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://metacpan.org/dist/Bio-Tools-Run-Alignment-Clustalw
Software package for performing multiple sequence alignment from set of unaligned sequences and/or sub-alignments by means of the clustalw program.
Proper citation: Bio-Tools-Run-Alignment-Clustalw (RRID:SCR_024067) Copy
https://metacpan.org/dist/Bio-Tools-Phylo-PAML
Software package used to parse output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00. You can use the Bio-Tools-Run-Phylo-PAML modules to actually run some of the PAML programs, but this module is only useful to parse the output.
Proper citation: Bio-Tools-Phylo-PAML (RRID:SCR_024069) Copy
https://metacpan.org/dist/Bio-Graphics
Software package to generate GD images of Bio::Seq objects.
Proper citation: Bio-Graphics (RRID:SCR_024061) Copy
https://github.com/genouest/biomaj-cli
Software package to use BioMAJ providing biomaj-cli.
Proper citation: CLI for BioMAJ (RRID:SCR_023980) Copy
Software pipeline for taxonomic classification of contigs and metagenome-assembled genomes. Contig Annotation Tool and Bin Annotation Tool for the taxonomic classification of long DNA sequences and metagenome assembled genomes of both known and unknown microorganisms, as generated by contemporary metagenomics studies.
Proper citation: CAT and BAT (RRID:SCR_023988) Copy
https://github.com/bioinfo-ut/GenomeTester4
Software toolkit for performing set operations - union, intersection and complement on k-mer lists.
Proper citation: GenomeTester4 (RRID:SCR_024026) Copy
https://github.com/nextstrain/augur
Software package to track evolution from sequence and serological data. Provides collection of commands which are designed to be composable into larger processing pipelines.
Proper citation: Augur (RRID:SCR_023964) Copy
https://cme.h-its.org/exelixis/web/software/exabayes/
Software package for Bayesian tree inference. Used for large-scale analyses on computer clusters.
Proper citation: ExaBayes (RRID:SCR_024019) Copy
Software to support biomedical image computing.
Proper citation: CTK (RRID:SCR_024002) Copy
https://github.com/a-slide/pycoQC
Software application to compute metrics and generate interactive QC plots for Oxford Nanopore technologies sequencing data.
Proper citation: pycoqc (RRID:SCR_024185) Copy
https://bioconductor.org/packages/release/bioc/html/annotate.html
Software R package for using R enviroments for annotation.
Proper citation: annotate (RRID:SCR_024221) Copy
https://bioconductor.org/packages/release/bioc/html/altcdfenvs.html
Software R package contains convenience data structures and functions to handle cdfenvs.
Proper citation: altcdfenvs (RRID:SCR_024225) Copy
https://cran.r-project.org/web/packages/biwt/index.html
Software R package for compute multivariate location, scale, and correlation estimates based on Tukey's biweight M-estimator.
Proper citation: biwt (RRID:SCR_024271) Copy
https://cran.r-project.org/web/packages/Epi/index.html
Software R package provides functions for demographic and epidemiological analysis in Lexis diagram, i.e. register and cohort follow-up data. In particular representation, manipulation, rate estimation and simulation for multistate data - the Lexis suite of functions, which includes interfaces to 'mstate', 'etm' and 'cmprsk' packages. Contains functions for Age-Period-Cohort and Lee-Carter modeling and function for interval censored data and some useful functions for tabulation and plotting, as well as number of epidemiological data sets.
Proper citation: Epi (RRID:SCR_024272) Copy
https://bioconductor.org/packages/preprocessCore/
Software library of core preprocessing routines.
Proper citation: preprocesscore (RRID:SCR_024254) Copy
https://bioconductor.org/packages/qusage/
Software R package is implementation Quantitative Set Analysis for Gene Expression method. Used to provide faster, more accurate, and easier to understand test for gene expression studies.
Proper citation: qusage (RRID:SCR_024255) Copy
https://bioconductor.org/packages/Rsamtools/
Software R package provides interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating Sequence Alignment Map, FASTA, binary variant call and compressed indexed tab-delimited files.
Proper citation: rsamtools (RRID:SCR_024257) Copy
https://bioconductor.org/packages/savR/
Software R package to parse Illumina Sequence Analysis Viewer files, access data, and generate QC plots.
Proper citation: savr (RRID:SCR_024258) Copy
https://bioconductor.org/packages/NanoStringQCPro/
Software R package to assess quality of NanoString mRNA gene expression data, to identify outlier probes and outlier samples. Provides different background subtraction and normalization approaches for this data. It outputs suggestions for flagging samples/probes and easily sharable html quality control output.
Proper citation: nanostringqcpro (RRID:SCR_024250) Copy
https://github.com/mroosmalen/nanosv
Software package that can be used to identify structural genomic variations in long-read sequencing data, such as data produced by Oxford Nanopore Technologies� MinION, GridION or PromethION instruments, or Pacific Biosciences RSII or Sequel sequencers.
Proper citation: NanoSV (RRID:SCR_024127) 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 NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF 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 NIF then you can log in from here to get additional features in NIF 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 NIF 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 NIF 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.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
