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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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TileQC Resource Report Resource Website |
TileQC (RRID:SCR_001229) | TileQC | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May,10, 2021.Software providing a visually oriented tile based approach to error detection for Solexa next-gen sequencing data. It is written in R and has both qualitative and quantitative error detection features. This software was written with the idea that the researcher's visual pattern recognition is the best way to detect novel errors and contains variety of ways to visualize that data. Once a new type of error is identified the data extraction features of the program may then be used as a starting point for the programmatic detection and/or filtration of similar errors. A supplementary role of tileQC is to convert the Eland and Q-score data contained within the Solexa "*_prb.txt" and "*_eland_results.txt" text files to a more flexible database form. Once in database form, tileQC simplifies the mechanics of interacting with that data and supplements standard SQL with an expression subsitution mechanism that allows R to be easily comingled with SQL. This system requires access to a mySQL server and the R package RMySQL as well as a few standard UNIX tools (also available on Windows and Macintosh). | next-generation sequencing, quality control, solexa, r, tile, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Oregon State University; Oregon; USA |
PMID:18507856 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:tileqc, OMICS_02114 | https://bio.tools/tileqc | SCR_001229 | TileQC: A tile based approached to quality control | 2026-02-14 01:59:56 | 0 | |||||
|
VAAL Resource Report Resource Website |
VAAL (RRID:SCR_001184) | VAAL | software resource | A polymorphism discovery algorithm for short reads. To run it, you provide reads (and quality scores) from a "sample genome" as input, along with a vector sequence to trim from the reads, and a reference sequence for a related genome to compare to. VAAL produces as output a an assembly for the sample genome, together with a mask showing which bases are "trusted". It then deduces from that a list of differences between the sample and related genomes. Alternatively, it can be provided as input read data for two sample genomes, together with a reference sequence for a related genome. In this case, VAAL produces assemblies for each of the sample genomes, and compares them to each other, thereby deducing a list of differences between them. VAAL has been tested on bacteria, using single lanes of 36 bp unpaired reads from the Illumina platform. Note: This software package is no longer supported and information on this page is provided for archival purposes only. | dna sequence, polymorphism, parallel sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Broad Institute |
PMID:19079253 | biotools:vaal, OMICS_02170 | https://bio.tools/vaal | SCR_001184 | 2026-02-14 02:00:01 | 0 | |||||||
|
Bionimbus Resource Report Resource Website 1+ mentions |
Bionimbus (RRID:SCR_001189) | Bionimbus | service resource | A cloud-based infrastructure for managing, analyzing and sharing genomics datasets. | data sharing, cloud, genomics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Open Science Data Cloud |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:bionimbus, OMICS_02160 | https://bio.tools/bionimbus | SCR_001189 | 2026-02-14 02:00:01 | 2 | |||||||
|
RCASPAR Resource Report Resource Website |
RCASPAR (RRID:SCR_001253) | RCASPAR | software resource | Software package for survival time prediction based on a piecewise baseline hazard Cox regression model. It is meant to help predict survival times in the presence of high-dimensional explanatory covariates. | gene expression, genetics, proteomics, visualization, acgh |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02087 | SCR_001253 | 2026-02-14 01:59:58 | 0 | ||||||||
|
CNVtools Resource Report Resource Website 10+ mentions |
CNVtools (RRID:SCR_001250) | CNVtools | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package to facilitate the testing of Copy Number Variant data for genetic association, typically in case-control studies. | genetic variability, copy number variant, genetic association |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:18776912 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02090 | SCR_001250 | CNVtools - A package to test genetic association with CNV data | 2026-02-14 01:59:56 | 12 | ||||||
|
SABER Resource Report Resource Website 50+ mentions |
SABER (RRID:SCR_001257) | SABER | software resource | Software program suitable for genome-scale data which uses a Markov-hidden Markov model (MHMM) to estimate local ancestry. The MHMM makes it possible to identify genomic blocks of a particular ancestry by use of any high-density single-nucleotide-polymorphism panel. One application is to perform admixture mapping without genotyping special ancestry-informative-marker panels. | r, linux, ancestry, admixed, genetic, population, linkage disequilibrium, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Stanford University School of Medicine; California; USA |
PMID:16773560 | Free, Available for download, Freely available | biotools:saber, OMICS_02081 | https://bio.tools/saber | SCR_001257 | 2026-02-14 01:59:58 | 72 | ||||||
|
multtest Resource Report Resource Website 10+ mentions |
multtest (RRID:SCR_001255) | multtest | software resource | Software package for non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). Single-step and step-wise methods are available. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. When probing hypotheses with t-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. Results are reported in terms of adjusted p-values, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments. | differential expression, microarray, multiple comparison, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | biotools:multtest, OMICS_02085 | https://bio.tools/multtest | SCR_001255 | multtest - Resampling-based multiple hypothesis testing | 2026-02-14 01:59:59 | 35 | ||||||
|
BFCounter Resource Report Resource Website 1+ mentions |
BFCounter (RRID:SCR_001248) | BFCounter | software resource | Software program for counting k-mers in DNA sequence data. It identifies all the k-mers that occur more than once in a DNA sequence data set using a Bloom filter, a probabilistic data structure that stores all the observed k-mers implicitly in memory with greatly reduced memory requirements. | c++, k-mer, dna sequence, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Stanford University; Stanford; California |
PMID:21831268 | Free, Available for download, Freely available | biotools:bfcounter, OMICS_02093 | https://bio.tools/bfcounter | http://pritch.bsd.uchicago.edu/bfcounter.html, http://pritchardlab.stanford.edu/bfcounter.html | SCR_001248 | BF Counter: Memory efficient K-mer counting Software | 2026-02-14 02:00:03 | 5 | ||||
|
freeIbis Resource Report Resource Website 10+ mentions |
freeIbis (RRID:SCR_001241) | freeIbis | software resource | A software basecaller for Illumina sequencers with calibrated quality scores. | illumina, basecaller, sequencer | is listed by: OMICtools | PMID:23471300 | Free, Freely available | OMICS_02217 | SCR_001241 | freeIbis - Improved Base Identification System | 2026-02-14 01:59:56 | 12 | ||||||
|
TALLYMER Resource Report Resource Website 1+ mentions |
TALLYMER (RRID:SCR_001244) | Tallymer | software resource | A collection of flexible and memory-efficient software programs for k-mer counting and indexing of large sequence sets. It is based on enhanced suffix arrays which gives a much larger flexibility concerning the choice of the k-mer size. It can process large data sizes of several billion bases. | k-mer, counting, sequence, genome annotation, genome, annotation, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Hamburg; Hamburg; Germany |
PMID:18976482 | Free, Freely available | biotools:tallymer, OMICS_02096 | https://bio.tools/tallymer | SCR_001244 | 2026-02-14 02:00:03 | 7 | ||||||
|
Tally Resource Report Resource Website 1+ mentions |
Tally (RRID:SCR_001239) | Tally | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software program for deduplicating sequence fragments. It minimises memory usage by compressing sequences and using compact memory allocation techniques. A built-in parser allows a variety of input file formats and a simple specification language allows flexible output file formats. It can be made aware of paired-end reads, and it can handle degenerate sequence inserts intended to reveal amplification biases. Tally comes with reaper, a program for demultiplexing, trimming and filtering short read sequencing data. | paired end read processing, deduplication, sequence fragment |
is listed by: OMICtools has parent organization: European Bioinformatics Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02100 | SCR_001239 | Tally - Deduplication of sequence fragments | 2026-02-14 02:00:03 | 7 | |||||||
|
ITALICS Resource Report Resource Website |
ITALICS (RRID:SCR_001274) | ITALICS | software resource | Software package to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set. | affymetrix, copy number variation, microarray |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:18252739 | Free, Available for download, Freely available | OMICS_02064 | SCR_001274 | 2026-02-14 01:59:59 | 0 | |||||||
|
mBPCR Resource Report Resource Website |
mBPCR (RRID:SCR_001273) | mBPCR | software resource | Software package that estimates the DNA copy number profile to detect regions with copy number changes. | copy number variation, microarray, snp, acgh |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02065 | SCR_001273 | mBPCR - Bayesian Piecewise Constant Regression for DNA copy number estimation | 2026-02-14 02:00:04 | 0 | |||||||
|
CGHregions Resource Report Resource Website 1+ mentions |
CGHregions (RRID:SCR_001278) | CGHregions | software resource | Software package for dimension Reduction for Array CGH Data with Minimal Information Loss. | copy number variation, microarray, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19455235 | Free, Available for download, Freely available | OMICS_02058 | SCR_001278 | CGHregions - Dimension Reduction for Array CGH Data with Minimal Information Loss | 2026-02-14 02:00:04 | 4 | ||||||
|
quantsmooth Resource Report Resource Website 1+ mentions |
quantsmooth (RRID:SCR_001271) | quantsmooth | software resource | Software package for quantile smoothing and genomic visualization of array data. | copy number variation, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:15572474 | Free, Available for download, Freely available | OMICS_02067, BioTools:quantsmooth, biotools:quantsmooth | https://bio.tools/quantsmooth https://bio.tools/quantsmooth https://bio.tools/quantsmooth |
SCR_001271 | 2026-02-14 01:59:57 | 1 | ||||||
|
SNPchip Resource Report Resource Website 10+ mentions |
SNPchip (RRID:SCR_001269) | SNPchip | software resource | Software package that contains classes and methods useful for storing, visualizing and analyzing high density SNP data. Originally developed from the SNPscan web-tool, SNPchip utilizes S4 classes and extends other open source R tools available at Bioconductor, including the R packages Biobase and oligo. This has numerous advantages, including the ability to build statistical models for SNP-level data that operate on instances of the class, and to communicate with other R packages that add additional functionality. | dna copy number, snp, genetic variability, visualization, high throughput, snp chip, microarray, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor has parent organization: Johns Hopkins Bloomberg School of Public Health; Maryland; USA |
PMID:17204461 | Free, Available for download, Freely available | OMICS_02069, biotools:snpchip | https://bio.tools/snpchip | SCR_001269 | 2026-02-14 02:00:04 | 13 | ||||||
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ADMIXTURE Resource Report Resource Website 1000+ mentions |
ADMIXTURE (RRID:SCR_001263) | ADMIXTURE | software resource | A software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. It uses a block relaxation approach to alternately update allele frequency and ancestry fraction parameters. Each block update is handled by solving a large number of independent convex optimization problems, which are tackled using a fast sequential quadratic programming algorithm. Convergence of the algorithm is accelerated using a novel quasi-Newton acceleration method., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | ancestry, macos x, linux, admixture, allele, genome, single nucleotide polymorphism, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Los Angeles; California; USA |
PMID:19648217 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:admixture, OMICS_02077 | http://www.genetics.ucla.edu/software/admixture/ | SCR_001263 | ADMIXTURE: fast ancestry estimation | 2026-02-14 01:59:59 | 2679 | |||||
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frappe Resource Report Resource Website 50+ mentions |
frappe (RRID:SCR_001264) | frappe | software resource | Software using a f frequentist approach for estimating individual ancestry proportion. | ancestry, admixture, genome, allele |
is listed by: OMICtools has parent organization: Stanford University School of Medicine; California; USA |
PMID:15712363 | Free, Available for download, Freely available | OMICS_02076 | SCR_001264 | 2026-02-14 02:00:04 | 55 | |||||||
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ipPCA Resource Report Resource Website 1+ mentions |
ipPCA (RRID:SCR_001262) | ipPCA, i2pPCA | software resource | Software implementing a population structure analysis algorithm which assigns individuals to subpopulations and infers the total number of subpopulations present. Additional functions have been included that result in improved population assignment accuracy. # Universal genotype data encoding scheme which allows the population analysis of all types of genetic markers; Single Nucleotide Polymorphism (SNP), Short Tandem Repeat (STR) and RFLP. # New termination criterion called ?EigenDev? which is more robust to population sampling, thus provides the better estimation of number of assigned subpopulations (K) and higher accuracy for the analysis of large complex population datasets. | principal component analysis, population, genetic marker, single nucleotide polymorphism, short tandem repeat, rflp | is listed by: OMICtools | PMID:21699684 PMID:19930644 |
Free, Available for download, Freely available | OMICS_02078 | http://www4a.biotec.or.th/GI/tools/ippca | SCR_001262 | i2pPCA, Iterative pruning Principal Component Analysis | 2026-02-14 01:59:57 | 1 | |||||
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VegaMC Resource Report Resource Website 1+ mentions |
VegaMC (RRID:SCR_001267) | VegaMC | software resource | Software package that enables the detection of driver chromosomal imbalances including loss of heterozygosity (LOH) from array comparative genomic hybridization (aCGH) data. It performs a joint segmentation of a dataset and uses a statistical framework to distinguish between driver and passenger mutation. VegaMC has been implemented so that it can be immediately integrated with the output produced by PennCNV tool. In addition, it produces in output two web pages that allows a rapid navigation between both the detected regions and the altered genes. In the web page that summarizes the altered genes, the link to the respective Ensembl gene web page is reported. | copy number variation, acgh, chromosomal imbalance |
is listed by: OMICtools is related to: PennCNV has parent organization: Bioconductor |
Cancer | PMID:22815357 | Free, Available for download, Freely available | OMICS_02071 | SCR_001267 | VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer | 2026-02-14 01:59:57 | 1 |
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