Biocview "Genetics"

Affected pathway ranking in differential gene expression analysis
Affymetrix SNP Probe-Summarization using Non-Negative Matrix Factorization
Affymetrix SNP Probe-Summarization using Non-Negative Matrix Factorization
A GAM based framework for analysis of ChIP-Seq data
A GAM based framework for analysis of ChIP-Seq data
A GAM based framework for analysis of ChIP-Seq data
A graphical interface for the metagene package
A graphical interface for the metagene package
A graphical interface for the metagene package
Agreement of Differential Expression Analysis
Agreement of Differential Expression Analysis
Analysis of Parent-Specific DNA Copy Numbers
Analysis of Parent-Specific DNA Copy Numbers
Analysis of sequencing data from ribosome profiling experiments
Analysis of sequencing data from ribosome profiling experiments
Analytical Tools for MassArray Data
Analytical Tools for MassArray Data
Ancestry Specific Allele Frequency Estimation
Ancestry Specific Allele Frequency Estimation
Ancestry Specific Allele Frequency Estimation
An integrated analysis package of Gene expression and Copy number alteration
An integrated analysis package of Gene expression and Copy number alteration
An integrated analysis package of miRNA and mRNA expression data
An integrated analysis package of miRNA and mRNA expression data
An integrated analysis package of miRNA and mRNA expression data
Annotation of Genetic Variants
Annotation of Genetic Variants
Annotation of Genetic Variants
Annotation package for the Leishmania.major.Friedlin object
Annotation package for the Solanum.lycopersicum object
Annotation package for the Trypanosoma.cruzi.CLBrener.Esmeraldo object
Annotation package for TxDb object(s)
Annotation package for TxDb object(s)
Annotation package for TxDb object(s)
Annotation package for TxDb object(s)
Annotation package for TxDb object(s)
Annotation package for TxDb object(s)
Annotation package for TxDb object(s)
Annotation package for TxDb object(s) for Brachypodium distachyon (JGI version 3.1)
An R package for nucleosome positioning prediction
An R package for nucleosome positioning prediction
An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates
An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates
A package for survival time prediction based on a piecewise baseline hazard Cox regression model.
A package for survival time prediction based on a piecewise baseline hazard Cox regression model.
A package to produce metagene plots
A package to produce metagene plots
A package to produce metagene plots
A small RNA-seq visualizer and analysis toolkit
A small RNA-seq visualizer and analysis toolkit
Assess Differential Gene Expression Experiments with ERCC Controls
Assess Differential Gene Expression Experiments with ERCC Controls
Assess Differential Gene Expression Experiments with ERCC Controls
Assess Differential Gene Expression Experiments with ERCC Controls
Association analysis of genomic regions based on permutation tests
Association analysis of genomic regions based on permutation tests
A tool for quantification of associations between genotypes and phenotypes with statistical learning techniques such as random forests and support vector machines as well as with Bayesian inference using hierarchical models
A tool for quantification of associations between genotypes and phenotypes with statistical learning techniques such as random forests and support vector machines as well as with Bayesian inference using hierarchical models
A tool for quantification of associations between genotypes and phenotypes with statistical learning techniques such as random forests and support vector machines as well as with Bayesian inference using hierarchical models
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
Base package for enabling powerful shiny web displays of Bioconductor objects
Base package for enabling powerful shiny web displays of Bioconductor objects
BEAT - BS-Seq Epimutation Analysis Toolkit
BEAT - BS-Seq Epimutation Analysis Toolkit
Big Data Management of Whole-genome Sequence Variant Calls
Big Data Management of Whole-genome Sequence Variant Calls
Big Data Management of Whole-genome Sequence Variant Calls
Cancer mutation analysis
Cancer mutation analysis
Candidate gene prioritization based on convergent evidence
Candidate gene prioritization based on convergent evidence
Candidate gene prioritization based on convergent evidence
Candidate gene prioritization based on convergent evidence
Candidate gene prioritization based on convergent evidence
Check Yeast Deletion Barcodes
ChIP-Seq Analysis with Windows
ChIP-Seq Analysis with Windows
ChIP-Seq Analysis with Windows
Chromosome Instability Index
Chromosome Instability Index
Cicer arietinum (Chickpea) full genome (NCBI version ASM33114v1)
Classes and functions for Array Comparative Genomic Hybridization data.
Classes and functions for Array Comparative Genomic Hybridization data.
Clustering of Time Series Gene Expression data
Clustering of Time Series Gene Expression data
Clustering of Time Series Gene Expression data
cn.mops - Mixture of Poissons for CNV detection in NGS data
cn.mops - Mixture of Poissons for CNV detection in NGS data
CNV detection tool for targeted NGS panel data
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns.
Compare multiple ChIP-Seq experiments.
Computational pipeline for computing probability of modification from structure probing experiment data
Computational pipeline for computing probability of modification from structure probing experiment data
Computational pipeline for computing probability of modification from structure probing experiment data
Copy number analysis of high-throughput sequencing cancer data
Copy number analysis of high-throughput sequencing cancer data
Copy Number study and Segmentation for multivariate biological data
Copy Number study and Segmentation for multivariate biological data
Copy number variant detection from exome sequencing read depth
Copy number variant detection from exome sequencing read depth
Count summarization and normalization for RNA-Seq data
Count summarization and normalization for RNA-Seq data
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
Cross omic genetic fingerprinting
Detecting SNPs with interactive effects on a quantitative trait
Detecting SNPs with interactive effects on a quantitative trait
Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges
Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges
Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges
Detection of subclonal SNVs in deep sequencing data.
Detection of subclonal SNVs in deep sequencing data.
Detection of subclonal SNVs in deep sequencing data.
Detection of subclonal SNVs in deep sequencing data.
Differential Binding of Transcription Factor with ChIP-seq
Differential Binding of Transcription Factor with ChIP-seq
Differential Coverage package
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
Distributed computing by file or by range
Distributed computing by file or by range
Distributed computing by file or by range
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA IP-seq data analysis
Empirical Analysis of Digital Gene Expression Data in R
Empirical Analysis of Digital Gene Expression Data in R
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
Epistasis Analysis for Quantitative Traits by Functional Regression Model
Epistasis Analysis for Quantitative Traits by Functional Regression Model
Estimation of genetic and molecular regulatory networks from high-throughput genomics data
Estimation of genetic and molecular regulatory networks from high-throughput genomics data
Evolutionary and plasticity analysis based on orthologous groups distribution
Evolutionary and plasticity analysis based on orthologous groups distribution
Expression Weighted Celltype Enrichment
Expression Weighted Celltype Enrichment
Feature-based association and gene-set enrichment for copy number alteration analysis in cancer
Feature-based association and gene-set enrichment for copy number alteration analysis in cancer
Filtering of coding and non-coding genetic variants
Filtering of coding and non-coding genetic variants
Filtering of coding and non-coding genetic variants
Full genome sequences for Brachypodium distachyon (JGI version 3.0 assembly)
Full genome sequences for Caenorhabditis elegans (UCSC version ce10)
Full genome sequences for Drosophila melanogaster (flybase version dm3)
Full genome sequences for Homo sapiens (UCSC version hg19)
Full genome sequences for Medicago truncatula (JCVI version Mt4.0v1)
Full genome sequences for P. falciparum 3D7
functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets
functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets
Functional Network Analysis
Functional Network Analysis
Functional Network Analysis
Functions for designing genetics studies
Functions for designing genetics studies
functions for genome-wide application of Liquid Association
functions for genome-wide application of Liquid Association
Gene Break Detection
Gene Break Detection
Gene Environment Wide Interaction Search Threshold
Gene Environment Wide Interaction Search Threshold
Generally Applicable Gene-set Enrichment for Pathway Analysis
Generally Applicable Gene-set Enrichment for Pathway Analysis
Generate synthetic nucleosome maps
Generate synthetic nucleosome maps
Generate synthetic nucleosome maps
Gene set analysis methods for SNP association p-values that lie in genes in given gene sets
Gene set analysis methods for SNP association p-values that lie in genes in given gene sets
Genetic Algorithms for Understanding Clonal Heterogeneity and Ordering
Genetic Algorithms for Understanding Clonal Heterogeneity and Ordering
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
Gene transfer format files for common ChIP-seq model organisms
Genome sequencing project metadata
Genome sequencing project metadata
Genome sequencing project metadata
Genometric Correlation package
Genomic Visualisation Routines
genotyping and copy number study tools
genotyping and copy number study tools
Genotyping and QTL Mapping in DO Mice
Genotyping and QTL Mapping in DO Mice
Genotyping and QTL Mapping in DO Mice
Get inversion status in predefined regions
Get inversion status in predefined regions
Get the QTL/gene/SNP data functions
GGBase infrastructure for genetics of gene expression package GGtools
GGBase infrastructure for genetics of gene expression package GGtools
Global visualization tool of genomic data
Global visualization tool of genomic data
gQTLBase: infrastructure for eQTL, mQTL and similar studies
gQTLBase: infrastructure for eQTL, mQTL and similar studies
gQTLstats: computationally efficient analysis for eQTL and allied studies
gQTLstats: computationally efficient analysis for eQTL and allied studies
gRx Differential Clustering
gRx Differential Clustering
GWAS Incorporating Networks in R
GWAS trait-associated SNP enrichment analyses in genomic intervals
GWAS trait-associated SNP enrichment analyses in genomic intervals
hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data
hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data
HLA Genotype Imputation with Attribute Bagging
HLA Genotype Imputation with Attribute Bagging
HLA Genotype Imputation with Attribute Bagging
Hybrid Multiple Testing
Hybrid Multiple Testing
Identification of SNP Interactions
Identification of SNP Interactions
Illumina 450K methylation array spatial analysis methods
Improved Allele-Specific Copy Number of SNP Microarrays for Downstream Segmentation
Improved Allele-Specific Copy Number of SNP Microarrays for Downstream Segmentation
Improves Early Build Genome Assemblies using Strand-Seq Data
Improves Early Build Genome Assemblies using Strand-Seq Data
Improves Early Build Genome Assemblies using Strand-Seq Data
Inference on agreement between ordered lists
Inference on agreement between ordered lists
Inference on agreement between ordered lists
Infers clonal composition of a tumor
Infers clonal composition of a tumor
Infrastructure for Biostrings-based genome data packages
Infrastructure for Biostrings-based genome data packages and support for efficient SNP representation
Infrastructure for Biostrings-based genome data packages and support for efficient SNP representation
Infrastructure to work with genomewide position-specific scores
Infrastructure to work with genomewide position-specific scores
Infrastructure to work with genomewide position-specific scores
Integrative analysis of structural variations
Integrative analysis of structural variations
Integrative Statistics of alleLe Dependent Expression
Integrative Statistics of alleLe Dependent Expression
Interface for Popular Multiple Sequence Alignment Tools
Interface to the Basic Local Alignment Search Tool (BLAST)
Interface to the RDP Classifier
Interface to the RDP Classifier
Investigates Allele Specific Expression
Investigates Allele Specific Expression
Investigates Allele Specific Expression
iSTOP - Induced STOP Experiment Design
iSTOP - Induced STOP Experiment Design
Joint analysis of multiple ChIP-Seq data sets
Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level
Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level
Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene, Pathway and Network Level
Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene, Pathway and Network Level
Linear model and normality based transformation method (Linnorm)
Linear model and normality based transformation method (Linnorm)
Linear Models for Microarray Data
Linear Models for Microarray Data
LiquidAssociation
LiquidAssociation
Marker Gene Finder in Microarray gene expression data
Marker Gene Finder in Microarray gene expression data
Marker Gene Finder in RNA-seq data
Marker Gene Finder in RNA-seq data
Metabolomic Quantitative Trait Locus Mapping for 1H NMR data
Metabolomic Quantitative Trait Locus Mapping for 1H NMR data
Methylation array and sequencing spatial analysis methods
Methylation array and sequencing spatial analysis methods
Methylation array and sequencing spatial analysis methods
Metrics to estimate a level of similarity between two ChIP-Seq profiles
Metrics to estimate a level of similarity between two ChIP-Seq profiles
Metrics to estimate a level of similarity between two ChIP-Seq profiles
Microarray Analysis of Differential Expression
Microbial Assemblage Normalized Transcript Analysis
Microbial Assemblage Normalized Transcript Analysis
mirhostgenes: putting miRNAs into genomic context
MLP
MLP
Model higher-order methylation profiles
Model higher-order methylation profiles
Model higher-order methylation profiles
Model higher-order methylation profiles
MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)
MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)
MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)
Multiple Sequence Alignment with MUSCLE
Multiple Sequence Alignment with MUSCLE
Normalization and difference calling in ChIP-seq data
Normalization and difference calling in ChIP-seq data
Normalization and difference calling in ChIP-seq data
Nucleosome positioning package for R
Nucleosome positioning package for R
Nucleosome positioning package for R
Objective Assessment of Copy-Number Estimates
Obtain total affinity and occupancies for binding site matrices on a given sequence
Obtain total affinity and occupancies for binding site matrices on a given sequence
Obtain total affinity and occupancies for binding site matrices on a given sequence
Operations on genomic intervals
Operations on genomic intervals
Optimal Gene Extensions From Histone Modification ChIP-seq Data
Optimized Functional Annotation Of ChIP-seq Data
Optimized Functional Annotation Of ChIP-seq Data
Optimized Functional Annotation Of Histone Modification ChIP-seq Data
Package for enabling powerful shiny web displays of Bioconductor objects
Package for enabling powerful shiny web displays of Bioconductor objects
Pairwise Integration of Functional Genomics Data
Pairwise INTegration of functional genomics data
Pairwise INTegration of functional genomics data
pairwise sequence alignment similarity simple.
Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
Parallel implmentation of bounded memory GEE
Pedigree Analysis and Familial Aggregation
Pedigree Analysis and Familial Aggregation
Pedigree Analysis and Familial Aggregation
Pedigree and genetic relationship functions
Pedigree and genetic relationship functions
Perform Chromosomal Ancestry Differences (CAnD) Analyses
Perform Chromosomal Ancestry Differences (CAnD) Analyses
Perform Methylation Analysis on Next Generation Sequencing Data
Perform Methylation Analysis on Next Generation Sequencing Data
Phenotype Consensus ANalysis (PCAN)
Phenotype Consensus ANalysis (PCAN)
Population Genetics
Population Genetics
Position-Dependent Kernel Association Test
Position-Dependent Kernel Association Test
Position Related Data Analysis
Position Related Data Analysis
Processing and analyzing bisulfite sequencing data
Processing and analyzing bisulfite sequencing data
Produce heatmaps for RNA-Seq HIV data
psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders
psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders
QA/QC of a gVCF or VCF file
QA/QC of a gVCF or VCF file
Quality control for target capture experiments
Quality control for target capture experiments
Quantify and Annotate Short Reads in R
Quantify and Annotate Short Reads in R
Quantitative comparison of multiple ChIP-seq datasets
Quantitative comparison of multiple ChIP-seq datasets
Quantitative DNA sequencing for chromosomal aberrations
Quantitative DNA sequencing for chromosomal aberrations
Quantitative DNA sequencing for chromosomal aberrations
R-based analysis of ChIP-seq And Differential Expression - a tool for integrating a count-based ChIP-seq analysis with differential expression summary data
R-based analysis of ChIP-seq And Differential Expression - a tool for integrating a count-based ChIP-seq analysis with differential expression summary data
R Client for Google Genomics API
R Client for Google Genomics API
R Client for Google Genomics API
Representation and manipulation of genomic intervals and variables defined along a genome
Representation and manipulation of genomic intervals and variables defined along a genome
Representation and manipulation of genomic intervals and variables defined along a genome
Representation and manipulation of short genomic alignments
Representation and manipulation of short genomic alignments
representing and modeling data in the EMBL-EBI GWAS catalog
representing and modeling data in the EMBL-EBI GWAS catalog
Rhythmicity Analysis Incorporating Non-parametric Methods
Rhythmicity Analysis Incorporating Non-parametric Methods
R package for RIVER (RNA-Informed Variant Effect on Regulation)
R package for RIVER (RNA-Informed Variant Effect on Regulation)
R package for RIVER (RNA-Informed Variant Effect on Regulation)
R package for RIVER (RNA-Informed Variant Effect on Regulation)
R SDK for BaseSpace RESTful API
R SDK for BaseSpace RESTful API
Run metabarcoding alalyses for multiple amplicons
Segmentation of single- and multi-track copy number data by penalized least squares regression.
Segmentation of single- and multi-track copy number data by penalized least squares regression.
Shape-based Analysis of Variation in ChIP-seq using Functional PCA
Shape-based Analysis of Variation in ChIP-seq using Functional PCA
snp.plotter
software and data for analyses in genetics of gene expression
software and data for analyses in genetics of gene expression
Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)
Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)
Statistical tools for the analysis of ChIP-seq data
Statistical tools for the analysis of ChIP-seq data
Storing annotation in TranscriptDb objects
Strength of Selected Codon Usage
Strength of Selected Codon Usage
String objects representing biological sequences, and matching algorithms
String objects representing biological sequences, and matching algorithms
Studying patterns in base substitution catalogues
Studying patterns in base substitution catalogues
Studying patterns in base substitution catalogues
Studying patterns in base substitution catalogues
Subclonal copy number and LOH prediction from whole genome sequencing of tumours
Subclonal copy number and LOH prediction from whole genome sequencing of tumours
Subclonal copy number and LOH prediction from whole genome sequencing of tumours
Subread sequence alignment for R
Subread sequence alignment for R
Suite of Functions for Pooled Crispr Screen QC and Analysis
Suite of Functions for Pooled Crispr Screen QC and Analysis
Suite of Functions for Pooled Crispr Screen QC and Analysis
SummarizedExperiment container
SummarizedExperiment container
SummarizedExperiment container
Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation Analysis
Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation Analysis
Synthetic Lethal Genetic Interaction
Synthetic Lethal Genetic Interaction
systemPipeRdata: NGS workflow templates and sample data
systemPipeR: NGS workflow and report generation environment
systemPipeR: NGS workflow and report generation environment
"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"
"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"
"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"
Testing of SNPs and SNP Interactions in Case-Parent Trio Studies
Testing of SNPs and SNP Interactions in Case-Parent Trio Studies
Testing of SNPs and SNP Interactions in Case-Parent Trio Studies
The Discordant Method: A Novel Approach for Differential Correlation
The Discordant Method: A Novel Approach for Differential Correlation
The Discordant Method: A Novel Approach for Differential Correlation
This package classifies putative polyadenylation sites as true or false/internally oligodT primed
This package classifies putative polyadenylation sites as true or false/internally oligodT primed
Tool for converting GFF3 file format data to a GRanges Object
Tools for curating, analyzing, and manipulating biological sequences
Tools for curating, analyzing, and manipulating biological sequences
Tools for Exploratory Analysis of Variant Calls
Tools for Exploratory Analysis of Variant Calls
Tools for making and manipulating transcript centric annotations
Tools for making and manipulating transcript centric annotations
Tools for Testing Gene-Gene Interaction at the Gene Level
Tools for Testing Gene-Gene Interaction at the Gene Level
Tools for Testing Gene-Gene Interaction at the Gene Level
Tools for variant data
Tools for variant data
Tools for visualizing genomics data
Tools for visualizing genomics data
Tools for visualizing genomics data
Tools for working with ScreenMill data
Transcriptional Regulatory Inference from Genetics of Gene ExpRession
Transcriptional Regulatory Inference from Genetics of Gene ExpRession
Transcriptional Regulatory Inference from Genetics of Gene ExpRession
Transcription Start Site Identification
Transcription Start Site Identification
Transcriptome instability analysis
Transcriptome instability analysis
TVTB: The VCF Tool Box
TVTB: The VCF Tool Box
TVTB: The VCF Tool Box
TVTB: The VCF Tool Box
Utilities for manipulating chromosome and other 'seqname' identifiers
Utilities for manipulating chromosome and other 'seqname' identifiers
Utilities to create and use an Ensembl based annotation database
Utilities to create and use Ensembl-based annotation databases
Utilities to create and use Ensembl-based annotation databases
Utilities to create and use Ensembl-based annotation databases
Utility functions for high throughput sequencing