R-universe search: topic:geneticvariability

bioc

phyloseq:Handling and analysis of high-throughput microbiome census data

phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.

Maintained by Paul J. McMurdie. Last updated 5 months ago.

immunooncology sequencing microbiome metagenomics clustering classification multiplecomparison geneticvariability

597 stars 13.90 score 8.4k scripts 37 dependents

bioc

metagenomeSeq:Statistical analysis for sparse high-throughput sequencing

metagenomeSeq is designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. metagenomeSeq is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.

Maintained by Joseph N. Paulson. Last updated 3 months ago.

immunooncology classification clustering geneticvariability differentialexpression microbiome metagenomics normalization visualization multiplecomparison sequencing software

69 stars 11.90 score 494 scripts 7 dependents

bioc

GWASTools:Tools for Genome Wide Association Studies

Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.

Maintained by Stephanie M. Gogarten. Last updated 11 days ago.

snp geneticvariability qualitycontrol microarray

17 stars 10.67 score 396 scripts 5 dependents

bioc

GENESIS:GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness

The GENESIS package provides methodology for estimating, inferring, and accounting for population and pedigree structure in genetic analyses. The current implementation provides functions to perform PC-AiR (Conomos et al., 2015, Gen Epi) and PC-Relate (Conomos et al., 2016, AJHG). PC-AiR performs a Principal Components Analysis on genome-wide SNP data for the detection of population structure in a sample that may contain known or cryptic relatedness. Unlike standard PCA, PC-AiR accounts for relatedness in the sample to provide accurate ancestry inference that is not confounded by family structure. PC-Relate uses ancestry representative principal components to adjust for population structure/ancestry and accurately estimate measures of recent genetic relatedness such as kinship coefficients, IBD sharing probabilities, and inbreeding coefficients. Additionally, functions are provided to perform efficient variance component estimation and mixed model association testing for both quantitative and binary phenotypes.

Maintained by Stephanie M. Gogarten. Last updated 2 months ago.

snp geneticvariability genetics statisticalmethod dimensionreduction principalcomponent genomewideassociation qualitycontrol biocviews

36 stars 10.44 score 342 scripts 1 dependents

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snpStats:SnpMatrix and XSnpMatrix classes and methods

Classes and statistical methods for large SNP association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.

Maintained by David Clayton. Last updated 2 days ago.

microarray snp geneticvariability zlib

9.68 score 674 scripts 23 dependents

bioc

Rsubread:Mapping, quantification and variant analysis of sequencing data

Alignment, quantification and analysis of RNA sequencing data (including both bulk RNA-seq and scRNA-seq) and DNA sequenicng data (including ATAC-seq, ChIP-seq, WGS, WES etc). Includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. Can be applied to all major sequencing techologies and to both short and long sequence reads.

Maintained by Wei Shi. Last updated 9 days ago.

sequencing alignment sequencematching rnaseq chipseq singlecell geneexpression generegulation genetics immunooncology snp geneticvariability preprocessing qualitycontrol genomeannotation genefusiondetection indeldetection variantannotation variantdetection multiplesequencealignment zlib

9.24 score 892 scripts 10 dependents

bioc

SeqVarTools:Tools for variant data

An interface to the fast-access storage format for VCF data provided in SeqArray, with tools for common operations and analysis.

Maintained by Stephanie M. Gogarten. Last updated 5 months ago.

snp geneticvariability sequencing genetics

3 stars 8.76 score 384 scripts 2 dependents

bioc

qpgraph:Estimation of Genetic and Molecular Regulatory Networks from High-Throughput Genomics Data

Estimate gene and eQTL networks from high-throughput expression and genotyping assays.

Maintained by Robert Castelo. Last updated 1 days ago.

microarray geneexpression transcription pathways networkinference graphandnetwork generegulation genetics geneticvariability snp software openblas

3 stars 8.72 score 20 scripts 3 dependents

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missMethyl:Analysing Illumina HumanMethylation BeadChip Data

Normalisation, testing for differential variability and differential methylation and gene set testing for data from Illumina's Infinium HumanMethylation arrays. The normalisation procedure is subset-quantile within-array normalisation (SWAN), which allows Infinium I and II type probes on a single array to be normalised together. The test for differential variability is based on an empirical Bayes version of Levene's test. Differential methylation testing is performed using RUV, which can adjust for systematic errors of unknown origin in high-dimensional data by using negative control probes. Gene ontology analysis is performed by taking into account the number of probes per gene on the array, as well as taking into account multi-gene associated probes.

Maintained by Belinda Phipson. Last updated 27 days ago.

normalization dnamethylation methylationarray genomicvariation geneticvariability differentialmethylation genesetenrichment

7.24 score 300 scripts 1 dependents

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SIAMCAT:Statistical Inference of Associations between Microbial Communities And host phenoTypes

Pipeline for Statistical Inference of Associations between Microbial Communities And host phenoTypes (SIAMCAT). A primary goal of analyzing microbiome data is to determine changes in community composition that are associated with environmental factors. In particular, linking human microbiome composition to host phenotypes such as diseases has become an area of intense research. For this, robust statistical modeling and biomarker extraction toolkits are crucially needed. SIAMCAT provides a full pipeline supporting data preprocessing, statistical association testing, statistical modeling (LASSO logistic regression) including tools for evaluation and interpretation of these models (such as cross validation, parameter selection, ROC analysis and diagnostic model plots).

Maintained by Jakob Wirbel. Last updated 5 months ago.

immunooncology metagenomics classification microbiome sequencing preprocessing clustering featureextraction geneticvariability multiplecomparison regression

6.72 score 147 scripts

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deepSNV:Detection of subclonal SNVs in deep sequencing data.

This package provides provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The deepSNV algorithm is used for a comparative setup with a control experiment of the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate sequencing errors and subclonal SNVs. The shearwater algorithm computes a Bayes classifier based on a beta-binomial model for variant calling with multiple samples for precisely estimating model parameters - such as local error rates and dispersion - and prior knowledge, e.g. from variation data bases such as COSMIC.

Maintained by Moritz Gerstung. Last updated 5 months ago.

geneticvariability snp sequencing genetics dataimport curl bzip2 xz-utils zlib cpp

6.53 score 38 scripts 1 dependents

bioc

gwasurvivr:gwasurvivr: an R package for genome wide survival analysis

gwasurvivr is a package to perform survival analysis using Cox proportional hazard models on imputed genetic data.

Maintained by Abbas Rizvi. Last updated 5 months ago.

genomewideassociation survival regression genetics snp geneticvariability pharmacogenomics biomedicalinformatics

12 stars 6.43 score 75 scripts

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RAIDS:Accurate Inference of Genetic Ancestry from Cancer Sequences

This package implements specialized algorithms that enable genetic ancestry inference from various cancer sequences sources (RNA, Exome and Whole-Genome sequences). This package also implements a simulation algorithm that generates synthetic cancer-derived data. This code and analysis pipeline was designed and developed for the following publication: Belleau, P et al. Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58.

Maintained by Pascal Belleau. Last updated 5 months ago.

genetics software sequencing wholegenome principalcomponent geneticvariability dimensionreduction biocviews ancestry cancer-genomics exome-sequencing genomics inference r-language rna-seq rna-sequencing whole-genome-sequencing

5 stars 6.23 score 19 scripts

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martini:GWAS Incorporating Networks

martini deals with the low power inherent to GWAS studies by using prior knowledge represented as a network. SNPs are the vertices of the network, and the edges represent biological relationships between them (genomic adjacency, belonging to the same gene, physical interaction between protein products). The network is scanned using SConES, which looks for groups of SNPs maximally associated with the phenotype, that form a close subnetwork.

Maintained by Hector Climente-Gonzalez. Last updated 5 months ago.

software genomewideassociation snp geneticvariability genetics featureextraction graphandnetwork network bioinformatics genomics gwas network-analysis snps systems-biology cpp

4 stars 6.16 score 30 scripts

bioc

GBScleanR:Error correction tool for noisy genotyping by sequencing (GBS) data

GBScleanR is a package for quality check, filtering, and error correction of genotype data derived from next generation sequcener (NGS) based genotyping platforms. GBScleanR takes Variant Call Format (VCF) file as input. The main function of this package is `estGeno()` which estimates the true genotypes of samples from given read counts for genotype markers using a hidden Markov model with incorporating uneven observation ratio of allelic reads. This implementation gives robust genotype estimation even in noisy genotype data usually observed in Genotyping-By-Sequnencing (GBS) and similar methods, e.g. RADseq. The current implementation accepts genotype data of a diploid population at any generation of multi-parental cross, e.g. biparental F2 from inbred parents, biparental F2 from outbred parents, and 8-way recombinant inbred lines (8-way RILs) which can be refered to as MAGIC population.

Maintained by Tomoyuki Furuta. Last updated 12 days ago.

geneticvariability snp genetics hiddenmarkovmodel sequencing qualitycontrol cpp

4 stars 5.92 score 6 scripts

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RTN:RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

A transcriptional regulatory network (TRN) consists of a collection of transcription factors (TFs) and the regulated target genes. TFs are regulators that recognize specific DNA sequences and guide the expression of the genome, either activating or repressing the expression the target genes. The set of genes controlled by the same TF forms a regulon. This package provides classes and methods for the reconstruction of TRNs and analysis of regulons.

Maintained by Mauro Castro. Last updated 5 months ago.

transcription network networkinference networkenrichment generegulation geneexpression graphandnetwork genesetenrichment geneticvariability

5.80 score 53 scripts 2 dependents

bioc

TVTB:TVTB: The VCF Tool Box

The package provides S4 classes and methods to filter, summarise and visualise genetic variation data stored in VCF files. In particular, the package extends the FilterRules class (S4Vectors package) to define news classes of filter rules applicable to the various slots of VCF objects. Functionalities are integrated and demonstrated in a Shiny web-application, the Shiny Variant Explorer (tSVE).

Maintained by Kevin Rue-Albrecht. Last updated 5 months ago.

software genetics geneticvariability genomicvariation datarepresentation gui dnaseq wholegenome visualization multiplecomparison dataimport variantannotation sequencing coverage alignment sequencematching

2 stars 5.76 score 16 scripts

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QSutils:Quasispecies Diversity

Set of utility functions for viral quasispecies analysis with NGS data. Most functions are equally useful for metagenomic studies. There are three main types: (1) data manipulation and exploration—functions useful for converting reads to haplotypes and frequencies, repairing reads, intersecting strand haplotypes, and visualizing haplotype alignments. (2) diversity indices—functions to compute diversity and entropy, in which incidence, abundance, and functional indices are considered. (3) data simulation—functions useful for generating random viral quasispecies data.

Maintained by Mercedes Guerrero-Murillo. Last updated 5 months ago.

software genetics dnaseq geneticvariability sequencing alignment sequencematching dataimport

5.56 score 8 scripts 1 dependents

bioc

RIVER:R package for RIVER (RNA-Informed Variant Effect on Regulation)

An implementation of a probabilistic modeling framework that jointly analyzes personal genome and transcriptome data to estimate the probability that a variant has regulatory impact in that individual. It is based on a generative model that assumes that genomic annotations, such as the location of a variant with respect to regulatory elements, determine the prior probability that variant is a functional regulatory variant, which is an unobserved variable. The functional regulatory variant status then influences whether nearby genes are likely to display outlier levels of gene expression in that person. See the RIVER website for more information, documentation and examples.

Maintained by Yungil Kim. Last updated 5 months ago.

geneexpression geneticvariability snp transcription functionalprediction generegulation genomicvariation biomedicalinformatics functionalgenomics genetics systemsbiology transcriptomics bayesian clustering transcriptomevariant regression functional-variants variant

11 stars 5.52 score 5 scripts

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CrispRVariants:Tools for counting and visualising mutations in a target location

CrispRVariants provides tools for analysing the results of a CRISPR-Cas9 mutagenesis sequencing experiment, or other sequencing experiments where variants within a given region are of interest. These tools allow users to localize variant allele combinations with respect to any genomic location (e.g. the Cas9 cut site), plot allele combinations and calculate mutation rates with flexible filtering of unrelated variants.

Maintained by Helen Lindsay. Last updated 5 months ago.

immunooncology crispr genomicvariation variantdetection geneticvariability datarepresentation visualization sequencing

5.51 score 32 scripts

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omicsPrint:Cross omic genetic fingerprinting

omicsPrint provides functionality for cross omic genetic fingerprinting, for example, to verify sample relationships between multiple omics data types, i.e. genomic, transcriptomic and epigenetic (DNA methylation).

Maintained by Davy Cats. Last updated 5 months ago.

qualitycontrol genetics epigenetics transcriptomics dnamethylation transcription geneticvariability immunooncology

5.20 score 32 scripts

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scQTLtools:An R package for single-cell eQTL analysis and visualization

This package specializes in analyzing and visualizing eQTL at the single-cell level. It can read gene expression matrices or Seurat data, or SingleCellExperiment object along with genotype data. It offers a function for cis-eQTL analysis to detect eQTL within a given range, and another function to fit models with three methods. Using this package, users can also generate single-cell level visualization result.

Maintained by Xiaofeng Wu. Last updated 3 days ago.

software geneexpression geneticvariability snp differentialexpression genomicvariation variantdetection genetics functionalgenomics systemsbiology regression singlecell normalization visualization rna-seq sc-eqtl

3 stars 5.02 score

yuelyu21

SCIntRuler:Guiding the Integration of Multiple Single-Cell RNA-Seq Datasets

The accumulation of single-cell RNA-seq (scRNA-seq) studies highlights the potential benefits of integrating multiple datasets. By augmenting sample sizes and enhancing analytical robustness, integration can lead to more insightful biological conclusions. However, challenges arise due to the inherent diversity and batch discrepancies within and across studies. SCIntRuler, a novel R package, addresses these challenges by guiding the integration of multiple scRNA-seq datasets.

Maintained by Yue Lyu. Last updated 6 months ago.

sequencing geneticvariability singlecell cpp

2 stars 4.85 score 3 scripts

thomaschln

snplinkage:Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations

Linkage disequilibrium visualizations of up to several hundreds of single nucleotide polymorphisms (SNPs), annotated with chromosomic positions and gene names. Two types of plots are available for small numbers of SNPs (<40) and for large numbers (tested up to 500). Both can be extended by combining other ggplots, e.g. association studies results, and functions enable to directly visualize the effect of SNP selection methods, as minor allele frequency filtering and TagSNP selection, with a second correlation heatmap. The SNPs correlations are computed on Genotype Data objects from the 'GWASTools' package using the 'SNPRelate' package, and the plots are customizable 'ggplot2' and 'gtable' objects and are annotated using the 'biomaRt' package. Usage is detailed in the vignette with example data and results from up to 500 SNPs of 1,200 scans are in Charlon T. (2019) <doi:10.13097/archive-ouverte/unige:161795>.

Maintained by Thomas Charlon. Last updated 4 months ago.

geneticvariability microarray snp

4.62 score 14 scripts

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epistasisGA:An R package to identify multi-snp effects in nuclear family studies using the GADGETS method

This package runs the GADGETS method to identify epistatic effects in nuclear family studies. It also provides functions for permutation-based inference and graphical visualization of the results.

Maintained by Michael Nodzenski. Last updated 5 months ago.

genetics snp geneticvariability openblas cpp

1 stars 4.48 score 5 scripts

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trio:Testing of SNPs and SNP Interactions in Case-Parent Trio Studies

Testing SNPs and SNP interactions with a genotypic TDT. This package furthermore contains functions for computing pairwise values of LD measures and for identifying LD blocks, as well as functions for setting up matched case pseudo-control genotype data for case-parent trios in order to run trio logic regression, for imputing missing genotypes in trios, for simulating case-parent trios with disease risk dependent on SNP interaction, and for power and sample size calculation in trio data.

Maintained by Holger Schwender. Last updated 3 months ago.

snp geneticvariability microarray genetics

4.36 score 19 scripts

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MAGAR:MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data

"Methylation-Aware Genotype Association in R" (MAGAR) computes methQTL from DNA methylation and genotyping data from matched samples. MAGAR uses a linear modeling stragety to call CpGs/SNPs that are methQTLs. MAGAR accounts for the local correlation structure of CpGs.

Maintained by Michael Scherer. Last updated 5 months ago.

regression epigenetics dnamethylation snp geneticvariability methylationarray microarray cpgisland methylseq sequencing mrnamicroarray preprocessing copynumbervariation twochannel immunooncology differentialmethylation batcheffect qualitycontrol dataimport network clustering graphandnetwork

4.30 score 3 scripts

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microSTASIS:Microbiota STability ASsessment via Iterative cluStering

The toolkit 'µSTASIS', or microSTASIS, has been developed for the stability analysis of microbiota in a temporal framework by leveraging on iterative clustering. Concretely, the core function uses Hartigan-Wong k-means algorithm as many times as possible for stressing out paired samples from the same individuals to test if they remain together for multiple numbers of clusters over a whole data set of individuals. Moreover, the package includes multiple functions to subset samples from paired times, validate the results or visualize the output.

Maintained by Pedro Sánchez-Sánchez. Last updated 5 months ago.

geneticvariability biomedicalinformatics clustering multiplecomparison microbiome

2 stars 4.30 score 1 scripts

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GeneGeneInteR:Tools for Testing Gene-Gene Interaction at the Gene Level

The aim of this package is to propose several methods for testing gene-gene interaction in case-control association studies. Such a test can be done by aggregating SNP-SNP interaction tests performed at the SNP level (SSI) or by using gene-gene multidimensionnal methods (GGI) methods. The package also proposes tools for a graphic display of the results. <doi:10.18637/jss.v095.i12>.

Maintained by Mathieu Emily. Last updated 5 months ago.

genomewideassociation snp genetics geneticvariability cpp

4.30 score 2 scripts

bioc

Clomial:Infers clonal composition of a tumor

Clomial fits binomial distributions to counts obtained from Next Gen Sequencing data of multiple samples of the same tumor. The trained parameters can be interpreted to infer the clonal structure of the tumor.

Maintained by Habil Zare. Last updated 5 months ago.

genetics geneticvariability sequencing clustering multiplecomparison bayesian dnaseq exomeseq targetedresequencing immunooncology

4.30 score 3 scripts

bioc

gmoviz:Seamless visualization of complex genomic variations in GMOs and edited cell lines

Genetically modified organisms (GMOs) and cell lines are widely used models in all kinds of biological research. As part of characterising these models, DNA sequencing technology and bioinformatics analyses are used systematically to study their genomes. Therefore, large volumes of data are generated and various algorithms are applied to analyse this data, which introduces a challenge on representing all findings in an informative and concise manner. `gmoviz` provides users with an easy way to visualise and facilitate the explanation of complex genomic editing events on a larger, biologically-relevant scale.

Maintained by Kathleen Zeglinski. Last updated 5 months ago.

visualization sequencing geneticvariability genomicvariation coverage

4.30 score 9 scripts

bioc

BUMHMM:Computational pipeline for computing probability of modification from structure probing experiment data

This is a probabilistic modelling pipeline for computing per- nucleotide posterior probabilities of modification from the data collected in structure probing experiments. The model supports multiple experimental replicates and empirically corrects coverage- and sequence-dependent biases. The model utilises the measure of a "drop-off rate" for each nucleotide, which is compared between replicates through a log-ratio (LDR). The LDRs between control replicates define a null distribution of variability in drop-off rate observed by chance and LDRs between treatment and control replicates gets compared to this distribution. Resulting empirical p-values (probability of being "drawn" from the null distribution) are used as observations in a Hidden Markov Model with a Beta-Uniform Mixture model used as an emission model. The resulting posterior probabilities indicate the probability of a nucleotide of having being modified in a structure probing experiment.

Maintained by Alina Selega. Last updated 5 months ago.

immunooncology geneticvariability transcription geneexpression generegulation coverage genetics structuralprediction transcriptomics bayesian classification featureextraction hiddenmarkovmodel regression rnaseq sequencing

4.15 score 14 scripts

bioc

VariantTools:Tools for Exploratory Analysis of Variant Calls

Explore, diagnose, and compare variant calls using filters.

Maintained by Michael Lawrence. Last updated 5 months ago.

genetics geneticvariability sequencing

4.09 score 41 scripts

bioc

microbiomeExplorer:Microbiome Exploration App

The MicrobiomeExplorer R package is designed to facilitate the analysis and visualization of marker-gene survey feature data. It allows a user to perform and visualize typical microbiome analytical workflows either through the command line or an interactive Shiny application included with the package. In addition to applying common analytical workflows the application enables automated analysis report generation.

Maintained by Janina Reeder. Last updated 5 months ago.

classification clustering geneticvariability differentialexpression microbiome metagenomics normalization visualization multiplecomparison sequencing software immunooncology

4.00 score 8 scripts

bioc

OMICsPCA:An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples

OMICsPCA is an analysis pipeline designed to integrate multi OMICs experiments done on various subjects (e.g. Cell lines, individuals), treatments (e.g. disease/control) or time points and to analyse such integrated data from various various angles and perspectives. In it's core OMICsPCA uses Principal Component Analysis (PCA) to integrate multiomics experiments from various sources and thus has ability to over data insufficiency issues by using the ingegrated data as representatives. OMICsPCA can be used in various application including analysis of overall distribution of OMICs assays across various samples /individuals /time points; grouping assays by user-defined conditions; identification of source of variation, similarity/dissimilarity between assays, variables or individuals.

Maintained by Subhadeep Das. Last updated 5 months ago.

immunooncology multiplecomparison principalcomponent datarepresentation workflow visualization dimensionreduction clustering biologicalquestion epigeneticsworkflow transcription geneticvariability gui biomedicalinformatics epigenetics functionalgenomics singlecell

4.00 score 1 scripts

bioc

GSReg:Gene Set Regulation (GS-Reg)

A package for gene set analysis based on the variability of expressions as well as a method to detect Alternative Splicing Events . It implements DIfferential RAnk Conservation (DIRAC) and gene set Expression Variation Analysis (EVA) methods. For detecting Differentially Spliced genes, it provides an implementation of the Spliced-EVA (SEVA).

Maintained by Bahman Afsari. Last updated 5 months ago.

generegulation pathways geneexpression geneticvariability genesetenrichment alternativesplicing

3.98 score 16 scripts

bioc

RLMM:A Genotype Calling Algorithm for Affymetrix SNP Arrays

A classification algorithm, based on a multi-chip, multi-SNP approach for Affymetrix SNP arrays. Using a large training sample where the genotype labels are known, this aglorithm will obtain more accurate classification results on new data. RLMM is based on a robust, linear model and uses the Mahalanobis distance for classification. The chip-to-chip non-biological variation is removed through normalization. This model-based algorithm captures the similarities across genotype groups and probes, as well as thousands other SNPs for accurate classification. NOTE: 100K-Xba only at for now.

Maintained by Nusrat Rabbee. Last updated 5 months ago.

microarray onechannel snp geneticvariability

3.90 score 1 scripts

bioc

trigger:Transcriptional Regulatory Inference from Genetics of Gene ExpRession

This R package provides tools for the statistical analysis of integrative genomic data that involve some combination of: genotypes, high-dimensional intermediate traits (e.g., gene expression, protein abundance), and higher-order traits (phenotypes). The package includes functions to: (1) construct global linkage maps between genetic markers and gene expression; (2) analyze multiple-locus linkage (epistasis) for gene expression; (3) quantify the proportion of genome-wide variation explained by each locus and identify eQTL hotspots; (4) estimate pair-wise causal gene regulatory probabilities and construct gene regulatory networks; and (5) identify causal genes for a quantitative trait of interest.

Maintained by John D. Storey. Last updated 3 days ago.

geneexpression snp geneticvariability microarray genetics

3.48 score 3 scripts

bioc

chopsticks:The 'snp.matrix' and 'X.snp.matrix' Classes

Implements classes and methods for large-scale SNP association studies

Maintained by Hin-Tak Leung. Last updated 4 months ago.

microarray snpsandgeneticvariability snp geneticvariability

3.48 score 5 scripts

bioc

hapFabia:hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data

A package to identify very short IBD segments in large sequencing data by FABIA biclustering. Two haplotypes are identical by descent (IBD) if they share a segment that both inherited from a common ancestor. Current IBD methods reliably detect long IBD segments because many minor alleles in the segment are concordant between the two haplotypes. However, many cohort studies contain unrelated individuals which share only short IBD segments. This package provides software to identify short IBD segments in sequencing data. Knowledge of short IBD segments are relevant for phasing of genotyping data, association studies, and for population genetics, where they shed light on the evolutionary history of humans. The package supports VCF formats, is based on sparse matrix operations, and provides visualization of haplotype clusters in different formats.

Maintained by Andreas Mitterecker. Last updated 5 months ago.

genetics geneticvariability snp sequencing visualization clustering sequencematching software

3.30 score 9 scripts

bioc

BBCAnalyzer:BBCAnalyzer: an R/Bioconductor package for visualizing base counts

BBCAnalyzer is a package for visualizing the relative or absolute number of bases, deletions and insertions at defined positions in sequence alignment data available as bam files in comparison to the reference bases. Markers for the relative base frequencies, the mean quality of the detected bases, known mutations or polymorphisms and variants called in the data may additionally be included in the plots.

Maintained by Sarah Sandmann. Last updated 5 months ago.

sequencing alignment coverage geneticvariability snp

3.30 score 1 scripts

bioc

FRGEpistasis:Epistasis Analysis for Quantitative Traits by Functional Regression Model

A Tool for Epistasis Analysis Based on Functional Regression Model

Maintained by Futao Zhang. Last updated 5 months ago.

genetics networkinference geneticvariability software

3.30 score 6 scripts

bioc

appreci8R:appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity and high PPV

The appreci8R is an R version of our appreci8-algorithm - A Pipeline for PREcise variant Calling Integrating 8 tools. Variant calling results of our standard appreci8-tools (GATK, Platypus, VarScan, FreeBayes, LoFreq, SNVer, samtools and VarDict), as well as up to 5 additional tools is combined, evaluated and filtered.

Maintained by Sarah Sandmann. Last updated 5 months ago.

variantdetection geneticvariability snp variantannotation sequencing

3.30 score 1 scripts

bioc

ISoLDE:Integrative Statistics of alleLe Dependent Expression

This package provides ISoLDE a new method for identifying imprinted genes. This method is dedicated to data arising from RNA sequencing technologies. The ISoLDE package implements original statistical methodology described in the publication below.

Maintained by Christelle Reynès. Last updated 5 months ago.

immunooncology geneexpression transcription genesetenrichment genetics sequencing rnaseq multiplecomparison snp geneticvariability epigenetics mathematicalbiology generegulation openmp

2.30 score 2 scripts