrot plots, deformation movies), which can be exported at publication-quality resolution level.
Filters genome wide scan data based on frequencies of resolved and unresolved sites.