Curator Dashboard

Software R package for sequence alignment and counting for R. Used for analyses of second and third generation sequencing data, for read mapping, read counting, SNP calling, short and long read alignment, quantification and mutation discovery. Includes assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software package for low-level analyses of single-cell RNA-seq data. Used for quality control, data exploration and normalization, cell cycle phase assignment, identification of highly variable and correlated genes, clustering into subpopulations and marker gene detection.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software package of python scripts made to simplify the processing of crystal diffraction images.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool as an algorithm to infer gene regulatory networks from spatial and temporal datasets. Spatial dataset or any data that can provide information about coexpression is used by the first step of the algorithm to perform clustering and separate the genes in the network in smaller coexpressed groups. Temporal dataset is used by the second step of the algorithm to infer regulations among the genes, based on Bayesian networks.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Web tool for synthetic single-guide RNA design of CRISPR-system in plants. Allows to search for high specificity Cas9 target sites within DNA sequences of interest, which also provides off-target loci prediction for specificity analyses and marks restriction enzyme cutting site to every sgRNA for further convenient in experiment.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool for data analysis and exploration. Statistics software for Mac.

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• RRID-Legacy
• 8 years ago - by Anonymous

Software tool to annotate structural variant calls with sequence depth information that can add or remove confidence to SV predicted to affect copy number. Indicates the presence of a rapid change in depth relative to the regions surrounding the breakpoints. Allows the run time to be nearly independent of the number of variants important for large, jointly called projects with many samples. Annotates structural variant predictions made from both short read and long read data.

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• SciCrunch
• 8 years ago - submitted by Brent Pedersen

Consortium to coordinate epigenome mapping and characterization worldwide to avoid redundant research effort, to implement high data quality standards, to coordinate data storage, management and analysis and to provide free access to the high resolution reference human epigenome maps for normal and disease cell types to the research community. Promotes data sharing. You may view, search and download the data already released by the different IHEC associated projects via the IHEC Data Portal.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Public university in Hangzhou, the capital of Zhejiang Province, China. It is a comprehensive university with an excellence in teacher training and professional development.

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

Data collected from subjects scanned 3 times (V1, V2, V3), with V1 and V2 on a scanner, V3 on another scanner in another site. Resting state blood oxygenation level dependent functional MRI (BOLD fMRI), pseudo continuous arterial spin labeling (pCASL), and high resolution 3D T1 imaging were performed under eyes open (EO) and eyes closed (EC) conditions.

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• NIF
• 8 years ago - submitted by Matt Travers

Software library to help with the conversion between imaging research formats and the standard DICOM representation for image analysis results. Used to implement conversion of the data stored in commonly used research formats into the standard DICOM representation. Available as a precompiled binary package for every major operating system, as a Docker image, and as an extension to 3D Slicer.

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• RRID-Legacy
• 8 years ago - submitted by Andrey Fedorov

Docker image that is used to process all of the data present in the Digital Expression Explorer 2 dataset. It can be freely used by anyone to process data on NCBI SRA or process their own RNA-seq fastq files. Used for bulk reprocessing of public RNA-seq data from SRA. The pipeline tallies the reads assigned to each gene or transcript.

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• SciCrunch
• 8 years ago - submitted by Mark Ziemann

GitHub repository of the Digital Expression Explorer 2 resource. It contains information related to the pipeline, docker image, backend analysis, webserver, and R package getDEE2.

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• SciCrunch
• 8 years ago - submitted by Mark Ziemann

Software tool as a repository of uniformly processed RNA-seq data mined from public data obtained from NCBI Short Read Archive . DEE2 consists of three parts: Webserver where end-users can search for and obtain data-sets of interest, Pipeline that can download and process SRA data as well as users own fastq files, Back-end that collects, filters and organises data provided by contributing worker nodes.

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• SciCrunch
• 8 years ago - submitted by Mark Ziemann

Equipment with product number MED VFC SCT M supplied by Med Associates. Fear conditioning package eliminates the need for bright visible light, visible light can be used within a session as a cue without impacting the video recording, real time video recordings allows software to distinguish between subtle movements such as whisker twitch or tail flick, as well as freezing behavior.

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• RRID-Legacy
• 8 years ago - by Anonymous

Web tool to identify putative transcription factor binding sites (TFBS) in DNA sequences from a species or groups of species of interest. Used for detection of known transcription regulatory elements using species-tailored searches.

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• RRID-Legacy
• 8 years ago - by Anonymous

Research project to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development and diseases. Portal provides free access to datasets, software packages, and protocols to advance biomedical research of nuclear architecture. Aims to develop and apply approaches to map the structure and dynamics of the human and mouse genomes.

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• dkNET
• 8 years ago - submitted by Ko-Wei Lin

Program to improve understanding of properties and functions of proteins that are currently unannotated within three most commonly drug protein families: targeted G-protein coupled receptors, ion channels, and protein kinases. Includes Data and Resource Generating Centers (DRGC), Knowledge Management Center (KMC), and Resource Dissemination and Outreach Center (RDOC).

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• dkNET
• 8 years ago - submitted by Ko-Wei Lin

Research consortium from many different fields to plan, perform and analyze the studies that are needed to help researchers conduct future prevention and intervention for Lower Urinary Tract Symptoms (LUTS) in women.

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• dkNET
• 8 years ago - submitted by Ko-Wei Lin

Project to facilitate research on single cells within tissues by supporting data generation and technology development to explore the relationship between cellular organization and function, as well as variability in normal tissue organization at the level of individual cells. Framework for functional mapping the human body with cellular resolution.Designed to support diverse spatial and non-spatial omics and imaging data types and to integrate with a wide range of analysis workflows.

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• dkNET
• 8 years ago - submitted by Ko-Wei Lin