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Facilitates understanding of the interconnection of pathways. Caleydo enables a non-distracting relation to gene expression data. It is based on simultaneous consideration of gene expression information and pathways. It allows to explore relationships between multiple, handcrafted pathways, and relationship of pathways to actual measurements of gene expression regulation directly. It can improve the process of understanding the complex network of pathways and the individual effects of gene expression regulation considerably.
ADAGE / Analysis using Denoising Autoencoders for Gene Expression
Allows users to integrate diverse gene expression data to aid in the interpretation of existing and new experiments. ADAGE is a neural network model. Using an unsupervised machine learning approach, the community-wide Pseudomonas aeruginosa gene expression data were integrated to create an ADAGE model that captures patterns corresponding to biological states or processes in gene expression data. The eADAGE algorithm combines multiple ADAGE models into one ensemble model to address model variability due to stochasticity and local minima.
CSTEA / Cell State Transition Expression Atlas
Provides both visualization and analysis of valuable time-series gene expression data during cell state transitions. CSTEA focuses on expounding important genes and their corresponding functions at intermediate time points during the dynamic transition process. The text mining served for collection of public datasets in order to propose a comprehensive roadmap describing the diverse cell state transitions. The purpose of this tool is to provide a valuable resource for both experimental and computational biologists.
DCQ / Digital cell quantifier
Allows users to infer changes in quantities of immune cell sub-populations. DCQ is a digital cell quantifier that deduces changes in cell quantities between the two conditions based on a cell surface markers motivated model. It permits the prediction of over 200 immune cell types simultaneous and can discriminate between closely related immune subtypes and different levels of activity. Moreover, this software can generate detailed testable hypotheses concerning the role of specific immune cells under particular conditions.
LungGENS / Lung Gene Expression iN Single-cell
Facilitates the retrieval of lung cell-specific gene expression information from extensive data sets derived from RNA sequencing of single cells. LungGENS is a web-based bioinformatics resource for querying single-cell gene expression databases by entering a gene symbol or a list of genes or selecting a cell type of their interest. It also integrates the data with previous RNA expression studies from mouse lung at various developmental times.
Provides functions to perform ensemble minimum redundancy maximum relevance (mRMR) feature selection by taking full advantage of parallel computing. mRMRe can be beneficial from both a predictive (lower bias and lower variance) and biological (more thorough feature space exploration) point of view. This makes it particularly attractive for high-throughput genomic data analysis. This package contains a set of function to compute mutual information matrices from continuous, categorical and survival variables.
URSA / Unveiling RNA Sample Annotation
Leverages the relationships between tissues and cell-types. URSA is able to identify specific tissue/cell-type signals present in a given gene expression profile. It permits to automatically annotate samples in public gene expression repositories where most samples are currently lacking tissue/cell-type-specific information. The tool can be used to test and identify possible sample contaminations or resolve cancer samples of unknown primary origin.
Stores and analyses Live Cell Array (LCA) data. BasyLiCA is a user-friendly software dedicated to wet lab biologists for the analysis of large amounts of LCA data in microplates. The user-friendly interface allows (i) the automatic insertion of LCA measurements; (ii) the manual or semi-automatic insertion of the characteristics of wells, strains and injection; (iii) the administration and the management of the database as a simple user or as an administrator and (iv) data treatment.
A resourced-based, well-documented web system that provides publicly available information on genes, biological pathways, Gene Ontology terms, gene-gene interaction networks (importantly, with the directionality of interactions), and links to key related PubMed documents. The PathwaysWeb API simplifies the construction of applications that need to retrieve and interrelate information across multiple, pathway-related data types from a variety of original data sources. PathwaysBrowser is a companion website that enables users to explore the same integrated pathway data. The PathwaysWeb system facilitates reproducible analyses by providing access to all versions of the integrated data sets. Although its Gene Ontology subsystem includes data for mouse, PathwaysWeb currently focuses on human data. However, pathways for mouse and many other species can be inferred with a high success rate from human pathways.
Infers transcriptome conservation patterns. myTAI can be used to screen for stages of high or low transcriptome conservation within a biological process of interest. This tool can be used for investigating the developmental hourglass model of embryo development on the transcriptomic level. Moreover, it provides functionality for: taxonomic information retrieval, gene age enrichment analyses, differential gene expression analyses of age categories, and additional metrics for quantifying transcriptome conservation.
NEMATIC / NEMatode-Arabidopsis Transcriptomic Interaction Compendium
Provides a spreadsheet application to perform plant–nematode interactions analysis. NEMATIC gathers transcriptomic data linked to other external transcriptomes and groups of genes to allow quick data management. The program allows users access to various features such as: (i) searching, selecting and filtering the genes of interest; (ii) selecting and filtering genes by Genevestigator expression values and; (iii) obtaining compiled information about filtered genes.
VoCAL / Variation of Cell-type Abundance Loci
Reveals the genetic basis of variation in immune cell traits based on gene expression data. VoCAL is a deconvolution-based method that uses expression profiles from a complex tissue across a population of individuals to calculate relative cell type abundance values in each individual, and then identify the underlying genetic variants on the basis of the predicted cell type abundance. The software avoids cell quantification by inferring the immune traits indirectly. It has been implemented in the freely available R package ComICS.
Provides computational biology resources that are related to the genome/transcriptome of the model plant Physcomitrella patens (Aphanoregma patens). Cosmoss is a web app that offer both the transcriptome representation (including a BLAST and retrieval service) and splice site prediction of Physcomitrella. The moss Physcomitrella patens is an emerging plant model system due to its high rate of homologous recombination, haploidy, simple body plan, physiological properties as well as phylogenetic position.
WormBase Converter
Enables the conversion of lists of genes with different identifiers and from different WormBase (WB) versions to a single coherent format. In order to permit accurate cross-release comparisons, WormBase Converter has to take into account all successive changes in gene annotation and modifies the list of gene identifiers accordingly. It can handle such lists and also displays any gene name for which an associated WB ID gene identifier cannot be found. Furthermore, if a new WB version is released, the tool automatically retrieves the new data from the server this making it easy to keep lists up to date.
CACTI / CASAA Application for Coding Treatment Interactions
Rates digital audio recordings of psychotherapy sessions and other behavioral interactions. CACTI is a flexible and transcript-free program for facilitating the parsing and sequential coding of auditory behavioral interactions between two or more participants (such as those between clinician and client in a psychotherapy session). The software employs three modes: (1) parsing continuous behavioral data from a WAV audio file into codable utterances, (2) sequentially coding previously parsed utterances, and (3) assigning Likert-type global ratings.
Provides support for the composition of RESTful web services semantically annotated using SAWSDL. SemanticSCo is a supporting platform that supports the definition of constraints/conditions regarding the order in which service operations should be invoked, thus enabling the definition of complex service behaviours. It also provides support for the definition of analysis workflows at a high-level of abstraction, thus enabling users to focus on biological research issues rather than on the technical details of the composition process.
NvERTx / Nematostella vectensis Embryogenesis and Regeneration Transcriptomics
Offers a platform for gene expression comparisons between embryogenesis and regeneration in Nematostella. NvERTx is a web application supplying transcript models for the identification of gene sequences. The application gives access to a repository that can be browsed by gene name, JGI ID or by retrieving a personal sequence through a BLAST tool. In addition, users can test for conservation of regeneration gene batteries, investigate gene expression clusters, mine data and detects groups of co-expressed genes.
peaBrain / Promoter-and-Enhancer-derived Abundance Brain
Predicts the mean tissue-specific abundance of all genes. peaBrain can provides individual abundance on a subject-by-subject basis by including the transcriptomic consequences of genotype variation. This software models the transcriptional machinery of a tissue via a two-stage process. In addition to predicting disease-associated variants, it can search the discriminative ability of derived scores in identifying allele-specific transcription factor binding sites.
RASLseqTools / RNA-mediated oligonucleotide Annealing, Selection, and Ligation Tools
Provides a collection of tools to design and investigate RASL-seq experiments. RASLseqTools furnishes empirical estimates of experimental, sequencing, and alignment error. It can be used for: (1) assessing the sequence similarity of barcodes and RRASL probes, (2) demultiplexing and aligning RRASL-seq FASTQ reads, (3) annotating demultiplexed and mapped reads with meta-data, (4) displaying batch effects, and (5) correcting systematic error using normalization methods.
EPIC / Estimate the Proportion of Immune and Cancer cells
Allows estimation of the proportion of immune and cancer cells from bulk tumor gene expression data. EPIC incorporates reference gene expression profiles from each major immune and other non-malignant cell type for modelling bulk RNA-Seq data as a superposition of these reference profiles. The software can be used with reference gene expression profiles pre-compiled from circulating or tumor-infiltrating cells, or provided by the user.
Allows selection of a subset of time points in time course experiment in a variety of experimental design situations. NITPicker is a statistical tool that selects informative time points for follow-up experiments, given a set of example curves from a high-resolution time course. The software uses methods from functional data analysis to find these optimal points. It was tested on several simulated and real-life datasets, and its flexibility was assessed by addressing different experimental design questions in each case.
Classifies gene expression profiles. SampleClassifier uses some functions (i) to classify microarray gene expression, (ii) to display the classification predictions as a heatmap and (iii) to classify microarray gene expression profiles using support vector machines (SVM). Each query profile is compared to all sample types in the reference matrix and a similarity score is calculated. The similarity score is based on the number of marker genes that are shared between the query and the reference.
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SRPDB / Signal Recognition Particle Database
Provides aligned, annotated and phylogenetically ordered sequences of the Signal recognition particle (SRP) components. SRPDB is a database that provides alphabetically and phylogenetically ordered lists of SRP RNA and SRP protein sequences. This online resource is also organized for additional proteins that play a role in SRP-mediated protein transport or are related to SRP components. The SRPDB lists 115 sequences from all phylogenetic groups.
CREEDS / CRowd Extracted Expression of Differential Signatures
Provides an access to the three collections of gene expression signatures for knowledge reuse and exploration. The CREEDS database visualizes all of the signatures in a packed circles layout in which similar signatures are closer to each other. It also includes interactive heatmaps of hierarchically clustered matrices of all signatures. A search engine is available in order to allow users to search by text or by providing lists of up and down DEGs (differentially expressed genes).
PRIMe / Platform for RIKEN Metabolomics
Allows to search and analyze ranging from metabolomics to transcriptomics. PRIMe represents a web service which measures standard metabolites by means of multi-dimensional nuclear magnetic resonance (NMR) spectroscopy, gas chromatography-mass spectrometry (GC/MS), liquid chromatography-mass spectrometry (LC/MS), and capillary electrophoresis-mass spectrometry (CE/MS). It includes several tools which help to work about metabolomics, transcriptomics, and integrated analysis of a range of other "-omics" data.
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