Curator Dashboard

Software package for single cell RNA-seq data analysis using k-NN graph partitions. Used to analyze group of scRNA profiles that are highly similar and provides features for deriving them. Can be used with large datasets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

• Resource
• RRID-Legacy
• 8 years ago - by Anonymous

Software R package for identifying and characterizing continuous developmental trajectories in single cell data. Cell lineage and pseudotime inference for single-cell transcriptomics.

• Resource
• RRID-Legacy
• 8 years ago - by Anonymous

Software tool for generating multi omics data with disease status. Simulates genomics (SNPs and copy number variations), epigenomics ( whole genome bisulphite sequencing), transcriptomics ( RNA seq), and proteomics (normalized reverse phase protein array) data at the whole genome level. Available as desktop and web application version.

• Resource
• SciCrunch
• 8 years ago - submitted by Ren-Hua Chung

Software tools for next generation sequencing based bulked segregation analysis for outbreeding species including fruit trees such as apple or cirtus. Used to improve gene mapping efficiency of next generation sequencing based segregant analysis in outbreeding species and realize rapid candidate gene mining based on multi-omics data.

• Resource
• SciCrunch
• 8 years ago - submitted by Fei Shen

University in Turin in Piedmont region of north western Italy. One of the oldest universities in Europe, and continues to play an important role in research and training.

• Organization
• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software R package to execute next generation sequencing computing applications, e.g. reads mapping and counting, wrapped in docker containers.

• Resource
• SciCrunch
• 8 years ago - submitted by Raffaele Calogero

Software package for reproducible classification analysis of single cell sequencing data.

• Resource
• SciCrunch
• 8 years ago - submitted by Raffaele Calogero

Software tool for data management in clinical studies to improve care for patients with Traumatic Brain Injury (TBI). Used to search and find study variables with the associated information and export study data for further analysis.

• Resource
• RRID-Legacy
• 8 years ago - by Anonymous

Software tool for molecular characterization and quantification of lipid species from electrospray mass spectrometry data. Enables lipid profiling by searching parent and fragment ion masses against lipid fragment database and reports numerical and graphical output for various lipid molecular species, lipid classes, fatty acids, and long chain bases.

• Resource
• RRID-Legacy
• 8 years ago - by Anonymous

Gene expression data portal developed for stem cell community, containing public gene expression datasets derived from microarray, RNA sequencing and single cell profiling technologies. Portal to visualize and download curated stem cell data. Provides easy to use and intuitive tools for biologists to visually explore data, including interactive gene expression profiles, principal component analysis plots and hierarchical clusters, among others.

• Resource
• SciCrunch
• 8 years ago - submitted by Victoria Perreau

Portal provides access to data and web based applications created for benefit of global research community by Allen Institute for Brain Science. Projects to ombine genomics with neuroanatomy by creating gene expression maps for mouse and human brain. Mouse Brain Atlas, Human Brain Atlas, Developing Mouse Brain Atlas, Developing Human Brain Atlas, Mouse Connectivity Atlas, Non-Human Primate Atlas, and Mouse Spinal Cord Atlas and three related projects Glioblastoma, Mouse Diversity, and Sleep data banks, are used to advance various fields of science especially in neurobiological diseases.

• Resource
• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Cellular Taxonomy of Mouse Visual Cortex by analyzing gene expression patterns at single cell level. Construction of cellular taxonomy of one cortical region, primary visual cortex, in adult mice done on basis of single cell RNA sequencing.

• Resource
• RRID-Legacy
• 8 years ago - submitted by Victoria Perreau

Atlas of brain cell types, derived from single cell RNA-Seq data from Linnarsson Lab. Can be browsed by taxon, cell type, tissue, and gene, with information on enriched genes, specific markers, anatomical location and more. Single cell gene expression atlas of mouse nervous system.

• Resource
• RRID-Legacy
• 8 years ago - by Anonymous

Resource of targeted proteomics assays to detect and quantify proteins in complex proteome digests by mass spectrometry. Used to quantify the complete human proteome.

• Resource
• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool as a framework for fitting and describing connectivity patterns between regions that is a simple extension from the current population receptive field models in the visual neuroscience literature. The connectivity from each voxel in a designated seed region to a mapping region is modeled as a 3-dimensional Gaussian, providing location parameters and spread parameters. This allows the direct description of the relative mapping from one region to another.

• Resource
• NIF
• 8 years ago - by Anonymous

Software tool for evaluating RNA-Seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database. Capable to estimate gene database coverage by raw reads and de novo quality assessment using third party software.

• Resource
• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool for analysis of variant antigens in African trypanosomes. Used for quantitative analysis of antigenic diversity in systems data of genomes, transcriptomes, and proteomes, called Variant Antigen Profiling to understand how antigenic diversity relates to clinical outcome, how antigen genes may be used as epidemiological markers of virulence, and in measuring gene expression during experimental infections.

• Resource
• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool for assembling transcripts from RNA-Seq data. Explores surprising computational parallels between assembly of transcriptomes and single cell genomes. Suitable for all kind of organisms. Part of SPAdes package since version 3.9.

• Resource
• SciCrunch
• 8 years ago - submitted by Elena Bushmanova

Software tool as universal assay calculator for RIA, ELISA, IRMA, colorimetric or any other type of assay by Biosoft. Maintains record for each assay, and enables standard curve and QCs to be compared and adjusted. Can process data from 96 and 384-well plate readers in any order.

• Resource
• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool to automate cell type identification, cell type-specific pathway analyses, graph theory-based analysis of gene regulation, and detection of autocrine-paracrine signaling networks. Finds Gene and Autocrine-Paracrine Networks from Human Islet scRNA-Seq.

• Resource
• SciCrunch
• 8 years ago - submitted by Edyta Vieth