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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-09-05 06:24:31 | 12 | ||||||
|
CGEN Resource Report Resource Website 10+ mentions |
CGEN (RRID:SCR_001251) | CGEN | data analysis software, data processing software, software application, software resource | Software R package for analysis of case-control studies in genetic epidemiology. | genetic, epidemiology, r, case-control, clustering, multiple comparison, snp |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:21387464 | Free, Available for download, Freely available | OMICS_02089 | SCR_001251 | CGEN - An R package for analysis of case-control studies in genetic epidemiology | 2026-09-05 06:24:31 | 18 | ||||||
|
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 | 2026-09-05 06:24:31 | 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 | 2026-09-05 06:24:31 | 37 | ||||||
|
Mutation Surveyor Resource Report Resource Website 500+ mentions |
Mutation Surveyor (RRID:SCR_001247) | data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for DNA sequencing analysis that integates with Sanger Sequencing files generated by Applied Biosystems Genetic Analyzers, MegaBACE, and Beckman CEQ electrophoresis systems. It can be used to find single nucleotide polymorphisms (SNPs), insertions and deletions (INDELS), and somatic mutations in direct sequencing, PCR sequencing, mitochondrial DNA sequencing, and resequencing projects. | dna, sequencing, dna-seq, sanger sequencing, sequence analysis software | is listed by: OMICtools | PMID:21780000 PMID:20938837 |
Restricted | OMICS_01816 | Mutation Surveyor software version 5.0 | http://www.softgenetics.com/mutationSurveyor.html | SCR_001247 | 2026-09-05 06:24:31 | 668 | ||||||
|
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 | 2026-09-05 06:24:31 | 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 | 2026-09-05 06:24:31 | 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 | 2026-09-05 06:24:31 | 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 | 2026-09-05 06:24:31 | 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 | 2026-09-05 06:24:32 | 0 | |||||||
|
GenoSet Resource Report Resource Website |
GenoSet (RRID:SCR_001275) | GenoSet | data analysis software, data processing software, software application, software resource | Software package to load, manipulate, and plot copynumber and BAF data by providing classes similar to ExpressionSet for copy number analysis. The class extends ExpressionSet by adding a locData slot for a RangedData or GRanegs object. This object contains feature genome location data and provides for efficient subsetting on genome location. CNSet and BAFSet extend GenoSet and require assayData matrices for Copy Number (cn) or Log-R Ratio (lrr) and B-Allele Frequency (baf) data. Implements and provides convenience functions for processing of copy number and B-Allele Frequency data. | copy number variation, data representation, infrastructure, microarray, snp |
is listed by: OMICtools has parent organization: Bioconductor |
Artistic License, v2 | OMICS_02063 | SCR_001275 | genoset - Provides classes similar to ExpressionSet for copy number analysis | 2026-09-05 06:24:32 | 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 | 2026-09-05 06:24:32 | 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 | 2026-09-05 06:24:32 | 4 | ||||||
|
CGHbase Resource Report Resource Website 1+ mentions |
CGHbase (RRID:SCR_001279) | CGHbase | data analysis software, data processing software, software application, software resource | Software package that contains functions and classes that are needed by arrayCGH packages. | copy number variation, infrastructure, microarray |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02057 | SCR_001279 | CGHbase: Base functions and classes for arrayCGH data analysis | 2026-09-05 06:24:32 | 1 | |||||||
|
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 | 2026-09-05 06:24:32 | 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 | 2026-09-05 06:24:32 | 14 | ||||||
|
Simpleaffy Resource Report Resource Website 50+ mentions |
Simpleaffy (RRID:SCR_001302) | Simpleaffy | data analysis software, data processing software, software application, software resource | Software package that provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. It makes heavy use of the affy library. It also has some basic scatter plot functions and mechanisms for generating high resolution journal figures. | affymetrix, annotation, data import, differential expression, microarray, one channel, preprocessing, quality control, report writing, transcription, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:16076888 | GNU General Public License, v2 or newer | OMICS_02034 | SCR_001302 | Simpleaffy - Very simple high level analysis of Affymetrix data | 2026-09-05 06:24:32 | 85 | ||||||
|
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 | 2026-09-05 06:24:32 | 2699 | |||||
|
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 | 2026-09-05 06:24:32 | 56 | |||||||
|
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 | 2026-09-05 06:24:32 | 1 |
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