Searching across hundreds of databases
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
Integrated Software is a virtual database indexing software and tools from: SciCrunch, NITRC, Visiome Platform, Cerebellar Platform, Brain Machine Interface Platform and Genetic Analysis Software (GAS).
(last updated: Mar 5, 2022)
Physical Resource or Software Tool Software| Database | Name | Author/Location | Description | Notes | Reference |
|---|---|---|---|---|---|
| SciCrunch Registry | Rcorrector | Software tool as kmer based error correction method for RNAseq data. Can also be applied to other types of sequencing data where read coverage is nonuniform, such as single cell sequencing. Used for error correction for Illumina RNAseq reads. | Resource type:software resource,software application,data analysis software,data processing software, Availability:Free, Available for download, Freely available, supercategory:Resource | DOI:10.1186/s13742-015-0089-y | |
| SciCrunch Registry | CoLoRMap | Software tool as hybrid method for correcting noisy long reads, such as the ones produced by PacBio sequencing technology. Used for correcting long reads by mapping short reads. | Resource type:software resource,software application,data analysis software,data processing software, Availability:Free, Available for download, Freely available, supercategory:Resource | DOI:10.1093/bioinformatics/btw463 | |
| SciCrunch Registry | SparkAn | Software tool for custom calcium imaging analysis. | Resource type:software resource,image analysis software,data processing software,software application, Availability:Free, Freely available, supercategory:Resource | ||
| SciCrunch Registry | AMR meta | Software tool as k-mer and metafeature approach to classify antimicrobial resistance from high throughput short read metagenomics data. Kmer- and matrix factorization based classifier for metagenomics data. | Resource type:software resource,software application,data analysis software,data processing software, Availability:Free, Available for download, Freely available, supercategory:Resource | ||
| SciCrunch Registry | PlaForNEA | Software allows estimating growth and production at stand level of main forest species implanted in Argentine Mesopotamia such as Pino taeda, Eucalyptus grandis, Pino elliottii and Araucaria angustifolia. Areas for which models were adjusted correspond to province of Misiones, northeast of Corrientes and Concordia in province of Entre Ríos. | Resource type:software resource,software application,simulation software, Availability:Free, Available for download, Freely available, supercategory:Resource | ||
| SciCrunch Registry | Zentracker | Software tool as multiworm tracker. Can be used as analysis toolkit for extracting morphological and behavioural data from videos of objects moving in 2D environment. | Resource type:2d time-series analysis software,data analysis software,data processing software,software application,time-series analysis software,software resource, Availability:Free, Available for download, Freely available, supercategory:Resource | ||
| SciCrunch Registry | Rascaf | Software tool for scaffolding with RNA-seq read alignments. Used for improving genome assembly with RNA sequencing data. | Resource type:software resource,software application,data processing software, Availability:Free, Available for download, Freely available, supercategory:Resource | DOI:10.3835/plantgenome2016.03.0027 | |
| SciCrunch Registry | BayeScan | University of Bern; Bern; Switzerland, SIB Swiss Institute of Bioinformatics | Software tool to identify candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. | Resource type:software resource,software application,data analysis software,data processing software, Availability:Free, Available for Download, Freely available, supercategory:Resource | DOI:10.1534/genetics.108.092221 DOI:10.1111/j.1365-294X.2010.04820.x DOI:10.1111/j.1365-294X.2011.05015.x |
| SciCrunch Registry | StAMPP | Software R package for statistical analysis of mixed ploidy populations.Used for calculation of population structure and differentiation based on single nucleotide polymorphism genotype data from populations of any ploidy level, and/or mixed ploidy levels. | Resource type:software resource,software application,data analysis software,data processing software, Availability:Free, Available for download, Freely available, supercategory:Resource | DOI:10.1111/1755-0998.12129 | |
| SciCrunch Registry | gFACs | Software package provides comprehensive framework for evaluating, filtering, and analyzing gene models from range of input applications and preparing these annotations for formal publication or downstream analysis. | Resource type:software resource,software application,data processing software, Availability:Free, Available for download, Freely available, supercategory:Resource | DOI:10.1016/j.gpb.2019.04.002 | |
| SciCrunch Registry | ntCard | Software tool for estimating k-mer coverage histogram of genomics data. Streaming algorithm for estimating frequencies of k-mers in genomics datasets. | Resource type:software resource, Availability:Free, Available for download, Freely available, supercategory:Resource | DOI:10.1093/bioinformatics/btw832 | |
| SciCrunch Registry | Neuronanalyser | Software analysis toolkit for tracking blobs and extracting intensity values from imaging data, designed for use with ratiometric fluorescent sensors. | Resource type:2d time-series analysis software,data analysis software,data processing software,software application,time-series analysis software,software resource, Availability:Free, Available for download, Freely available, supercategory:Resource | ||
| SciCrunch Registry | PretextMap | Software tool to convert SAM formatted read pairs into genome contact maps. Prepares alignments for visualization with PretextView. | Resource type:software resource,software application,data processing software, Availability:Free, Available for download, Freely available, supercategory:Resource | ||
| SciCrunch Registry | AlienTrimmer | Allows detecting and removing multiple alien sequences in both ends of sequence reads. | Resource type:software resource, Availability:Free, supercategory:Resource | PMID:23912058 | |
| SciCrunch Registry | SALSA | Software tool for scaffold long read assemblies with Hi-C data. | Resource type:software resource,software application,data analysis software,data processing software, Availability:Free, Available for download, Freely available, supercategory:Resource | DOI:10.1371/journal.pcbi.1007273 DOI:10.1186/s12864-017-3879-z | |
| SciCrunch Registry | LEA | Software R package for landscape and ecological associations studies.Dedicated to genomewide association tests in general, with emphasis on association with ecological gradients. Runs analyses of population structure and scans for genomic signatures of local adaptation. | Resource type:software resource,software toolkit, Availability:Free, Available for download, Freely available, supercategory:Resource | DOI:10.1111/2041-210X.12382 | |
| SciCrunch Registry | calN50 | Software tool as simple script to calculate N50/NG50 and auN/auNG. | Resource type:data analytics software,software application,software resource, Availability:Free, Available for download, Freely available, supercategory:Resource | ||
| SciCrunch Registry | pcadapt | Software R package for fast Principal Component Analysis for outlier detection.Used to detect genetic markers involved in biological adaptation. Performs genome scans for selection based on principal component analysis. | Resource type:software resource,software toolkit, Availability:Free, Available for download, Freely available, supercategory:Resource | DOI:10.1111/1755-0998.12592 | |
| SciCrunch Registry | Blue Brain Nexus | Software system for knowledge graph management and data driven science. Ecosystem allows to organize and better leverage data through use of Knowledge Graph. | Resource type:software resource,software application,data management software, Availability:Free, Freely available, supercategory:Resource | ||
| SciCrunch Registry | SMART JUNIOR | Monitor-recognition software | Resource type:software resource,commercial organization, supercategory:Commercial Organization |
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.
You are currently on the Community Resources tab looking through categories and sources that RRID 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 RRID then you can log in from here to get additional features in RRID 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:
If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
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.
