Curator Dashboard

Commercial organization providing laboratory solutions in the fields of psychophysiology, neuroscience, social science, life science, child and behavioral development. Offers a wide array of products and services including signal acquisition hardware used to collect a variety of measures including Cardiac Impedance, HRV, GSR/GSC, ECG/EKG, HR, BP, and EMG supplemented with software suite of analysis applications.

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• RRID-Legacy
• 8 years ago - by Anonymous

Software tool for generic streaming read processing tasks that have low memory or computational demands, such as format conversion, sub sampling, and various filtering operations.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool to merge two overlapping paired reads into a single read. Used in amplicon studies and in assembly, where longer reads allow the use of longer kmers or fewer comparisons.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool for trimming and filtering sequencing data. Used to combine data quality related trimming, filtering, and masking operations into a single tool adapter. BBDuk2 allows multiple kmer based operations in a single pass.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software suite of bioinformatics tools for analysis of DNA and RNA sequence data. Used for file formats such as fastq, fasta, sam, scarf, fasta plus qual, compressed or raw, with autodetection of quality encoding and interleaving. Written in Java and works on any platform supporting Java, including Linux, MacOS, and Microsoft Windows.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool for finding and removing adapters from Oxford Nanopore reads.

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• SciCrunch
• 8 years ago - by Anonymous

Software tool written in Python to perform its filtering based on mean read quality and GC content and read length. Used for filtering and trimming of long read sequencing data.

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• SciCrunch
• 8 years ago - by Anonymous

Software tool as a short read aligner for DNA and RNA seq data. Used for large genomes with millions of scaffolds. Can align reads from Illumina, PacBio, 454, Sanger, Ion Torrent, Nanopore. Fast and accurate, particularly with highly mutated genomes or reads with long indels, even whole gene deletions over 100kbp long. It has no upper limit to genome size or number of contigs. Written in Java, can run on any platform.

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• SciCrunch
• 8 years ago - by Anonymous

Software tool to identify Topological Domains, which are basic builiding blocks of genome structure. Detects topological domains in a linear time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Web application providing transmembrane topology prediction. Server incorporates topology information from existing experimental and computational sources using the probabilistic framework of hidden Markov model. Provides the option to precede the topology prediction with signal peptide prediction and transmembrane globular protein discrimination. Given the amino acid sequence of a putative α helical transmembrane protein, CCTOP predicts its topology i.e. localization of membrane spanning regions and orientation of segments between them.

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• RRID-Legacy
• 8 years ago - by Anonymous

Software tool to provide fast all in one preprocessing for FastQ files. Developed in C++ with multithreading supported to afford high performance. Performs quality control, adapter trimming, quality filtering, per read quality pruning and many other operations with a single scan of the FASTQ data.

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• SciCrunch
• 8 years ago - submitted by Julien Bane

Software tools to make developing R packages easier by providing R functions that simplify and expedite common tasks.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software R package for making and manipulating transcript centric annotations. Used to download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool as a full probabilistic model for mapping ancient methylomes using sequencing data underlying an ancient specimen.

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• SciCrunch
• 8 years ago - submitted by kristian hanghoej

Portal for Science Dynamics projects with open source framework to provide way to query datasets. Code framework, including tutorials for project, titled Over Optimization of Academic Publishing Metrics Observing Goodhart Law in Action, to interactively explore and understand how various properties of journals have changed over time. Datasets, software implementations, code tutorials and interactive web interface for investigating studied networks.

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• SciCrunch
• 8 years ago - submitted by Michael Fire

Pipeline for the analysis of 10x single cell RNA sequencing data. Collection of python3 pipelines and Rscripts to analyze data generated with the 10x Genomics platform. The pipelines are based on 10x's Cell Ranger pipeline for mapping and quantitation and the R Seurat package for downstream analysis.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Manually curated collection of human epigenetic factors, their complexes, corresponding genes and products.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software written in R for determining cluster count and membership by stability evidence in unsupervised analysis. Provides quantitative and visual stability evidence for estimating the number of unsupervised classes in a dataset with item tracking, item consensus and cluster consensus plots.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

ImageJ plugins and macros for whisker tracking. Set of Fiji plugins and macros for tracking a single whisker.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth