Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://github.com/BackofenLab/StoatyDive
Software tool to evaluate and classify predicted peak profiles to assess binding specificity of protein to its targets. Can be used for sequencing data such as CLIP-seq or ChIP-Seq, or any other type of peak profile data.
Proper citation: StoatyDive (RRID:SCR_018796) Copy
https://milaboratory.com/software/mixcr/
Software tool to processes big immunome data from raw sequences to quantitated clonotypes by MiLaboratory LLC. Universal software for analysis of T- and B-cell receptor repertoire high throughput sequencing data. Software for comprehensive adaptive immunity profiling.
Proper citation: MiXCR (RRID:SCR_018725) Copy
https://github.com/cochran4/GEMB
Software tool to introduce gene set enrichment for mathematical biology. Measures association between disease of interest and set of genes related to biological pathway. Used for defining gene contributions based on biophysical properties, by leveraging mathematical models of biology to predict effects of genetic perturbations on particular downstream function.
Proper citation: GEMB (RRID:SCR_018904) Copy
https://github.com/HicServices/DicomTypeTranslation
Open source software tool to extract metadata from DICOM files for indexing and storage in SQL database.
Proper citation: DicomTypeTranslator (RRID:SCR_018878) Copy
https://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi
Web tool for detection of structural and functional domains in protein sequences. Allows computation and download of conserved domain annotation for large sets of protein queries. Allows to view results graphically. Shows domain footprints, alignment details, and conserved features on any individual query sequence.
Proper citation: Batch Web CD-Search Tool (RRID:SCR_018756) Copy
https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/
Software tool as analysis pipeline for ribosome profiling experiments, which exploits triplet periodicity of ribosomal footprints to call translated regions. Statistical approach that identifies translated regions on basis of characteristic three nucleotide periodicity of Ribo-seq data.
Proper citation: RiboTaper (RRID:SCR_018880) Copy
Software tool for efficiently solving large scale sequence matching tasks.
Proper citation: Vmatch (RRID:SCR_018968) Copy
https://github.com/oushujun/LTR_FINDER_parallel
Software tool for parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons.
Proper citation: LTR_FINDER_parallel (RRID:SCR_018969) Copy
https://github.com/SouthGreenPlatform/metaXplor
Web interfaced application to store, share, explore and manipulate metagenomic data. Interactive viral and microbial metagenomic data manager. Stores large volumes of user defined sample, sequence and assignment information while providing filtering web interface. Offers means to share datasets with collaborators, BLAST external sequences against them, and confirm assignments by running phylogenetic placement. Available as set of Docker containers that make it simple to deploy on various infrastructures.
Proper citation: metaXplor (RRID:SCR_019025) Copy
https://github.com/LCSB-BioCore/GigaSOM.jl
Software tool for huge scale, high performance flow cytometry data clustering and visualization in Julia. High performance clustering and visualization of huge cytometry datasets.
Proper citation: GigaSOM.jl (RRID:SCR_019020) Copy
https://github.com/acg-team/tral
Software tool to make annotation of tandem repeats in amino acid and nucleic data simple. Includes modules for detecting tandem repeats with both de novo software and sequence profile HMMs. Used for statistical significance analysis of putative tandem repeats, and filtering of redundant predictions.
Proper citation: TRAL (RRID:SCR_018979) Copy
http://crdd.osdd.net/raghava/vicmpred/index.html
Software tool as SVM based method for prediction of functional proteins of gram negative bacteria using amino acid patterns and composition. Webserver for functional classification of proteins of bacteria into virulence factors, information molecule, cellular process and metabolism molecule.
Proper citation: VICMpred (RRID:SCR_019039) Copy
Web tool for visualization of genome annotations across large phylogenetic trees.Used for visualization and exploration of functionally annotated microbial tree of life. Integrates taxonomic, phylogenetic and functional annotation data from bacterial and archaeal genomes.
Proper citation: Annotree (RRID:SCR_018980) Copy
http://pyntacle.css-mendel.it/
Software Python package and command line tool for graphs analysis. Used to search for important components of graphs. Implements and provides ancillary methods for community finding, set operations between graphs, and quick data type conversion tools.
Proper citation: Pyntacle (RRID:SCR_019030) Copy
https://github.com/Gaius-Augustus/BRAKER
Software tool as pipeline for accurate and automated gene prediction in novel eukaryotic genomes. Automated gene prediction training and gene prediction pipeline.BRAKER1 is eukaryotic genome annotation pipeline. BRAKER2 is extension of BRAKER1 which allows for fully automated training of gene prediction tools GeneMark EX R14, R15, R17, F1 and AUGUSTUS from RNA Seq and/or protein homology information, and that integrates extrinsic evidence from RNA-Seq and protein homology information into prediction.
Proper citation: BRAKER (RRID:SCR_018964) Copy
http://www.imgt.org/StatClonotype/
Software tool to evaluate and visualize statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per variable,diversity, and joining gene of given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. Antibody clonotype analysis based on NGS sequences.
Proper citation: IMGT/StatClonotype (RRID:SCR_018963) Copy
https://github.com/auranic/ClinTrajan
Software Python package for analysis of trajectories in clinical datasets.
Proper citation: ClinTrajAn (RRID:SCR_019018) Copy
Software fast and lightweight tool for processing sequences in FASTA or FASTQ format.
Proper citation: Seqtk (RRID:SCR_018927) Copy
https://github.com/sandmanns/CopyDetective
Software tool for detection threshold aware CNV calling in matched whole exome sequencing data.
Proper citation: CopyDetective (RRID:SCR_018909) Copy
https://github.com/ShaokunAn/D-EE
Software tool for distributed dimensionality reduction and visualization. Distributed software for visualizing intrinsic structure of large scale single cell data written in C language. Its distributed storage and distributed computation technique allows efficiently analyze large scale single cell data at cost of constant time speedup.
Proper citation: D-EE (RRID:SCR_019058) Copy
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on dkNET then you can log in from here to get additional features in dkNET such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
You can save any searches you perform for quick access to later from here.
We recognized your search term and included synonyms and inferred terms along side your term to help get the data you are looking for.
If you are logged into dkNET you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the sources that were queried against in your search that you can investigate further.
Here are the categories present within dkNET that you can filter your data on
Here are the subcategories present within this category that you can filter your data on
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
Email: info_at_ dknet.org
