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http://purl.bioontology.org/ontology/ICD11-BODYSYSTEM

Ontology of a set of body-system terms used in the ICD (International Classification of Diseases) 11 revision

Proper citation: Body System Terms from ICD11 (RRID:SCR_001252) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/RCASPAR.html

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.

Proper citation: RCASPAR (RRID:SCR_001253) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/CNVtools.html

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.

Proper citation: CNVtools (RRID:SCR_001250) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/CGEN.html

Software R package for analysis of case-control studies in genetic epidemiology.

Proper citation: CGEN (RRID:SCR_001251) Copy   

•   Source: SciCrunch Registry

http://med.stanford.edu/tanglab/software/saber.html

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.

Proper citation: SABER (RRID:SCR_001257) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/multtest.html

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.

Proper citation: multtest (RRID:SCR_001255) Copy   

•   Source: SciCrunch Registry

http://www.softgenetics.com/mutationSurveyor.php

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.

Proper citation: Mutation Surveyor (RRID:SCR_001247) Copy   

•   Source: SciCrunch Registry

https://github.com/pmelsted/BFCounter

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.

Proper citation: BFCounter (RRID:SCR_001248) Copy   

•   Source: SciCrunch Registry

https://github.com/grenaud/freeIbis

A software basecaller for Illumina sequencers with calibrated quality scores.

Proper citation: freeIbis (RRID:SCR_001241) Copy   

•   Source: SciCrunch Registry

http://www.zbh.uni-hamburg.de/?id=211

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.

Proper citation: TALLYMER (RRID:SCR_001244) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/~stijn/reaper/tally.html

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.

Proper citation: Tally (RRID:SCR_001239) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/ITALICS.html

Software package to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set.

Proper citation: ITALICS (RRID:SCR_001274) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/genoset.html

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.

Proper citation: GenoSet (RRID:SCR_001275) Copy   

•   Source: SciCrunch Registry

https://www.benaroyaresearch.org/

Non-profit organization based out of Seattle, Washington that conducts medical research on autoimmune disease.

Proper citation: Benaroya Research Institute (RRID:SCR_001272) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.14/bioc/html/mBPCR.html

Software package that estimates the DNA copy number profile to detect regions with copy number changes.

Proper citation: mBPCR (RRID:SCR_001273) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/devel/bioc/html/CGHregions.html

Software package for dimension Reduction for Array CGH Data with Minimal Information Loss.

Proper citation: CGHregions (RRID:SCR_001278) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.14/bioc/html/CGHbase.html

Software package that contains functions and classes that are needed by arrayCGH packages.

Proper citation: CGHbase (RRID:SCR_001279) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/quantsmooth.html

Software package for quantile smoothing and genomic visualization of array data.

Proper citation: quantsmooth (RRID:SCR_001271) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.0/bioc/html/SNPchip.html

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.

Proper citation: SNPchip (RRID:SCR_001269) Copy   

•   Source: SciCrunch Registry

https://dalexander.github.io/admixture/download.html

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.

Proper citation: ADMIXTURE (RRID:SCR_001263) Copy   

•   Source: SciCrunch Registry