Curator Dashboard

Open source software designed in modular way, aimed at facilitating user interaction with Docker environments in three different computational layers like infrastructure, platform and application.

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• SciCrunch
• 8 years ago - submitted by Fabiano Menegidio

Software R package for calculating, applying, evaluating and plotting results of polygenic risk scores analysis. Performs simulation study to estimate P value significance threshold for high resolution PRS studies and produces plots for inspection of results. Operating Unix/Linux.

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• SciCrunch
• 8 years ago - submitted by Shing Wan Choi

Software tool for nucleotide sequence alignment. Graphical version of multiple sequence alignment program for DNA and proteins. Windows interface for ClustalW multiple sequence alignment program. Provides integrated environment for performing multiple sequence and profile alignments and analyzing results. Available on Linux, Mac and Windows.

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• RRID-Legacy
• 8 years ago - submitted by JING LI

Collection of publicly available data of curated receptors, ligands and their interactions. Integrates existing datasets that pertain to cellular communication and new manually reviewed information. Used to search for particular ligand or receptor or to interrogate single cell transcriptomics data.

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

Software Python tool for sleep EEG analysis. Used for Closed and Open loop in Slow Ocillations, Sleep Stimulation in Auditory or Recording in full PSG using OpenBCI Cyton.

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• SciCrunch
• 8 years ago - submitted by Frederik D. Weber

Software application for performing Gene Ontology analysis on RNAseq data and other length biased data. Used to reduce complexity and highlight biological processes in genome wide expression studies.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software R package for computing and annotating genomic ranges. Used for storing and manipulating genomic intervals and variables defined along genome.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool as executable program that measures sizes and other properties of colonies arrayed in grid format from jpeg images. Intended for 768, 384, or 96 colonies on agar plates.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool as peak finder for joint analysis of NGS replicates. Used for peak finding in next generation sequencing broad and narrow datasets like ChIP-Seq, ATAC-Seq, DNase-Seq. Can integrate information from biological replicates and assign peak boundaries accurately.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Open source software package for handling Unique Molecular Identifiers in NGS data sets.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software Java graphical tool for single cell analysis, clustering and visualization. Provides multithreaded implementations of clustering algorithms, including nonparametric density based X shift, Hierarchical clustering, Mean shift and K medoids.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Cross platform open source extension loading library. Provides efficient run time mechanisms for determining which OpenGL extensions are supported on target platform. OpenGL core and extension functionality is exposed in single header file. Operating systems Windows, Linux, Mac OS X, FreeBSD, Irix, and Solaris.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Algorithm for identification of rare and abundant cell types from single cell transcriptome data. Based on transcript counts obtained with unique molecular identifies. Used for discovering rare cell types and corresponding marker genes in healthy and diseased organs. Operating system Unix/Linux, Mac OS, Windows.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

SPARC data repository as of 2023 is an open data repository developed as part of the NIH SPARC initiative and has been used by SPARC funded investigator groups to curate and publish high quality datasets related to the autonomic nervous system. We are thrilled that as of August 2022, SPARC is accepting datasets from investigators that are not funded through the NIH SPARC program. The NIH's Common Fund Stimulating Peripheral Activity to Relieve Conditions (SPARC) program aims to transform our understanding of these nerve-organ interactions and ultimately advance neuromodulation field toward precise treatment of diseases and conditions for which conventional therapies fall short.

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• SciCrunch
• 8 years ago - submitted by Anita Bandrowski

Software package for simple data retrieval and versioning.

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• SciCrunch
• 8 years ago - by Anonymous

Software package as de novo trascriptome assembler for RNA-Seq data. Framework for de novo transcriptome assembly using RNA-seq data. Can assemble all transcripts from short reads without using reference. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux.

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• SciCrunch
• 8 years ago - by Anonymous

Software tool as de novo trascriptome assembler for RNA-Seq data. Used to assemble full length transcripts by remodeling problem as tracking set of trajectories of items over splicing graph. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux.

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• SciCrunch
• 8 years ago - by Anonymous

Software tool for de novo transcriptome assembly from RNA-Seq data.

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• SciCrunch
• 8 years ago - by Anonymous

Software tool for quantifying expression of transcripts using RNA-seq data. Provides fast and bias-aware quantification of transcript expression. Transcriptome-wide quantifier to correct for fragment GC-content bias.

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• SciCrunch
• 8 years ago - by Anonymous

Software tool to evaluate de novo transcriptome assemblies from RNA-Seq data. Consists of RSEM-EVAL and REF-EVAL packages. RSEM-EVAL is reference-free evaluation method. REF-EVAL is reference based and can be used to compare sets of any kinds of genomic sequences.

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• SciCrunch
• 8 years ago - by Anonymous