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Cite this (BinPacker, RRID:SCR_017038)
URL: https://github.com/macmanes-lab/BinPacker/blob/master/README
Resource Type: Resource, software resource, software application, data analysis software, data processing software
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.Cite this (BioPortainer, RRID:SCR_017058)
URL: https://bioportainer.github.io/BioPortainer/
Resource Type: Resource, software resource, software application, data analysis software, data processing software
Open source software designed in modular way, aimed at facilitating user interaction with Docker environments in three different computational layers: infrastructure, platform and application.Cite this (Bridger, RRID:SCR_017039)
URL: https://github.com/fmaguire/Bridger_Assembler
Resource Type: Resource, software resource, software application, data analysis software, data processing software
Software package as de novo trascriptome assembler for 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.Cite this (CellPhoneDB, RRID:SCR_017054)
URL: https://www.cellphonedb.org/
Resource Type: Resource, data or information resource, database
Collection of publicly available data of curated receptors, ligands and their interactions. Subunit architecture is included for both ligands and receptors, representing heteromeric complexes accurately. Integrates existing datasets that pertain to cellular communication and new manually reviewed information. Used to search for particular ligand/receptor or interrogate your own single-cell transcriptomics data.Cite this (Clustal X , RRID:SCR_017055)
URL: http://www.clustal.org/clustal2/
Resource Type: Resource, image analysis software, data processing software, alignment software, software application, data visualization software, software resource
Software tool as 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.Cite this (Colony measure, RRID:SCR_017050)
URL: https://sourceforge.net/projects/ht-col-measurer/
Resource Type: Resource, software resource, software application, data analysis software, data processing software
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.Cite this (COsleep, RRID:SCR_017053)
URL: https://github.com/Frederik-D-Weber/cosleep
Resource Type: Resource, software resource, software application, data analysis software, data processing software
Software Python tool for sleep EEG analysis. Used for Closed and Open loop (Slow Ocillations) Sleep Stimulation (Auditory) or Recording in full PSG using OpenBCI Cyton.Cite this (datastorr, RRID:SCR_017040)
URL: https://github.com/ropenscilabs/datastorr
Resource Type: Resource, software resource, software application, data processing software
Software package for simple data retrieval and versioning.Cite this (Genomic Ranges, RRID:SCR_017051)
URL: http://bioconductor.org/packages/GenomicRanges/
Resource Type: Resource, software resource, software application, data analysis software, data processing software
Software R package for computing and annotating genomic ranges. Used for storing and manipulating genomic intervals and variables defined along genome.Cite this (GLEW, RRID:SCR_017046)
URL: http://glew.sourceforge.net/
Resource Type: Resource, software resource, software toolkit, software library
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.Cite this (Goseq, RRID:SCR_017052)
URL: https://bioconductor.org/packages/release/bioc/html/goseq.html
Resource Type: Resource, software resource, software application, data analysis software, data processing software
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.Cite this (HaTSPiL, RRID:SCR_017059)
URL: https://github.com/dodomorandi/hatspil
Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application
Software Python tool for high throughput sequencing analysis, focused on high reliability, modularity and customisability.Cite this (Italian Institute for Genomic Medicine; Turin; Italy, RRID:SCR_017062)
URL: https://www.iigm.it/site/index.php?l=ENG
Resource Type: Organization
Private research institute established by Compagnia di San Paolo, Universita degli Studi di Torino and Politecnico di Torino. Research programs addressed fields of human genetics, genomics and epigenomics. Investigation topics are immunogenetics, functional genomics, genomic epidemiology, tumour diagnostic and prognostic biomarker research, epigenetic modifications in disease, quantitative biology and computational neuroscience.Cite this (JAMM, RRID:SCR_017049)
URL: https://github.com/mahmoudibrahim/JAMM
Resource Type: Resource, software resource, software application, data analysis software, data processing software
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.Cite this (Kinarm End-Point Lab, RRID:SCR_017060)
URL: https://www.bkintechnologies.com/bkin-products/kinarm-end-point-lab/
Resource Type: Resource, material resource
Robotic manipulandum with display for studying arm movements. Allows to assess coordination of limbs at multiple joints while measuring joint specific force applied by subject as they perform individual tasks. Robotics research tool designed to make quantitative neurological assessments of sensorimotor, proprioception, and cognitive brain function by BKIN Technologies.Cite this (PRSice, RRID:SCR_017057)
URL: http://prsice.info/
Resource Type: Resource, software resource, software application, data analysis software, data processing software
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.Cite this (Queens University; Kingston; Canada, RRID:SCR_017061)
Resource Type: Organization, funding resource, undergraduate program resource, postdoctoral program resource, degree granting program, training resource
Public research university in Kingston, Ontario, Canada. Church of Scotland established Queen's College in 1841 with a royal charter from Queen Victoria. Canada's leading research intensive university.Cite this (RaceID, RRID:SCR_017045)
URL: https://github.com/dgrun/RaceID
Resource Type: Resource, software resource, algorithm resource
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.Cite this (Shannon, RRID:SCR_017037)
URL: https://github.com/sreeramkannan/Shannon
Resource Type: Resource, software resource, software application, data analysis software, data processing software
Software tool for de novo transcriptome assembly from RNA-Seq data.Cite this (UMI-tools, RRID:SCR_017048)
URL: https://github.com/CGATOxford/UMI-tools
Resource Type: Resource, software resource, software application, data analysis software, data processing software
Open source software package for handling Unique Molecular Identifiers in NGS data sets.Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
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