Curator Dashboard

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

Xylazine is an analogue of clonidine and an agonist at the α2 class of adrenergic receptor.[1] It is used for sedation, anesthesia, muscle relaxation, and analgesia in animals.

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• SciCrunch
• 8 years ago - submitted by Luping Yin

Ketamine hydrochloride is a cyclohexanone derivative used for induction of anesthesia. Its mechanism of action is not well understood, but ketamine can block NMDA receptors (RECEPTORS, N-METHYL-D-ASPARTATE) and may interact with sigma receptors.

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• SciCrunch
• 8 years ago - submitted by Luping Yin

sold under the trade name Forane among others, is a general anesthetic. It can be used to start or maintain anesthesia

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• SciCrunch
• 8 years ago - submitted by Luping Yin

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

Open source software tool for de novo transcriptome assembly reference free quality analysis. Used to examine assembly in detail and compare it to sequencing reads, reporting quality scores for contigs and assemblies to allow to choose between assemblers and parameters, filter out bad contigs from an assembly, and help decide when to stop trying to improve assembly.

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• SciCrunch
• 8 years ago - by Anonymous

Interactive web service for analysis of RNA-Seq read count data with principal component analysis (PCA) and agglomerative clustering. Includes features like read count normalization, filtering read counts by gene annotation and visualization options.

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• SciCrunch
• 8 years ago - by Anonymous