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/rvalieris/parallel-fastq-dump
Software wrapper to speed up downloading process by dividing the work into multiple threads.
Proper citation: parallel-fastq-dump (RRID:SCR_024150) Copy
https://github.com/FlorianThibord/OptimiR
Software miRSeq data alignment workflow. Used to integrate genetic information to assess the impact of variants on miRNA expression. Used for integrating genome wide genotype data into miRNA sequence alignment analysis.
Proper citation: OptimiR (RRID:SCR_024149) Copy
https://github.com/FePhyFoFum/phyx
Software phylogenetic tools for unix. Used to perform phylogenetics analyses on trees and sequences. Collection of programs written in C ++ to explore, manipulate, analyze and simulate phylogenetic objects.
Proper citation: Phyx (RRID:SCR_024164) Copy
https://qtltools.github.io/qtltools/
Software tool set for molecular Quantitative Trait Loci discovery and analysis. Allows to go from raw sequence data to collection of molecular Quantitative Trait Loci in few easy-to-perform steps.
Proper citation: qtltools (RRID:SCR_024200) Copy
Open source software for image computation with main focus on high performance volumetric registration, segmentation, and image processing of volumetric medical images.
Proper citation: Plastimatch (RRID:SCR_024168) Copy
Software command line utility and library for lossy compression of PNG images. The conversion reduces file sizes significantly and preserves full alpha transparency. Generated images are compatible with all web browsers and operating systems.
Proper citation: pngquant (RRID:SCR_024169) Copy
https://gitlab.com/RKIBioinformaticsPipelines/QCumber
Software for quality control, quality trimming, adapter removal and sequence content check of NGS data.
Proper citation: qcumber (RRID:SCR_024203) Copy
https://github.com/BIMSBbioinfo/pigx_rnaseq
Software reproducible genomics analysis pipelines with GNU Guix. Used for analysis of RNA sequencing, chromatin immunoprecipitation sequencing, bisulfite-treated DNA sequencing, and single-cell resolution RNA sequencing. All pipelines process raw experimental data and generate reports containing publication-ready plots and figures, with interactive report elements and standard observables.
Proper citation: PiGx-RNAseq (RRID:SCR_024160) Copy
https://cran.r-project.org/web/packages/Mediana/index.html
Software R package for clinical trial simulations based on Clinical Scenario Evaluation approach. The package supports broad class of data models, analysis strategies and commonly used evaluation criteria.
Proper citation: mediana (RRID:SCR_024281) Copy
https://github.com/scottgigante/picopore
Software tool for reducing the storage size of Oxford Nanopore Technologies datasets without loss of functionality.
Proper citation: picopore (RRID:SCR_024161) Copy
https://cran.r-project.org/web/packages/itertools/index.html
Software R package for creating iterators, many patterned after functions in the Python itertools module, and others patterned after functions in the 'snow' package.
Proper citation: itertools (RRID:SCR_024282) Copy
Platform independent JAVA software for analysis of sequence based typing methods that generate allelic profiles and their associated epidemiological data.Phylogenetic inference and data visualization for sequence based typing methods.
Proper citation: PHYLOViZ (RRID:SCR_024162) Copy
https://bioconductor.org/packages/RBGL/
Software R package as interface to the graph algorithms contained in the BOOST library.
Proper citation: rbgl (RRID:SCR_024251) Copy
https://bioconductor.org/packages/release/bioc/html/pcaMethods.html
Software R package providing PCA methods for incomplete data. Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and conventional SVD PCA. Cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation.
Proper citation: pcaMethods (RRID:SCR_024252) Copy
https://bioconductor.org/packages/Rcpi/
Software R package as molecular informatics toolkit with integration of bioinformatics and chemoinformatics tools for drug discovery.
Proper citation: rcpi (RRID:SCR_024253) Copy
https://bioconductor.org/packages/release/bioc/html/rgsepd.html
Software R package to help disambiguate transcriptome samples by automating differential expression, then gene set enrichment, and finally N-dimensional projection to quantify in which ways each sample is like either treatment group.
Proper citation: rgsepd (RRID:SCR_024256) Copy
https://bioconductor.org/packages/makecdfenv/
Software R package has two functions. One reads Affymetrix chip description file and creates hash table environment containing location/probe set membership mapping. The other creates package that automatically loads that environment.
Proper citation: makecdfenv (RRID:SCR_024248) Copy
https://cran.r-project.org/web/packages/beeswarm/index.html
Software R package implementing bee swarm plots. Bee swarm plot is one-dimensional scatter plot like "stripchart", but with closely packed, non overlapping points.
Proper citation: beeswarm (RRID:SCR_024262) Copy
https://cran.r-project.org/web/packages/adephylo/index.html
Software R package provides multivariate tools to analyze comparative data. Analysis of comparative evolutionary data. Used for investigating phylogenetic signal in biological traits.
Proper citation: adephylo (RRID:SCR_024267) Copy
https://bioconductor.org/packages/TFBSTools/
Software R package for analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.
Proper citation: tfbstools (RRID:SCR_024260) 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
