Biocview "Software"

Access Bioconductor docker images

Access HDF5 content from h5serv

Accessory Methods for the Analysis of Oxford Nanopore Technologies DNA Sequence Data

Access Pathways from Multiple Databases Through BioPAX and Pathway Commons

Accurate Inference of Genetic Ancestry from Cancer Sequencing

A collection of single-cell V(D)J tools

A collection of tools for imaging MS data processing

A comprehensive and high-efficiency tool for converting and retrieving the information of miRNAs in different miRBase versions

A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

Adaptive Signature Selection and InteGratioN (ASSIGN)

A `DataFrame` (`S4Vectors`) backend for `dplyr`

Advanced analysis of microbial flow cytometry data

A fast hierarchical graph-based clustering method

A Fast Scalable and Flexible Non Negative Matrix Factorization Method

Affinity test for identifying regularity Indels

Affinity test for identifying regulatory SNPs

Affymetrix-based RMA Processing Using Fixed Parameters

A Framework for Consensus Partitioning

A Framework for Quality Control

A Framework for visualizing gene set enrichment throughout neurodevelopment

A Framework to Combine, Analize and Interpret CNVs Calling Results

A gene-signature ranking method based on sample density in PCA space

A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC

A graphical user interface for MSstatsQC package

AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype

Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misalignment Detection

Allele-specific copy number genotyping for single cell sequencing data

A mass spectrometry imaging toolbox for statistical analysis

An algorithm for gene and gene set network inference

An alternative to dendrogram visualization and insertion of multiple layers of information

Analysis of alternative poly A site usage

Analysis of Brain Imaging Data

Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

Analysis of compositions of microbiomes with bias correction

Analysis of Copy Number Variation in Single-Cell-Sequencing Data

Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account

Analysis Of Differential Abundance Taking Sample Variation Into Account

Analysis of FACS data for the Jurkat crible project

Analysis of high-throughput microscopy-based screens

Analysis of Host-Associated Microbiomes from Hybrid Organisms

Analysis of Large-Scale Pharmacogenomic Data

Analysis of Large-Scale Radio-Genomic Data

Analysis of Large-Scale Toxico-Genomic Data

Analysis of patient-derived xenograft (PDX) data

Analysis of pooled genetic screens

Analysis of single-cell epigenomics datasets with a Shiny App

Analysis of Transposable Elements

Analysis Tools for 10X V(D)J Data

Analysis Tools for scATACseq Data with CoGAPS

Analyze comorbidities from electronic health record data

Analyze flow cytometric data using gate information

Analyze flow cytometric data using histogram information

Analyze Gene Sets Collections Properites

Analyze high-throughput sequencing of T and B cell receptors

Analyze massively parallel reporter assays

Analyze the Neighborhood (Upstream/Downstream Neighbors) of Genes

Analyzing tRNA sequences and structures

An Easy Pipeline for NanoString nCounter Data Analysis

An Implementation of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection

An integrated analysis package of Gene expression and Copy number alteration

An integrated analysis package of miRNA and mRNA expression data

An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification

An Interactive Consensus Clustering Framework for Multi-platform Data Analysis

An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps

An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps.

An interface to the Semantic MEDLINE database

annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions

Annotate sequences with KEGG pathways

Annotate the Gene Symbols for Probes in Expression Array

Annotate transcripts and predicted protein sequences

Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

Annotation and gene expression data retrieval from Bgee database

Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology

Annotation of Genomic Regions to Genomic Annotations

annotation of noncoding RNAs and coexpressed genes

Annotation translation functions

ANother Transcriptome Lineage ExploreR

a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data

An package for identification of novel peptides by customized database derived from RNA-Seq

An R Interface for Ribo Files

An R interface to the Common Workflow Language

An R interface to the Ontology Lookup Service

An R Package for Adjusting Bias in Gene Set Enrichment Analysis

an R package for analysis, visualization and biomarker discovery of microbiome

An R package for circadian and differential circadian analysis.

An R package for circadian and differential circadian analysis with repeated measurement

An R package for circadian differential R2.

An R Package for Comprehensive Filtration and Selection of Cancer Somatic Mutations

An R package for DiffCircaPipeline: A framework for multifaceted characterization of differential rhythmicity

An R package for fast computing for adaptively weighted fisher's method

An R Package for Integrating and Visualizing Single-Cell and Bulk Data to Resolve Regulatory Elements

An R package for subset-based association analysis of heterogeneous traits and subtypes

An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.

An R package for the creation of complex genomic profile plots

An R package for the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms

An R Package for Unbiased Splicing Pathway Analysis

An R Package for Unbiased Splicing Pathway Analysis in RNAseq data

an R package for visualization of tree and annotation data

An R Package To Add Geometric Layers On Circular Or Other Layout Tree Of "ggtree"

An R package to automate the analysis of double-strand break repair during meiosis

An R package to simulate DNA methylation data

An R/shiny package for microbiome functional enrichment analysis

An Ultra-Fast and All-in-One Fastq Preprocessor (Quality Control, Adapter, low quality and polyX trimming) and UMI Sequence Parsing).

AnVILBilling

A package for visualizing complex biological network

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

A package to search and retrieve data from Hub resources

A package with style requirements for the gDR suite

A pipeline for processing drug sensitivity screen data

A Pipeline Manager

A Pipeline to Process RNAseq Data

Application of t-sne to NGS Genomic Signal Profiles

A R/Bioconductor package to detect the interaction nodes from HiC/HiChIP/HiCAR data

ArrayAnalysis

ascend - Analysis of Single Cell Expression, Normalisation, and Differential expression

A search tool for single cell RNA-seq data by gene lists

A sensitive and fast tool for detection of TAD boundaries

A set of methods and tools for comprehensive analysis of phosphoproteomics data

A Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files

A Shiny App to accompany clusterExperiment

Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)

Assigning scRNA-seq to clone-of-origin using copy number from ultra-low-depth scDNA-seq

Assign Properties to TNBC Patients

Assign rfPred functional prediction scores to a missense variants list

Associates DNA Methylation with Matched gene Expression

A suite of functions to facilitate zFPKM transformations

A SummarizedExperiment for Ivy-GAP data

A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data

A Supervised Approach for Predicting Cell Cycle Progression Using Single-Cell RNA-seq Data

Asymmetric Within-Sample Transformation

Atlas and Analysis of Systems-Biology-Led Pathways

A Tool for Individualized Coherent Absolute Risk Estimation (iCARE)

A tool for unsupervised projection of single cell RNA-seq data

A toolkit for APA analysis using RNA-seq data

A Toolkit for Flow And Mass Cytometry Data

A toolkit for performing KNN-based statistics for flow and mass cytometry data

A toolkit for single-cell immune receptor profiling

A tool set for 3D Trans-Omic network visualization with Cytoscape

A tool to calculate and validate primers for Golden Gate Cloning

Augmenting Massively Parallel Cytometry Experiments Using Multivariate Non-Linear Regressions

Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics

Automated functions for comparing various omic data from cbioportal.org

Automated ingestion and conversion of various single-cell data formats.

Automated, probabilistic assignment of scRNA-seq to cell types

Automated Seurat Pipeline for scRNA-seq analysis

Automated spectraL Processing System for NMR

Automate package and project setup for Bioconductor packages

Automatically Aggregating and Summarizing lncRNA Analysis Results for Interactive Report

Automatic RNA-Seq present/absent gene expression calls generation

Automatic Statistical Identification in Complex Spectra

A visualization tool for single cell data of C.elegans embrogenesis

A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses

BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

BANDITS: Bayesian ANalysis of DIfferenTial Splicing

Bandwise normalization and batch correction of Hi-C data

Base Classes and Functions for Phylogenetic Tree Input and Output

Base Classes for Storing Genomic Interaction Data

BASiNET - Classification of mRNA and lncRNA sequences using complex network theory

Batch Effects Quality Control Software

Bayesian ANalysis Of Compositional Covariance

Bayesian Analysis of Differential Expression in RNA Sequencing Data

Bayesian Analysis of Single-Cell Sequencing data

Bayesian Enrichment Estimation in R

Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)

Bayesian hierarchical model for genome-wide profiling of nucleosome positions based on high-throughput short-read data (MNase-Seq data)

bcbioLite

BEAT - BS-Seq Epimutation Analysis Toolkit

Benchmark of differential abundance methods on microbiome data

Bias-free Footprint Enrichment Test

Big multivariate data plotted interactively

Binomial Random Forest Feature Selection

Bioconductor Quality Enhancement

Bioconductor software ecosystem building tools

biodb, a library and a development framework for connecting to chemical and biological databases

biodbChebi, a library for connecting to the ChEBI Database

biodbExpasy, a library for connecting to Expasy ENZYME database.

biodbHmdb, a library for connecting to the HMDB Database

biodbKegg, a library for connecting to the KEGG Database

biodbLipidmaps, a library for connecting to the Lipidmaps Structure database

biodbNci, a library for connecting to biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database

biodbUniprot, a library for connecting to the Uniprot Database

Biogeographic Regionalization and Macroecology

Bioinformatics pipelines based on Rcwl

Biological Network Reconstruction Omnibus

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

BioTIP: An R package for characterization of Biological Tipping-Point

Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful

BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data

Build Annotation From Online Database

Build, Predict and Analyse Artificial Intelligence Models

Bumpy Matrix of Non-Scalar Objects

Cache files downloaded from S3

Calculate and Visualize Synergy Scores for Drug Combinations

Calculate growth-rate inhibition (GR) metrics

Calculate, visualize and analyse overlap between genomic regions

Cancer mutation analysis

Cancer subtypes identification, validation and visualization based on multiple genomic data sets

Candidate Driver Analysis

Candidate Gene Miner

Candidate gene prioritization based on convergent evidence

Casc

ccrepe_and_nc.score

cell counter

Cell-Cycle using Mixture Models

Cell type annotation for unannotated single-cell RNA-Seq data

Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms

Cepo for the identification of differentially stable genes

Challenges for the Bioconductor community

Check Yeast Deletion Barcodes

CHiCAGO: Capture Hi-C Analysis of Genomic Organization

ChIPanalyser: Predicting Transcription Factor Binding Sites

ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

chromDraw is a R package for drawing the schemes of karyotypes in the linear and circular fashion.

Chromosome Instability Index

CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution

Classes and Functions to Serve as the Basis for Other 'Gx' Packages

Classes and Methods for Handling Genomic Interaction Data

Classes and methods for multi-omics data integration

Classes and methods for performing benchmark comparisons

Classification of RNA-seq data from ALL samples

Classification of RNA Sequences using Complex Network and Information Theory

Classification of RNA Sequences using Complex Network Theory

Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting molecules

Client for GREAT Analysis

Clonal ordering and visualization

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

Clone Identification from Single Cell Data

Cluster analysis of Spatial Transcriptomics data

Clustering Algorithms for Bioconductor

Clustering and pathway analysis using exponential distributions

Clustering and Resolution Enhancement of Spatial Transcriptomes

Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models

Clustering approach to solve complete Deconvolution problem

Clustering Deviation Index (CDI)

Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq

CMEA: An R package for Systematic Exploration of Single-Cell Morphological Phenotypes from Transcriptomic Profile

CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models

CNCDriver

CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.

Code for using BridgeDb identifier mapping framework from within R

Codon Usage Analysis and Prediction of Gene Expressivity

Co-Expression Analysis of Sequencing Data

co-expression of lincRNAs and protein-coding genes

Collate Gene Annotation Data from Uniprot and NIH Gene Databases

Collection of simple tools for learning about Bioconductor Packages

Collection of simple tools for learning about Bioc Packages

Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)

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.

Common utility functions

Comparative Evaluation and Visualization of Differential Expression Analyses

Compare Clusterings for Single-Cell Sequencing

Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets

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

Compares the genetic/epigenetic features between cancer cell lines with different dependencies of a gene set (signature)

Comparing tumour copy number profiles

Compensates for the bias introduced by median normalization in phosphoproteomics. This is done by taking enriched and non-enriched data and creating a normalization factor.

Competitive Balances for Taxonomic Enrichment Analysis in R

CompositeDriver

Comprehensive Analysis of Gene Interactivity Networks Based on Single-Cell RNA-Seq

Computation of functional similarities between GO terms and gene products; GO enrichment analysis

Compute coverage matrices from recount quickly using bwtool

Conditional Differential Analysis for Flow and Mass Cytometry Experiments

Conditional reciprocal best hits (CRBHits) in R

Conducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocation

Confidence estimation for intra-chromosomal contact maps

ConsensusClusterPlus

Construct Benchmarks for Single Cell Analysis Methods

Constructing gene regulatory networks from expression data through functional module inference

Context-Aware Transcript Quantification from Long Read RNA-Seq data

Conversion of single cell experiment output files to relational database

Convex Analysis of Mixtures for Tissue Heterogeneity Characterization

Convex Analysis of Mixtures Version 3

CopyKit

Copy Number Analysis for 450k Illumina Methylation Arrays

Copy number calling and SNV classification using targeted short read sequencing

Copy Number Variant Metrics

Core Engine for NxtIRF: a User-Friendly Intron Retention and Alternative Splicing Analysis using the IRFinder Engine

Correction for natural isotope abundance and tracer purity in MS and MS/MS data from stable isotope labeling experiments

Correction of batch effects in DNA methylation data

Correlated Meta-Analysis

Correlation analysis of RNA secondary structure mutation and differential expression

Correspondence Analysis for Single Cell Data

Coverage visualization package for R

Create R package

Creates and uses physio spaces as a dimension reduction mapping

Creates diffusion maps

Creates hatched patterns for scatterplots

Creating a DelayedMatrix of Regression Residuals

crisprseekplus

Crossover analysis and genetic map construction

CUE: CpG impUtation Ensemble for DNA Methylation Levels Across the HumanMethylation450 (HM450) BeadChip and HumanMethylation EPIC (HM850) BeadChip Platforms

Customize and Query Compound Annotation Database

Cutsomize and Query Compound Annotation Database

Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations

Cytometry dATa anALYSis Tools

Data-driven Annotation of the Transcriptome

Data Package for the annoFuse Bioconductor Package

DataSHIELD client site Omics association functions.

DataSHIELD server site Omic functions

Decomposing Heterogeneous Cohorts using Omic Data Profiling

Decomposition of individual tumors into mutational signatures by signature refitting

Deconvolution by Convex Analysis of Mixtures

Deconvolution of Expression for Nascent RNA Sequencing Data

decoupleR: Ensemble of computational methods to infer biological activities from omics data

DegNorm: degradation normalization for RNA-seq data

Delineate outstanding genomic zones of differential gene activity

Density-Preserving Data Visualization via Non-Linear Dimensionality Reduction

derfinder helper package

DEsingle for detecting three types of differential expression in single-cell RNA-seq data

Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions

detect different methylation level (DMR)

Detecting abberant splicing events from RNA-sequencing data

Detecting patterns of post-transcriptional modifications using machine learning

Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing

Detection, Characterization and Visualization of Kataegis in Sequencing Data

Detection of 2'-O methylations by RiboMethSeq

Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition

Detection of DE genes in time series data using impulse models

Detection of Differentially Methylated Regions

Detection of ligand-protein interactions from 2D thermal profiles (DLPTP)

Detection of m7G, m3C and D modification by AlkAnilineSeq

Detection of post-transcriptional modifications in high throughput sequencing data

Detection of site fixation in molecular evolution

Detect marker panel from scRNA-seq profile

Detect Programmed Ribosomal Frameshifting Events from mRNA/cDNA BLASTX Output

Determination of essential phenotypic elements of clusters in high-dimensional entities

Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data

Diagnostic Plots to Evaluate the Target Decoy Approach

Differential Abundance Analysis of Label-Free Mass Spectrometry Data

Differential abundance analysis with a right censored covariate in high-dimensional cytometry

Differential Alternative Polyadenylation Analysis From Compositions

Differential discovery in high-dimensional cytometry via high-resolution clustering

Differential Enrichment Scan

Differential Enrichment Scan 2

Differential Epigenetic Coregulation Test

Differential expression analysis and model fitting for single-cell RNA-seq data

Differential Expression Analysis based on the read count data generated by either of Salmon, Kallisto, featureCounts and perform statistical analysis to discover quantitative changes in expression levels between two different experimental groups

Differential expression analysis of longitudinal count data sets

Differential expression using kernel-based score test

Differential Gene Expression Analysis for Multi-subject scRNA-seq

Differentially Methylated Regions caller

Differentially regulated genes from scRNA-seq data

Differential neighbourhood abundance testing on a graph

Differential pattern analysis for Ribo-seq data

Differential RhythmicitY analysis

Differential Topology, Progression and Differentiation.

Different methods for the integrative analysis multiple omics data

Different test statistics based on co-citation.

DiffLogo: A comparative visualisation of biooligomer motifs

Direct Access to Orbitrap Data and Beyond

Discriminant Analysis for Evolutionary Inference

Disease-Gene-Variant Relations Mining from the Public Databases and Literature

Disease Ontology Semantic and Enrichment analysis

Displaying binary trees with focus on dendrogram leaves

distinct: a method for differential analyses via hierarchical permutation tests

Divergence Computations

Divergence: Functionality for assessing omics data by divergence with respect to a baseline

Do 16s Data Analysis and Generate Figures

doseLM

doseR

dPeak (Deconvolution of Peaks in ChIP-seq Analysis)

DtracePLN: Sparse precision matrix estimation via lasso penalized D-trace loss in the multivariate Poisson log-normal model

Dynamic Programming Based Alignment of MS2 Chromatograms

EaCoN : Easy Copy Number !

Earth Mover's Distance for Differential Analysis of Genomics Data

Easy Analysis of RNASeq DE

Easy single cell analysis platform for enrichment

echoverse module: echoversePackageTitle

EDLogo Plots Featuring String Logos and Adaptive Scaling of Position-Weight Matrices

Ejemplo de biocthis para cdsb2020

Ejemplo de biocthis para ConectaR2021

ELBOW - Evaluating foLd change By the lOgit Way

Empirical Bayes estimate of block diagonal covariance matrices

Enhanced copy-number variation analysis using Illumina DNA methylation arrays

Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

Enrichment Analysis using Multiple Ontologies and False Discovery Rate

Enrichment Approach to Predict Which Transcription Factors are Regulated

Ensemble of Gene Set Enrichment Analyses

Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

EpiMethEx Package

EpiMix: an integrative tool for the population-level analysis of DNA methylation

Epistasis Analysis for Quantitative Traits by Functional Regression Model

Equality of 2 (or k) Continuous Univariate and Multivariate Distributions

Eric Utilities

Estimates Isoform Specific RPF Footprint Densities

Estimate Systems Immune Response from RNA-seq data

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

EWCE for Multiple Gene Lists

ExCluster robustly detects differentially expressed exons between two conditions of RNA-seq data, requiring at least two independent biological replicates per condition

Exon Based Strategy for Expression Analysis of genes

Exploration of marker-gene sequence taxonomic annotations

Exploratory Data Analysis of LC-MS/MS data by spectral counts

Exploratory Systems Analysis Tools

Explore and download data from the recount3 project

Explore and download data from the recount project

Exploring the Human Cell Atlas Data Coordinating Platform

Exposes and makes available data from the cBioPortal web resources

Exposes and Makes Available Data from the cBioPortal Web Resources

Exposome exploration and outcome data analysis

Extending guilt by association by degree

Extra Base Functions for Bioconductor

Extract and manage matrix data from the Human Cell Atlas project

Facilities for Filtering Bioconductor Annotation Resources

Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data

Factor Loading Adaptive SHrinkage in R

Fast and Interpretable Consensus Clustering via Minipatch Learning

Fast calculation of uniConSig and CSEA

Fast Permutation-based Gene Set Analysis

FASTQ Quality Control

Fast Reading and Processing of Common Gene Annotation and Next Generation Sequencing Format Files

Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens

FDR-controlled analysis of 2D-TPP experiments with replicates

FDR-controlled analysis of SPP experiments

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

Feature Specific Quantile Normalization

FEVV: Functional Enrichment of Genomic Variants and Variations

Find breakpoints in Strand-seq data

Find common transcription factors in yeast expression data

find influential TF and Target based on multi-omics data

Finding Mutually Exclusive Groups of Alterations in Cancer Datasets

Find microbial interactions

Find Potential Disease-Related Genes

Find RAre Splicing Events in RNA-Seq Data

Find SNV/Indel differences between two bam files with near relationship

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

Fit a Gamma-Poisson Generalized Linear Model

Fix gene symbols that are messed up by Excel

flexible pipelines for secretome prediction

For Visualizing Differential Expression Analysis

Framework for Storing and Accessing Hi-C Data Through HDF Files

From functional enrichment results to biological networks

Frozen RMA and Barcode

Frozen RMA Tools

Functional interpretation of single cell RNA-seq latent manifolds

Functionality Visualization for Motifs

Functions for Analyzing Cellular Barcoding Data

Functions for analyzing SELEX-seq data

Functions for annotating GRanges objects

functions for genome-wide application of Liquid Association

Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering

Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects

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

Functions to help analyze data as phyloseq objects

Functions used to preprocess datasets stored in BioDataome

Further Utilities for Genomic Interactions

GC-SIM-MS data processing and alaysis tool

GEMINI: Variational inference approach to infer genetic interactions from pairwise CRISPR screens

Genearting Samples of Gene Expression Data with Variational Autoencoders

General utility functions for developing Bioconductor packages

Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search

Generate customized protein databases from NGS data for proteomics search

Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results

Generate Publication Ready Visualizations of Single Cell Transcriptomics Data

Generate Quality Surrogate Variable Analysis for Degradation Correction

Generate Summary Plots of FastQC Reports

Generate synthetic nucleosome maps

Generating Protein Sequences with Deep Generative Models

Generating SAM file for PSMs in shotgun proteomics data

Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions

Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions

Generation of cell pictures

Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences

Generic Omics Pathway Enrichment Analysis

Gene set analysis accounting for gene-gene correlations

Gene set analysis following differential expression using linear (mixed) modeling with dream

Gene Set Analysis in R

Gene Set Enrichment Analysis with Networks

Gene Set Enrichment / Projection Displays

Genetic Algorithms for Understanding Clonal Heterogeneity and Ordering

Genome Level Trellis Layout

GenoMetric Query Language for R/Bioconductor

Genome-wide assessment of differential translations with ribosome profiling data

Genomic Annotation in Livestock for Positional Candidate LOci

GenomicDistributions: fast analysis of genomic intervals with Bioconductor

Genomic Knowledge-guided Multiple Testing

GenomicOperations

GEOexplorer: a webserver for gene expression analysis and visualisation

GEOsearch

Get the QTL/gene/SNP data functions

gin in R

goProfiles: an R package for the statistical analysis of functional profiles

GO-terms Semantic Similarity Measures

GPA (Genetic analysis incorporating Pleiotropy and Annotation)

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

Graphical User Interface for High Performance BAM-based binary alternative splicing event quantitation, differential analysis, and visualisation

Graphical User Interface for IsoCorrectoR

GREAT Analysis - Functional Enrichment on Genomic Regions

GRO-seq Analysis Pipeline

GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction

GWAS Incorporating Networks

Handling Missing Individuals in Multi-Omics Data Integration

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

Helper Functions for LIBD Deconvolution

Hexbin plots for single cell omics data

HiC analysis using data.table

HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets

HiCdiff: Joint normalization and comparative analysis of multiple Hi-C datasets

Hi-C Direct Caller Plus

Hierarchical ensemble method based on factor graph

High-throughput prediction of DNA shape features

HLA typing clustering and visualization based on specific similarity metrics

HMMERutils

Human genome partitioning of dense sequencing data by identifying haplotype blocks

Identification and Analysis of ceRNA Regulation

Identification and analysis of miRNA sponge interaction networks and modules

Identification and analysis of miRNA sponge regulation

Identification and Annotation of Protein Hotspot Residues

Identification and classification of plant transcription factors

Identification Of Clinically Relevant Genomic Subtypes Using Outcome Weighted Learning

Identification of genetic Variants affecting Alternative Splicing

Identifying differential cell populations in flow cytometry data accounting for marker frequency

igvShiny: a wrapper of Integrative Genomics Viewer (IGV - an interactive tool for visualization and exploration integrated genomic data)

ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data

Immunoglobulin Clonal Lineage and Diversity Analysis

Implementation of MultiDataSet and ResultSet

Implementation of the dot bracket annotations with Biostrings

Implements the Affymetrix PLIER algorithm

Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format

Importing a tRNAscan-SE result file as GRanges object

Importing from tRNAdb and mitotRNAdb as GRanges objects

Import methods for 10X Genomics files

Improving replicability in single-cell RNA-Seq cell type discovery

Imputation-guided re-construction of complete methylomes from WGBS data

Imputation of label-free mass spectrometry peptides

Indentification of significantly activated ligand-receptor interactions across clusters of cells from single-cell RNA sequencing data

Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis

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

Inference And Analysis Of Synteny Networks

Inferring functionally related proteins using protein interaction networks

Inferring miRNA sponge modules in heterogeneous data

Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Inferring the Tree of Cells

Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and drug-protein profiling

Inferring unobserved perturbations from gene expression data

Information Accretion-based Function Predictor Evaluation

In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data

Install/Update Bioconductor and CRAN Packages

Integrated Differential Expression and Differential Network Analysis (INDEED)

Integration of Disease Similarity Methods

Integrative Analysis and Visualization of Epigenomic Sequencing Data

Integrative analysis of Multi-omics data for Alternative Splicing

Integrative analysis of multi-omics data to infer regulatory networks

Integrative analysis of structural variations

Integrative network analysis of omics data

interactive analysis and visualization of alternative splicing in R

Interactive Cytometry Gating in R

Interactive Differential Expression Analyzer

Interactive graphical application for clinical assessment of sequence coverage at the base-pair level

Interactive visualization and manipulation of nested networks

Interactive visualization in genomics

Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection

Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package

Interactive visualization of scRNA-seq data with Cerebro

Interactive Workflow for Discovering Rhythmicity in Biological Data

InterCellar: an R-Shiny app for interactive analysis and exploration of cell-cell communication in single-cell transcriptomics

Interpretable marker-based single-cell pseudotime using Bayesian parametric models

Interpretation and enrichment for metabolomics data

Intron-Exon Retention Estimator

iPath pipeline for detecting perturbed pathways at individual level

iSMNN: Batch Effect Correction for Single-cell RNA-seq data via Iterative Supervised Mutual Nearest Neighbor Refinement

Isoform expression estimation based on RNA-seq data

iSTOP - Induced STOP Experiment Design

Iterative Differential Clustering for single-cell

Iteratively Adjusted Surrogate Variable Analysis

Iterative Pruning to Capture Population Structure

Iterative Pruning to Capture Population Structure version 2

Joint Inference of Mutually Exclusive Driver Pathways and their Progression Dynamics

Judging Quality of Clustering Methods using Mutual Information

K-Mers Similarity Score Matrix and HeatMap

k-nearest neighbour batch effect test

KRSA: Kinome Random Sampling Analyzer

L1-regularization based methods for detection of differential splicing

Labels normalized cells for CyTOF data and assigns probabilities for each label

Landscape Expression Visualization Interface

Landscape Single Cell Entropy

LC-MS/MS Differential Expression Tests

LEA: an R package for Landscape and Ecological Association Studies

Learning from DNA to Predict Enhancers

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

Library for (single-cell) SNP array processing

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

Linear Subpsace identification to solve complete gene expression deconvolution problem

LinkHD: a versatile framework to explore and integrate heterogeneous data

LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

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

Long gene expression as a metric for neuronal identity

Longitudinal system suitability monitoring and quality control for proteomic experiments

LPEseq: local-pooled-error test for RNA-seq data with a small number of replicates

Maaslin

Maaslin2

Machine learning tools for automated transcriptome clustering analysis

MACS: Model-based Analysis for ChIP-Seq

Make Complex Heatmaps

Make Interactive Complex Heatmaps

Making 2D Hilbert Curve

Making Complex Heatmaps

Making Enriched Heatmaps

Manages subsets of data with Bioconductor Experiment objects

Managing Expiration for Cache Directories

Mass Cytometry S4 Class Structure Pipeline for Images

massiR: MicroArray Sample Sex Identifier

Massive and Integrative Gene Set Analysis

Massive correlating biclusters for gene expression data and associated methods

Matched Interaction across Tissues (MIxT) data analysis

Maximum Likelihood Decay Modeling of RNA Degradation Data

Maximum Likelihood Estimation of DNA Methylation and Hydroxymethylation Proportions

MBDDiff for processing MBDcap-seq datasets

Mean/Median-balanced quantile normalization

Mechanism-Aware Imputation

megadepth: BigWig and BAM related utilities

MEIGOR - MEtaheuristics for bIoinformatics Global Optimization

MeSH Enrichment and Semantic analyses

MeSH(Medical Subject Headings) Semantic Similarity Measures

Meta-analysis of Gene Set differential Co-expression Analysis

Metabolite Set Enrichment Analysis (MSEA)

Metabolomics Workbench in R

MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways

MetaCyto: A package for meta-analysis of cytometry data

Meta Gene Set Co-expression Analysis

MetFamily: Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies

Method for Combining LC-MS Metabolomics Feature Measurements

Methods for Single-Cell RNA-Seq Data Analysis

Methods for Spike-in Arrays

Methods for TCR single-cell embedding

Method to generate robust consensus from published cell deconvolution/aggregation methods

methometR: Extracting methylation information from Optical Genome Maps

Methylation Analysis Based on Signal Detection

MethylIT utility

Michaelis-Menten Modelling of Dropouts in single-cell RNASeq

Microbial community dIversity and Network Analysis

Microbiome analysis

Microbiome Analysis Plotting and Visualization

Microbiome Analysis Tools

Microbiome Data Simulation

Microbiome differential abudance and correlation analyses with bias correction

Microbiome Differential Abundance Simulation

Microbiome Exploration App

Microbiome Time Series Analysis

Mini-batch K-means Clustering for Single-Cell RNA-seq

Minimal Protein Set Explaining Peptide Spectrum Matches

Minimized Single-Cell Consensus Clustering

miRNAselector - a package for biomarker selection based on high-throughput experiments.

miRNAtap: microRNA Targets - Aggregated Predictions

mirTarRnaSeq

Missing Value Estimation of DNA Methylation Data

Mixtures of Matrix Variate Poisson-log Normal Distributions

Mixtures of Multivariate Poisson-Log Normal Model for Clustering Count Data

MLG Clustering

'(m,n)-mer' - A Simple Statistical Feature for Sequence Classification

Model based analysis for paired-end data

Model-Based Comparative Analysis of the TCR Repertoire

Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolite Profiles

Modified Concordance Index

Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

Molecular Signature identification using Biclustering

Motif Analysis In Gene Regulatory Networks

motif matching, comparison, and de novo discovery using the MEME Suite

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

Multilevel Model for Multivariate Responses with Missing Values

Multi-locus multi-purpose Crispr/Cas design

Multimodal Mediation Analysis

Multiomic Batch effect Correction

Multi Omic Master Regulator Analysis

Multi-omics Classification, Functional Enrichment and Network Inference analysis

Multi-Omics REgulation (MORE)

Multi-Omics Simulation (MOSim)

Multi-Omics (time-course) network-based integration and interpretation

Multiple co-inertia analysis of omics datasets

Multiple omics data integrative clustering and gene set analysis

Multiple Sample Peak Calling: Using combined evidence from replicates to evaluate ChIP-seq peaks

Multiplex PCR Primer Design and Analysis

Multi-sample multi-group scRNA-seq data analysis tools

Multi-Scale Target Explorer

"Multivariable Association Discovery in Population-scale Meta-omics Studies"

Multivariate Information Criteria to identify important predictors in high dimensional multivariate regression

Multiview Intercellular SpaTial modeling framework

Mutational Signature Comprehensive Analysis Toolkit

nanotatoR: next generation structural variant annotation and classification

Negative binomial model for scRNA-seq

Negative Binomial Models to detect Differential Splicing

Neighbor_net analysis

netboxr

Network Analysis for Omics Data

Network Analysis Supported by Boosting

Network Centrality Metrics for Elastic-Net Regularized Models

Network-Regularized Regression Models

NEUral network-based single-Cell Annotation tool

Next generation structural variant annotation and classification

Non-detects in qPCR data

Non-parametric analysis of response curves for thermal proteome profiling experiments

Normalisation Tools for Inter-Condition Variability of ChIP-Seq Data

Normalization of Single-Cell mRNA Sequencing Data

Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available

Novel Mutational Signature Analysis

Object design (S4) for AMARETTO

Obtain Raw Read Counts from RNASeq Data

Omics-Based Interaction Framework

OmicSelector - a package for biomarker selection based on high-throughput experiments.

Omixer: multivariate and reproducible sample randomization to proactively counter batch effects in omics studies

OmniPath web service client

OmniPath web service client and more

OnASSIs Ontology Annotation and Semantic SImilarity software

One-Dimensional Soli-Expression by Nonlinear Stochastic Embedding (OneSENSE)

Online error control

Online error rate control

ontology enrichment analysis

OpenAccess TCGA Data on Terra as MultiAssayExperiment

Open Cancer TherApeutic Discovery (OCTAD)

Open Reading Frames in Genomics

optimalFlow

Optimising the Definition of Expressed Regions

Optimized Functional Annotation Of ChIP-seq Data

Optimized LC-MS Spectra Processing

Outlier-aware and Count-based Compositional Analysis of Single-cell Data.

Outlier profile and pathway analysis in R

OVESEG-test to detect tissue/cell-specific markers

Package analyse 4C sequencing data

Package for CTDbase data query, visualization and downstream analysis

Package for Fold-specific GO Terms Recognition

Package for Single-cell Data Visualization and Analysis

Package pour l'introduction à la visualisation en R

Package to Perform High Throughput Biological Screening

Package to work with miRNAs and miRNA targets with R

PaIRKAT

Pancreatic Ductal Adenocarcinoma Tool-Kit

PathoStat Statistical Microbiome Analysis Package

Pathway Enrichment Based on Differential Causal Effects

Pathway enrichment using a regularized regression approach

Pathway Fingerprint Framework in R

PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons

Peak Matrix Processing and signal batch correction for metabolomics datasets

Peak Refinement Metric Gathering and Evalutation by Motif Enrichment

Peak saturation processing and analysis

Perform a maximum contrast projection of 3D images along the z-dimension into 2D

Perform methylation analysis

Perform methylation analysis and facilitates differential expression analyses

Perform Needleman-Wunsch algorithm

Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect

Permutation filtration for microbiome data

Phase template strands from Strand-seq data

PhenoGeneRanker: A gene and phenotype prioritization tool

Phenotype-driven module identification

Phenotyping of microbial Raman spectroscopy data

Phylogenetic partitioning based ILR transform for metagenomics data

Phylogenetic Reconstruction and Analysis

Phylogeny-based sequence clustering with site polymorphism

PhyloProfile

PhyloProfileCorona

PhyloProfileRibi

Pipeline for augmented co-expression analysis

Pipeline for identifying LINE1 insertoin in the WGS data

Pipeline for single cell multi-omic data pre-processing

pipeline for single cell RNA-seq data analysis

Pipeline framework for bioinformatics in R

PIVOT launcher

Placental DNA methylation analysis tools

PLNet: Sparse precision matrix estimation via lasso penalized D-trace loss in the multivariate Poisson log-normal model

Plot Gene Ontology and KEGG pathway Annotation and Abundance

Plot Multiple Sequence Alignment using 'ggplot2'

Plots of Statistics Collected by Qualimap from RNASeq Data

Plot the effect of one omics data on other omics data along the chromosome

Plotting functions for derfinder

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

PolyA counting and differential transcript usage analysis for scRNA-seq data

Pooling RNA-seq datasets for assembling transcript models

Population-Specific Expression Analysis.

Position Related Data Analysis

Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

preciseTAD: A machine learning framework for precise TAD boundary prediction

Predict Combined Function of Transcription Factors

Predict genes expressed selectively in specific cell types

Predicting Targets for Drosophila Intragenic miRNAs

Prediction of intronic splicing branchpoints

Predicts the genome build version of genomic track files

Predict transcription factor occupancy using DNase- or ATAC-seq data

Pre-process 1H-NMR FID signals

Pre-process DNA Copy Number (CN) Data for Detection of CN Events

Preprocessing of spectra data from high resolution mass spectrometry

Pre-processing PTR-TOF-MS Data

Pretrained learning models for cell type prediction on single cell RNA-sequencing data

Prize: an R package for prioritization estimation based on analytic hierarchy process

Probe-level Expression Change Averaging

Processing of adductomic mass spectral datasets

Processing Various Types of Data on GEO and TCGA

Professional Comprehensive Omics Data Analysis

Profiles and targets subpopulations with high Treatment EEFects

Profile score distributions

Protein co-expression network analysis (ProCoNA).

Protein Interactions and Networks with Compounds based on Sequences using Deep Learning

Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

Provide functions to retrieve and report on usage expenses in NHGRI AnVIL (anvilproject.org).

Provide methods for microarray analysis

Provides a GUI for DAPAR

Provides helper functions for microbiome preprocessing and analysis

psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders

Publish Packages and Other Resources to AnVIL Workspaces

PWM enrichment analysis

QC for enrichment based NGS

QTL mapping using Bulk Segregant Analysis of Next Generation Sequencing data.

Quality Control for Single-Cell RNA-seq Data

Quantification of the Tumor Immune contexture from RNA-seq data

Quantify and interpret divers of variation in multilevel gene expression experiments

Quantify and interpret drivers of variation in multilevel gene expression experiments

Quasispecies Diversity

qusage: Quantitative Set Analysis for Gene Expression

Randomize Samples for -omics Profiling

Random Rotation Methods for High Dimensional Data with Batch Structure

Rank-based single-sample gene set scoring method

Rank Constrained Similarity Learning for single cell RNA sequencing data

Rank Constrained Similarity Learning for Single Cell RNA Sequencing Data

Rank Product method for identifying differentially expressed genes with application in meta-analysis

Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr

Rapid Reconstruction of Time-Varying Gene Regulatory Networks

R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts

rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines

R Client for Seven Bridges Genomics API (v1)

Receiver Operating Characteristic Partial Area Indexes for evaluating classifiers

Recipes using seqsetvis

Reconstruction, visualization and analysis of branching trajectories

Reduce + Visualize GO

Reference-Based Single-Cell RNA-Seq Annotation

Reference-free Cell-Type Deconvolution of Multi-Cellular Spatially Resolved Transcriptomics Data

Reference-guided isoform reconstruction and quantification for long read RNA-Seq data

Refitting diploid region profiles using a clustering procedure

Regression Models with Multivariate Outcomes for Mass Cytometry Experiments

Remove Unwanted Variation from RNA-Seq Data

Replicate oriented Visualization of a genomic region

Representation of SQL tables in DataFrame metaphor

Representing Different Biological Sets

Reproducibility-Optimized Test Statistic

Retrieve and analyze data from the Human Protein Atlas

Reusable and reproducible Data Management

Re-using Content in Bioconductor Books

Revealing differentially expressed genes using nonlinear dimensionality reduction for single cell RNA-Seq data

R functions

RiboseQC, a Comprehensive Ribo-Seq Analysis Tool

Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation

'rifi' analyses data from rifampicin time series created by microarray or RNAseq

R implementation of informtion measures

R implementation of the LEfSE method for microbiome biomarker discovery

RNA Centric Annotation System

RNA-seq analysis using multiple algorithms

RNAseq and qPCR signal comparison

RNA-seq workflows at HCI

Robust differential co-expression test by copula

Robust Inference for Absolute Abundance in Microbiome Analysis

Robust prediction of clinical outcomes using cytometry data without cell gating

Robust statistical inference for quantitative LC-MS proteomics

Rothstein Lab SGA Analysis Tools

R package for analysing TFBSs in DNA sequences

R package for CRAG

R package for Manhattan Plots

R Package for Processing High Content Screening data

R package for sparse and out-of-core arithmetic and decomposition of Tensor

R package motivated by the SCTC Dream Challenges

R package of gene set enrichment analysis

R Package Template - Enhanced

R SDK for BaseSpace RESTful API

R SeqAn

R Tools for RNA-Seq Projects at Institut Pasteur (Biomics Platform)

Run workflows implemented in Terra/AnVIL workspace

`rutils` is a home for my commonly used R utility functions

R Wrapper for DGIdb

R wrapper for Progenetix

R wrapper for SpatialDE

R wrapper for the OMA REST API

R wrapper for the python openTSNE library

S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects

SAFE-clustering:Single-cell Aggregated (From Ensemble) Clustering for Single-cell RNA-seq Data

SAME: Single-cell RNA-seq Aggregated clustering via Mixture model Ensemble for Single-cell RNA-seq Data

samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation

Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications

Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs

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

Scaling normalization based on the Pareto distribution

SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions

scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction

Science-wise false discovery rate and proportion of true null hypotheses estimation

Scientific Data on Time of Lineage Divergence for Your Taxa

Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences

scMerge: Merging multiple batches of scRNA-seq data

scReClassify: post hoc cell type classification of single-cell RNA-seq data

scRecover for imputation of single-cell RNA-seq data

scRMD: Imputation for single cell RNA-seq data via robust matrix decomposition

ScRNA-seq Workflow CONCLUS - From CONsensus CLUSters To A Meaningful CONCLUSion

Secondary analyses of CNV data (HRD and more)

Selecting the number of mutational signatures using a perplexity-based measure and cross-validation

Selecting transcript model using PRO-seq

Set Based Visualizations for Next-Gen Sequencing Data

Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R

Shiny Application for Interactive CRISPR Screen Visualization, Exploration, Comparison, and Filtering

Shiny Application for Multiplex PCR Primer Design and Analysis

Shiny interface for Cardinal

SIAT: Symptom Intensity Tool Analysis

Signal batch correction for (LC)-MS data

Signature Overrepresentation Analysis

signet: Selection Inference in Gene NETworks

Significance Analysis of Function and Expression

SIMD Partial Order Alignment in R

Similar Binding Profiles

Similarity measures for chemical compounds

Simple Demo of S4 Methods and Classes for Bioconductor

Simple, sequence-based simulation of epi-genomes.

Simple Simulation of Single-cell RNA Sequencing Data

simple Two-Tier Mapper: an interface for Two-Tier Mapper

Simplification of scRNA-Seq Data by Merging Together Similar Cells

Simplify Functional Enrichment Results

Simulate Bulk RNA-seq Datasets from Single-Cell Datasets

Simulating Multi-omics Datasets with Arbitrary Association Structure

Simulating Whole-Genome Inherited Bisulphite Sequencing Data

Simulation of Rare Variant Genetic Data

Simulation, power evaluation, and sample size recommendation for single cell RNA-seq

Simulation tool for optimal design of high-dimensional MS-based proteomics experiment

SINCE - a robust algorithm for single-cell number of clusters estimation

Single-cell analysis toolkit for gene expression data in R

Single-Cell Analysis Toolkit for Gene Expression Data in R

Single-Cell Batch Correction Methods

Single-Cell Consensus Clustering

Single-Cell Data Visualisation Using Kernel Gene-Weighted Density Estimation

Single Cell Differential Expression

Single Cell Entropy

single-cell higher order testing

Single Cell Inference of Regulatory Activity

Single-Cell Operation for Neat Enrichment

Single Cell Overview of Normalized Expression data

Single-Cell RNA-Seq Analysis Utilities

Single Cell RNA-Seq UMI Filtering Facilitator (scruff)

Single-cell Targetted Network Inference

Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)

Single Nucleus Analysis Package for ATAC-Seq

Single-Sample Classifier of Medulloblastoma Subtypes for Medulloblastoma Patient Samples, Mouse Models, and Cell Lines

Singular Value Decomposition for Bioconductor Packages

Small-Count Analysis Methods for High-Dimensional Data

SMNN: Batch Effect Correction for Single-cell RNA-seq data with Supervised Mutual Nearest Neighbor Detection

SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data

some skill for me (Title Case)

Sparse Data Observations for Simulating Synthetic Abundance

Spatial Image Analysis of Tissues

Spatial Transcriptomics Analysis

SpectralTAD: Hierarchical TAD detection using spectral clustering

SQANTI Explorer

SRGnet: An R package for studying synergistic response to gene mutations from transcriptomics data

ssPATHS: Single Sample PATHway Score

S-system parameter estimation method

Stabilised mosaic single cell data integration using unshared features

stageR: stage-wise analysis of high throughput gene expression data in R

Standardize Antibody Names

Standard styles for vignettes and other Bioconductor documents

Stan implementation of BASiCS

StatePaintR: a tool for creating and documenting reproducible chromatin state annotations from StateHub

Statistical analysis for sparse high-throughput sequencing

Statistical Analysis of Metabolomic Data

Statistical Analysis of Molecular Profiles

Statistical Analysis of MPRA data

Statistical Analysis of RNA-Seq Tools

Statistical analysis of sequins

Statistical approaches for differential expression analysis in metatranscriptomics

Statistical Characterization of Post-translational Modifications

Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)

Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)

Statistical Modelling of AP-MS Data (SMAD)

Statistical Testing for ChIP-Seq data sets

Statistical tests for detecting differential distributions based on the 2-Wasserstein distance

stJoincount - Join count statistic for quantifying spatial correlation between clusters

Store and plot TFBS sites from HOCOMOCO v11 scored by FIMO

Storing and accessing epitranscriptomic information using the AnnotationDbi interface

Structure Learning for Count Data

Submitter and Monitor of the 'LSF Cluster'

Subtype Identification with Survival Data

Suite of Functions for Pooled Crispr Screen QC and Analysis

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

Summary Statistics for Rows and Columns of Sparse Matrices

Support for Springer monograph on Bioconductor

supraHex: a supra-hexagonal map for analysing tabular omics data

SVM2CRM: support vector machine for cis-regulatory elements detections

SWATH extended library generation and statistical data analysis

Switch-like differential expression across single-cell trajectories

Synteny Alignment and Analysis for Saccharomyces sensu stricto

Systematic quality checks on comparative genomics analyses

Systems EPigenomics Inference of Regulatory Activity

System-wise protein turnover curve fitting

TADCompare: Identification and characterization of differential TADs

TARgeted SEQuencing Experiment Quality Control

Target Inhibition Interaction using Maximization and Minimization Averaging

taxFun

TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

TCGA utility functions for data management

Ternary Network Estimation

Test branch renaming

Test, Document, Containerise, and Deploy R Packages

Test for differential expression for RNA-seq data

Testing AnnHub transition to Azure

Testing multiple biological mediators simultaneously

Test Single Package Builder

text mining for msigdb sets construed as documents

The Cancer Genome Atlas Data Integration

The Herper package is a simple toolset to install and manage conda packages and environments from R

The removal of batch effects from datasets using a PCA and constrained optimisation based technique

Thermal proximity co-aggregation with R

the R package for analyzing expression evolution based on RNA-seq data

The slim version of signac

The subREgion-based BurdEn Test (REBET)

This package is a single-cell ATAC-seq simulator

This R package for performing module repertoire analyses and generating fingerprint representations

Tidy Meta Profiles using Bioconductor and the Tidyverse

Time-Course Multi-Omics data integration

Time sensitive microRNA-mRNA integration, analysis and network generation tool

Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines

Tokenizing Text of Gene Set Enrichment Analysis

Tools for analysing methylation patterns at genomic tuples

Tools for Assessing Clustering

Tools for Connectivity Map-like analyses

Tools for Diagnostics and Corrections of Batch Effects in Proteomics

Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data

Tools for high-throughput metabolomics

Tools for making reports in various formats

Tools for Manipulating the FOBI Ontology

Tools for matrices with precision weights, test and explore weighted or sparse data

Tools for Metabolomics Data

Tools for Omics Data Analysis

Tools for ordering single-cell sequencing

Tools for processing of high-dimensional cytometry data

Tools for spliced gene structure manipulation and analysis

Tools for the Efficient Analysis of High-Resolution Genomics Data

Tools for working with diverse immune genes

Tools for working with ScreenMill data

Tools to aid the development of Bioconductor Workflow packages

Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells

Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells.

Tools to assess and compare miRNA expression estimatation methods

Tools to query the Bioconductor package binary repositories.

trajectory-based differential expression analysis for sequencing data

Trajectory functions for visualization and interpretation.

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

Transcriptional analysis based on transcriptograms

Transcriptional Data Guided fMRI Network Classification

Transcription Factor High Accumulation Zones

Transcription Factors Enrichment Analysis

Transcriptomic Ovarian Cancer Datasets

Tree Aggregation

tricycle: Transferable Representation and Inference of cell cycle

TSS sequencing data analysis

Tumor Mutational Burden Quantification From Gene Panels And WES

TVTB: The VCF Tool Box

Two-Tier Mapper: a clustering tool based on topological data analysis

Unified Statistical Modeling of Omics Data

Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data

Unlocking iSEE for transcript-level visualization

Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions

Untargeted LC-MS data annotation

uORF prediction in R

Useful bioinformation tools for R.

User Friendly Single-Cell and Bulk RNA Sequencing Visualization

User-friendly Workflow for Pre-processing and Statistical Analysis of Mass Spectrometry Data

Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression

Using self-organizing maps for visualization and interpretation of cytometry data

Using TileDB as a DelayedArray Backend

Utilities for handling genomic interaction data

Utilities to compute, compare, and plot the agreement between ordered vectors of features (ie. distinct genomic experiments). The package includes Correspondence-At-the-TOP (CAT) analysis.

Utilities to create and use Bioconductor Hubs

Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm

Validating Sample Identiy Through RNA-seq and DNA Genotyping Correlation

Variable Selection Oriented LASSO Bagging Algorithm

Variance Adaptive Shrinkage

Varying-Censoring Aware Matrix Factorization

View AnnotationHub and ExperimentHub Resources Interactively

Viscello for Visualization of Single Cell Data

Viscello for Visualization of Single Cell EHT Data

ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity

ViSEAGO: Easier data mining of biological functions organized into clusters using Gene Ontology and semantic similarity

Visual comparison of mutational processes in a set of tumors

Visual Exploration of Omic Datasets Using a Shiny App

Visualise methlation data from Oxford Nanopore sequencing

Visualise methylation data from Oxford Nanopore sequencing

Visualise microarray and RNAseq data using gene ontology annotations

Visualising Set Enrichment Analysis Results

Visualization of Functional Enrichment Result

Visualization of genomic structural variants

Visualization of highly multiplexed imaging data in R

Visualization of Phylogenetic Networks

Visualization Tool for Genetic Reassortment

Visualization Tool for Sequence Recombination and Reassortment

Visualizing Structure in ecological site-species abundance data

Weighting protein-protein interactions

What the Package Does (One Line, Title Case)

What the Package Does (TODO)

What the Package Does TODOELI

Workflow for Identifying Regulatory Elements from Chromatin Accessibility Assay Data

Workflow to process tandem MS files and build MassBank records

Working with modified nucleotide sequences

Wrench normalization for sparse count data

YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization

Yet Another Single-Cell Analysis Toolkit (Yeskit)

Zero-Inflated Negative Binomial Model for RNA-Seq Data

Zwyx

Biocview "Software"

R Package Documentation

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