Biocview "Genetics"

A/B compartment inference from ATAC-seq and methylation array data

Accessing and Processing a 'Mega2' Genetic Database

Accurate Inference of Genetic Ancestry from Cancer Sequencing

Affected pathway ranking in differential gene expression analysis

Affymetrix SNP Probe-Summarization using Non-Negative Matrix Factorization

A GAM based framework for analysis of ChIP-Seq data

A graphical interface for the metagene package

Agreement of Differential Expression Analysis

A lecture on sequence count data

Analysis and Visualisation of the Human Phenotype Ontology

Analysis of alternative poly A site usage

Analysis of Parent-Specific DNA Copy Numbers

Analysis of sequencing data from ribosome profiling experiments

Analytical Tools for MassArray Data

Analyze comorbidities from electronic health record data

Ancestry Specific Allele Frequency Estimation

An integrated analysis package of Gene expression and Copy number alteration

An integrated analysis package of miRNA and mRNA expression data

Annotation of Genetic Variants

Annotation package for the Leishmania.major.Friedlin object

Annotation package for the Solanum.lycopersicum object

Annotation package for the Trypanosoma.brucei.TREU927 object

Annotation package for the Trypanosoma.cruzi.CLBrener.Esmeraldo object

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 prediction of nucleosome positions

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

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 the CLIP data visualization

A package of creating an algorithm of identifying microRNA-competing endogenous RNA triplets

A package to produce metagene plots

A small RNA-seq visualizer and analysis toolkit

A Software Suite for Shallow Sequencing Copy Number Analysis

Assess Differential Gene Expression Experiments with ERCC Controls

Assess Gene Predictions Using Proteomics and Evolutionary Conservation

Association analysis of CNVs and imputed SNPs incorporating uncertainty

Association analysis of genomic regions based on permutation tests

A tool for quantification of associations between genotypes and phenotypes in genome wide association studies (GWAS) with Bayesian inference and statistical learning

a tool set for pathway based data integration and visualization

Automated functions for comparing various omic data from cbioportal.org

Automated genomic fine-mapping

Automatic calculation of literature relevance of genes

BANDITS: Bayesian ANalysis of DIfferenTial Splicing

Barycenter Single-Cell Differential Expression for Case-Control Studies

Base package for enabling powerful shiny web displays of Bioconductor objects

Bayesian clustering and imputationa of single cell methylomes

Bayesian modelling of cell-to-cell DNA methylation heterogeneity

BEAT - BS-Seq Epimutation Analysis Toolkit

Bias-free Footprint Enrichment Test

Bioconductor Tools for Human Mitochondrial Variant Analysis

BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data

Cancer mutation analysis

Candidate gene prioritization based on convergent evidence

Candidate Gene Prioritization for Non-Communicable Diseases Based on Functional Information

Check Yeast Deletion Barcodes

ChIP-Seq Analysis with Windows

Chromosomal DNA of Saccharomyces cerevisiae

Chromosome Instability Index

Chromosome plus MT plus rDNA sequences for riz (based on ensembl)

Classes and functions for Array Comparative Genomic Hybridization data

Clonal ordering and visualization

Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations

Clustering of Time Series Gene Expression data

cn.mops - Mixture of Poissons for CNV detection in NGS data

CNV detection tool for targeted NGS panel data

Coliphage Phi-X174 Complete Genome

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.

Compare Patient Samples to Cell Line Models Using Molecular Data and Weighted Similarity

Comparing tumour copy number profiles

Comparison, Benchmarking & QC of Epigenomic Datasets

Comprehensive genome-wide analysis of mutational processes

Comprehensive QTL annotation of GWAS results

Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

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

Computes estimates of the probability of related individuals sharing a rare variant

Conditional reciprocal best hits (CRBHits) in R

Conveniently access PyRanges functionalities from Bioconductor

Conveniently import and query gene models

Copy number analysis of high-throughput sequencing cancer data

Copy Number study and Segmentation for multivariate biological data

Copy number variant detection from exome sequencing read depth

Count summarization and normalization for RNA-Seq data

Covariate Assisted Large-scale Multiple testing

Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them

Cross omic genetic fingerprinting

Crossover analysis and genetic map construction

Data-Adaptive Statistics for High-Dimensional Multiple Testing

Data management of large-scale whole-genome sequence variant calls

Data Management of Large-Scale Whole-Genome Sequence Variant Calls

Data normalization by matrix raking

Decomposition of individual tumors into mutational signatures by signature refitting

Delineate outstanding genomic zones of differential gene activity

de novo Annotation of Pack-TYPE Transposable Elements

Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patients

Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges

Detection of subclonal SNVs in deep sequencing data.

Differential Binding of Transcription Factor with ChIP-seq

Differential Coverage package

Differential Expression Analysis for RNA-seq data through a robust variance component test

Differential gene usage in immune repertoires

Differentially regulated genes from scRNA-seq data

Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq

Diffusion scores on biological networks

Discriminant Analysis for Evolutionary Inference

distinct: a method for differential analyses via hierarchical permutation tests

Distributed computing by file or by range

distSTRING calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

DNA IP-seq data analysis

dPeak (Deconvolution of Peaks in ChIP-seq Analysis)

Dual redundant reference sequencing

echoverse module: Annotate fine-mapping results

echoverse module: Create package dependency graphs

echoverse module: echoversePackageTitle

echoverse module: Fine-mapping data access and formatting

echoverse module: Fine-mapping functions

echoverse module: Locus plot creation for fine-mapping and colocalization studies

Efficient manipulation of biological strings

Empirical Analysis of Digital Gene Expression Data in R

Ensemble of Gene Set Enrichment Analyses

Epistasis Analysis for Quantitative Traits by Functional Regression Model

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

Estimation of genetic and molecular regulatory networks from high-throughput genomics data

Evolutionary and plasticity analysis of orthologous groups

EWCE for Multiple Gene Lists

Expression Weighted Celltype Enrichment

Feature-based association and gene-set enrichment for copy number alteration analysis in cancer

Filtering of coding and non-coding genetic variants

Find Causal Cell-Types Underlying Complex Trait Genetics

Finding the DNA and protein sequences in a list of genomic or proteomic loci

Finding the DNA and Protein Sequences of Any Genomic or Proteomic Loci

Find RAre Splicing Events in RNA-Seq Data

FIREcaller: an R package for detecting frequently interacting regions from Hi-C data

Full Genome Sequence for Cryptococcus neoformans var. grubii KN99 (ASM221672v1)

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 mauritania (NCBI v1)

Full genome sequences for Drosophila melanogaster (flybase version dm3)

Full genome sequences for Homo sapiens (UCSC version hg19)

Full genome sequences for Homo sapiens (UCSC version hg38, based on GRCh38.p12) with injected major alleles (dbSNP151)

Full genome sequences for Homo sapiens (UCSC version hg38, based on GRCh38.p12) with injected minor alleles (dbSNP151)

Full genome sequences for Medicago truncatula (JCVI version Mt4.0v1)

Full genome sequences for P. falciparum 3D7

Full genome sequences for Zea mays PH207 (v1.0)

Full masked genome sequences for Mus musculus (UCSC version mm10)

functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets

Functionality Visualization for Motifs

Functional Network Analysis

Functions for designing genetics studies

functions for genome-wide application of Liquid Association

Functions to creation of low dimensional comparative matrices of Amino Acid Sequence occurrences

Gene Break Detection

Gene Environment Wide Interaction Search Threshold

Generally Applicable Gene-set Enrichment for Pathway Analysis

Generate synthetic nucleosome maps

Gene set analysis methods for SNP association p-values that lie in genes in given gene sets

genesis assocation testing code rewrite

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 inteRaction and EssenTiality neTwork mApper

Gene transfer format files for common ChIP-seq model organisms

Genome sequencing project metadata

Genometric Correlation package

Genome wide association studies of multiple traits with Bayesian multilvel models

Genomic Visualisation Routines

genotyping and copy number study tools

Genotyping and QTL Mapping in DO Mice

genphen: tool for quantification of genotype-phenotype associations in genome wide association studies (GWAS)

Get inversion status in predefined regions

Get the QTL/gene/SNP data functions

GGBase infrastructure for genetics of gene expression package GGtools

Gimpute: An efficient genetic data processing and imputation pipeline

gin in R

Global visualization tool of genomic data

GPA (Genetic analysis incorporating Pleiotropy and Annotation)

gQTLBase: infrastructure for eQTL, mQTL and similar studies

gQTLstats: computationally efficient analysis for eQTL and allied studies

GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data

graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture

gRx Differential Clustering

GWAS Incorporating Networks

GWAS trait-associated SNP enrichment analyses in genomic intervals

gwasurvivr: an R package for genome wide survival analysis

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

Higher-order chromatin domain inference in single samples from methylation arrays and single cells from scRNA-seq and scATAC-seq

HLA Genotype Imputation with Attribute Bagging

HMMRATAC - a semi-supervised machine learning approach for identifying open chromatin regions from ATAC-Seq data using Hidden Markov Models

Human ChIP-seq peaks data from ENCODE and ROADMAP Epigenomics

Hybrid Multiple Testing

Identification of cell-type-specific spatially variable genes accounting for excess zeros

Identification of SNP Interactions

Identify Different Architectures of Sequence Elements

Illumina 450K methylation array spatial analysis methods

Improved Allele-Specific Copy Number of SNP Microarrays for Downstream Segmentation

Improves Early Build Genome Assemblies using Strand-Seq Data

Infer Copy Number Variation from Single-Cell RNA-Seq Data

Inference of Chromosome-length Haplotypes using Genomic Data of Single Gamete Cells

Inference of Chromosome-Length Haplotypes Using Genomic Data of Single Gamete Cells

Inference on agreement between ordered lists

Infers clonal composition of a tumor

Infrastructure for Biostrings-based genome data packages

Infrastructure to work with genomewide position-specific scores

In-silico methods for genetic finemapping in inbred mice

Integrative analysis of structural variations

Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

Integrative Statistics of alleLe Dependent Expression

Interface for Popular Multiple Sequence Alignment Tools

Interface to the RDP Classifier

Interspecies gene mapping

Investigates Allele Specific Expression

iSTOP - Induced STOP Experiment Design

Iterative Pruning to Capture Population Structure

Iterative Pruning to Capture Population Structure version 2

KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level

Linear model and normality based normalization and transformation method (Linnorm)

Linear Models for Microarray Data

LiquidAssociation

Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs

m6Aboost

Mapping, quantification and variant analysis of sequencing data

Mapping Spectra to Mutational Signatures Based on Shot-Noise Modeling

Marker Gene Finder in Microarray gene expression data

Marker Gene Finder in RNA-seq data

Mean Alterations Using Discrete Expression

Metabarcoding and microbiome analysis using multiple amplicons

Metabolomic Quantitative Trait Locus Mapping for 1H NMR data

Methylated CpGs Set Enrichment Analysis

Methylation array and sequencing spatial analysis methods

Metrics to estimate a level of similarity between two ChIP-Seq profiles

Microarray Analysis of Differential Expression

Microbial Assemblage Normalized Transcript Analysis

Mining, Calling, and Importing Epigenomic Peaks in R

mirhostgenes: putting miRNAs into genomic context

MLP

Model higher-order methylation profiles

MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)

MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

Multi-function software that performs enrichment, functionally-informed genetic fine-mapping and gene mapping

Multiple Sequence Alignment with MUSCLE

Multi-Scale Target Explorer

Multivariate Analysis of Genotype–Phenotype Association and Visualization for 3D Image

Normalization and difference calling in ChIP-seq data

Nucleosome Dynamics

Nucleosome positioning package for R

Objective Assessment of Copy-Number Estimates

Obtain total affinity and occupancies for binding site matrices on a given sequence

Operations on genomic intervals

Optimized Functional Annotation Of ChIP-seq Data

OUTRIDER - OUTlier in RNA-Seq fInDER

Overlay omics data onto SBGN pathway diagram

Package for enabling powerful shiny web displays of Bioconductor objects

Pairwise INTegration of functional genomics data

pairwise sequence alignment similarity simple.

Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

Parallel implmentation of bounded memory GEE

PatchseqMap

Pedigree Analysis and Familial Aggregation

Pedigree and genetic relationship functions

Perform Chromosomal Ancestry Differences (CAnD) Analyses

Perform co-DE gene analysis

Perform Methylation Analysis on Next Generation Sequencing Data

Phenotype Consensus ANalysis (PCAN)

Poisson Models for Quantifying DNA Copy-number from FISH Images of Tissue Sections

Population Genetics

Position-Dependent Kernel Association Test

Position Related Data Analysis

Prediction of pri-miRNA Transcription Start Site

Preprocess epigenomic data for downstream analysis

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

QA/QC of a gVCF or VCF file

Quality control for target capture experiments

Quantify and Annotate Short Reads in R

Quantitative comparison of multiple ChIP-seq datasets

Quantitative DNA Sequencing for Chromosomal Aberrations

Quasispecies Diversity

Random Rotation Methods for High Dimensional Data with Batch Structure

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

Representation and manipulation of genomic intervals

Representation and manipulation of genomic intervals; demo with github actions binary generation

Representation and manipulation of short genomic alignments

representing and modeling data in the EMBL-EBI GWAS catalog

Retrotransposed transcript detection from structural variants

Rhythmicity Analysis Incorporating Non-parametric Methods

R Interface for the Basic Local Alignment Search Tool

RNA-binding protein motif analysis

RNASeqR: an R package for automated two-group RNA-Seq analysis workflow

Rothstein Lab SGA Analysis Tools

R package for immunogenomics data handling and association analysis

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

R SDK for BaseSpace RESTful API

R wrapper for the OMA REST API

sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R

"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"

Scalable Implementation of Generalized mixed models using GDS files in Phenome-Wide Association Studies

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 (with hg38 and mm10).

Semi-Supervised Mixture Model

Shape-based Analysis of Variation in ChIP-seq using Functional PCA

Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)

simple interfaces from OpenCRAVAT to Bioconductor

Simulation of Rare Variant Genetic Data

snp.plotter

software and data for analyses in genetics of gene expression

Software infrastructure for efficient representation of full genomes and their SNPs

Standardise summary statistics from GWAS

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

Storing annotation in TranscriptDb objects

Strength of Selected Codon Usage

Subclonal copy number and LOH prediction from whole genome sequencing of tumours

Suite of Functions for Pooled Crispr Screen QC and Analysis

SummarizedExperiment container

Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation Analysis

Summix2: A suite of methods to estimate, adjust, and leverage substructure in genetic summary data

Support package for GenomicFeatures

Synteny Alignment and Analysis for Saccharomyces sensu stricto

Synthetic Lethal Genetic Interaction

systemPipeRdata: Workflow templates and sample data

systemPipeR: NGS workflow and report generation environment

systemPipeR: workflow management and report generation environment

taxFun

"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"

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

The Discordant Method: A Novel Approach for Differential Correlation

This package classifies putative polyadenylation sites as true or false/internally oligodT primed

TnT applications with GWAS in dn8 format

Tools for building SNPlocs data packages

Tools for computing, querying and storing linkage-disequilibrium data

Tools for curating, analyzing, and manipulating biological sequences

Tools for Exploratory Analysis of Variant Calls

Tools for Testing Gene-Gene Interaction at the Gene Level

Tools for variant data

Tools for visualizing genomics data

Tools for working with diverse immune genes

Tools for working with ScreenMill data

Tools for Working With Synteny Objects

Transcript Annotation Tool (TransAT): an R package for retrieving annotations for transcript specific genetic variants

Transcriptional Regulatory Inference from Genetics of Gene ExpRession

Transcription Start Site Identification

Transcriptome instability analysis

TVTB: The VCF Tool Box

Use pyAnVIL and SMART infrastructure to work with AnVIL FHIR in R

Utilities for ATACseq QC, differential accessibility, and integration

Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

Utilities to create and use an Ensembl based annotation database

Utilities to create and use Ensembl-based annotation databases

Utility functions for high throughput sequencing

Variant annotations for structural variants

Visual comparison of mutational processes in a set of tumors

Visualization Tool for GWAS Result

visualize genome-wide association study with gene annotation and linkage disequiblism

Biocview "Genetics"

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