Curator Dashboard

Software tool for automatic transposable element classification. Used for searching for structural features and similarity to classify transposable elements.

• Resource
• SciCrunch
• 7 years ago - submitted by Shuang Jiang

Software tool for chromosome scale scaffolding of de novo genome assemblies based on chromatin interactions.Method exploits signal of genomic proximity in Hi-C datasets for ultra long range scaffolding of de novo genome assemblies.

• Resource
• SciCrunch
• 7 years ago - submitted by Shuang Jiang

Software tool as optimized and flexible pipeline for Hi-C data processing. Used to process Hi-C data, from raw fastq files, paired end Illumina data, to normalized contact maps.

• Resource
• SciCrunch
• 7 years ago - submitted by Shuang Jiang

Software tool as de novo genome assembly from long uncorrected reads. Used to correct raw contigs generated by rapid assembly methods which do not include consensus step. Supports data produced by Pacific Biosciences and Oxford Nanopore Technologies.

• Resource
• SciCrunch
• 7 years ago - submitted by Shuang Jiang

Software tool as image and photo editor for PCs that run Windows. Features user interface with support for layers, unlimited undo, special effects, and variety of useful and powerful tools.

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

Software toolbox for connectivity based parcellation of monkey brain. Integrated pipeline realizing tractography based brain parcellation with automatic processing and massive parallel computing. Highly automated process and high throughput performance supported by GPU option makes toolbox ready to be used by research community.

• Organization
• SciCrunch
• 7 years ago - submitted by he bin

Software tool for identifying and quantifying RNA splicing variation. Used to study sample and population variation in intron splicing. Identifies variable intron splicing events from short read RNA-seq data and finds alternative splicing events of high complexity. Used for detecting differential splicing between sample groups, and for mapping splicing quantitative trait loci (sQTLs).

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

Software tool to find restriction endonucleases. Helps restriction map nucleotide sequences. Tool with customizable interface, platform independent accessibility, interfaces to NCBI's GenBank, DNA sequence database, and NEB's REBase, and restriction enzyme database. In addition to restriction site mapping, Webcutter 2 also performs degenerate digests, including option of finding restriction sites that can be introduced into sequence by silent mutagenesis.

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

Software package for using multi locus genotype data to investigate population structure. Used for inferring presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Can be applied to most of commonly used genetic markers, including SNPS, microsatellites, RFLPs and Amplified Fragment Length Polymorphisms.

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

Web based program for collating results generated by program STRUCTURE. Provides assess and visualize likelihood values across multiple values of K and hundreds of iterations for easier detection of number of genetic groups that best fit data. Reformats data for use in downstream programs, such as CLUMPP.It is complement for using software Structure in genetics population. Website and program for visualizing STRUCTURE output and implementing Evanno method., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• RRID-Legacy
• 7 years ago - submitted by Anita Bandrowski

24 channel mobile electroencephalographic recording system. Supports synchronization with other sensors and simultaneous multi amplifier streaming via labstreaming layer. Wearable device that features motion sensors so body and head movements can be detected.

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

Software tool that uses long reads to enhance genome assembly. Fast and accurate gap closing software tool that uses low coverage of error-prone long reads generated by third generation sequence techniques (Pacbio, Oxford Nanopore, etc.) or preassembled contigs for large genomes.

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• RRID-Legacy
• 7 years ago - by Anonymous

Software for organizing and analyzing blot and gel images captured on iBright Imaging Systems. Available as desktop version PC and Mac OS compatible and cloud-based version accessible via web browser through Connect platform.

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

System for unified collection of measurement time series in research experiments that handles networking, time synchronization, near real time access as well as optionally centralized collection, viewing and disk recording of data. System for synchronizing streaming data for live analysis or recording.

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• RRID-Legacy
• 7 years ago - submitted by Anita Bandrowski

Software toolbox for neuroscientist data (EEG and reaction time for time being). Used to create shared language among different algorithms and softwares in this field (e.g. Fieldtrip, Eeglab, Chronux, Brainstorm, etc), in order to facilitate implementation of experimental analysis by users. Code and scripts for EEG analysis for MATLAB.

• Resource
• RRID-Legacy
• 7 years ago - submitted by Pablo Billeke

Miniaturized microscope that allows imaging from two brain regions. Integrates inertial measurement unit (IMU) and optogenetic LED driver. Used to perform dual miniscope recordings in multiple configurations and works with cross-platform software enabling operation on MSWindows, MacOS and Linux.

• Resource
• RRID-Legacy
• 7 years ago - submitted by Tycho Hoogland

Open source web application that tracks progress of jobs submitted to remote servers using Sun Grid Engine (SGE) on-demand scheduling system. Allows remote scheduling of pre-defined pipelines, as well as re-scheduling queued jobs. Telescope does not assume anything from the remote server, except for SSH connection. The connection is established using SSH key pairs that are stored after encrypted.

• Resource
• SciCrunch
• 7 years ago - submitted by Jaqueline Brito

Software tool to identify errors in genome assemblies without need for reference sequence. Can be used in any stage of assembly pipeline to automatically break incorrect scaffolds and flag other errors in assembly for manual inspection. Reports mis-assemblies and other warnings, and produces new broken assembly based on error calls.

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

Software tool for computing genome assembly likelihoods.Computes likelihood of reads with respect to assembly and statistical model which can be used as metric for evaluating assemblies. Novel likelihood based approach to assembly assessment in absence of ground truth.

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

Software package for identification of long terminal repeat retrotransposons (LTR-RTs). Removes false positives from initial software predictions. Achieves very high specificity, accuracy, and precision without significantly sacrificing sensitivity, hence significantly outperforming existing methods. Can construct LTR libraries directly from self-corrected PacBio reads prior to genome assembly.

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